diff --git a/testing/README.md b/testing/README.md index b6b4425..48bb85a 100644 --- a/testing/README.md +++ b/testing/README.md @@ -1,6 +1,6 @@ # Test data -This test data was compiled by Lijia Huang (CHEO Hospital), Bailey Gallinger (SickKids), and Orion Buske (University of Toronto/SickKids). +Test data was compiled by Lijia Huang (CHEO Hospital), Bailey Gallinger (SickKids), and Orion Buske (University of Toronto/SickKids). -TODO: - - Extract `end`, `referenceBases`, and `alternateBases` from HGVS variants. +There is currently one file containing test data: +* `benchmark_patients.json`: a benchmark data set of 50 test patients compiled from the literature. It contain a JSON-formatted list of patient objects, suitable for loading into a database or including in a match request. diff --git a/testing/test.json b/testing/benchmark_patients.json similarity index 64% rename from testing/test.json rename to testing/benchmark_patients.json index 3a3bb16..8c3265e 100644 --- a/testing/test.json +++ b/testing/benchmark_patients.json @@ -7,84 +7,68 @@ }, "disorders": [ { - "id": "MIM:610536", - "label": "#610536 MANDIBULOFACIAL DYSOSTOSIS, GUION-ALMEIDA TYPE; MFDGA ;;MANDIBULOFACIAL DYSOSTOSIS WITH MICROCEPHALY; MFDM;; GROWTH AND MENTAL RETARDATION, MANDIBULOFACIAL DYSOSTOSIS, MICROCEPHALY, AND CLEFT PALATE" + "id": "MIM:610536" } ], "features": [ { "id": "HP:0008773", - "label": "Aplasia/Hypoplasia of the middle ear", "observed": "yes" }, { "id": "HP:0000413", - "label": "Atresia of the external auditory canal", "observed": "yes" }, { "id": "HP:0000453", - "label": "Choanal atresia", "observed": "yes" }, { "id": "HP:0000405", - "label": "Conductive hearing impairment", "observed": "yes" }, { "id": "HP:0011451", - "label": "Congenital microcephaly", "observed": "yes" }, { "id": "HP:0011471", - "label": "Gastrostomy tube feeding in infancy", "observed": "yes" }, { "id": "HP:0010880", - "label": "Increased nuchal translucency", "observed": "yes" }, { "id": "HP:0000272", - "label": "Malar flattening", "observed": "yes" }, { "id": "HP:0000347", - "label": "Micrognathia", "observed": "yes" }, { "id": "HP:0008551", - "label": "Microtia", "observed": "yes" }, { "id": "HP:0011342", - "label": "Mild global developmental delay", "observed": "yes" }, { "id": "HP:0000545", - "label": "Myopia", "observed": "yes" }, { "id": "HP:0000384", - "label": "Preauricular skin tag", "observed": "yes" }, { "id": "HP:0001622", - "label": "Premature birth", "observed": "no" }, { "id": "HP:0009623", - "label": "Proximal placement of thumb", "observed": "yes" } ], @@ -98,11 +82,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_004247.3(EFTUD2):c.2770C>T", + "end": 42929131, + "referenceBases": "G", "referenceName": "17", - "start": 42929131 - } + "start": 42929130 + }, + "zygosity": 1 } ], "id": "P0000079", @@ -117,89 +104,72 @@ }, "disorders": [ { - "id": "MIM:614261", - "label": "#614261 MICROCEPHALY-CAPILLARY MALFORMATION SYNDROME; MICCAP" + "id": "MIM:614261" } ], "features": [ { "id": "HP:0100026", - "label": "Arteriovenous malformation", "observed": "yes" }, { "id": "HP:0003561", - "label": "Birth length less than 3rd percentile", "observed": "yes" }, { "id": "HP:0011451", - "label": "Congenital microcephaly", "observed": "yes" }, { "id": "HP:0009879", - "label": "Cortical gyral simplification", "observed": "yes" }, { "id": "HP:0011097", - "label": "Epileptic spasms", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0012469", - "label": "Infantile spasms", "observed": "yes" }, { "id": "HP:0001336", - "label": "Myoclonus", "observed": "yes" }, { "id": "HP:0000648", - "label": "Optic atrophy", "observed": "yes" }, { "id": "HP:0001622", - "label": "Premature birth", "observed": "no" }, { "id": "HP:0000253", - "label": "Progressive microcephaly", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0009882", - "label": "Short distal phalanx of finger", "observed": "yes" }, { "id": "HP:0001857", - "label": "Short distal phalanx of toe", "observed": "yes" }, { "id": "HP:0001518", - "label": "Small for gestational age", "observed": "yes" }, { "id": "HP:0001285", - "label": "Spastic tetraparesis", "observed": "yes" } ], @@ -213,11 +183,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_006463.4(STAMBP):c.125A>G", + "end": 74058108, + "referenceBases": "A", "referenceName": "2", - "start": 74058108 - } + "start": 74058107 + }, + "zygosity": 1 }, { "gene": { @@ -228,11 +201,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_006463.4(STAMBP):c.532C>T", + "end": 74074670, + "referenceBases": "C", "referenceName": "2", - "start": 74074670 - } + "start": 74074669 + }, + "zygosity": 1 } ], "id": "P0000083", @@ -247,79 +223,64 @@ }, "disorders": [ { - "id": "MIM:233400", - "label": "#233400 PERRAULT SYNDROME 1; PRLTS1 ;;OVARIAN DYSGENESIS WITH SENSORINEURAL DEAFNESS;; GONADAL DYSGENESIS, XX TYPE, WITH DEAFNESS" + "id": "MIM:233400" } ], "features": [ { "id": "HP:0001284", - "label": "Areflexia", "observed": "yes" }, { "id": "HP:0003447", - "label": "Axonal loss", "observed": "yes" }, { "id": "HP:0001272", - "label": "Cerebellar atrophy", "observed": "yes" }, { "id": "HP:0002474", - "label": "Expressive language delay", "observed": "yes" }, { "id": "HP:0001765", - "label": "Hammertoe", "observed": "yes" }, { "id": "HP:0011096", - "label": "Peripheral demyelination", "observed": "yes" }, { "id": "HP:0200070", - "label": "Peripheral retinal atrophy", "observed": "yes" }, { "id": "HP:0001761", - "label": "Pes cavus", "observed": "yes" }, { "id": "HP:0007240", - "label": "Progressive gait ataxia", "observed": "yes" }, { "id": "HP:0000510", - "label": "Retinitis pigmentosa", "observed": "yes" }, { "id": "HP:0007141", - "label": "Sensorimotor neuropathy", "observed": "yes" }, { "id": "HP:0000407", - "label": "Sensorineural hearing impairment", "observed": "yes" }, { "id": "HP:0003474", - "label": "Sensory impairment", "observed": "yes" }, { "id": "HP:0009088", - "label": "Speech articulation difficulties", "observed": "yes" } ], @@ -333,11 +294,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_000414.3(HSD17B4):c.1547T>C", + "end": 118860954, + "referenceBases": "T", "referenceName": "5", - "start": 118860954 - } + "start": 118860953 + }, + "zygosity": 1 }, { "gene": { @@ -348,11 +312,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_000414.3(HSD17B4):c.101C>T", + "end": 118792052, + "referenceBases": "C", "referenceName": "5", - "start": 118792052 - } + "start": 118792051 + }, + "zygosity": 1 } ], "id": "P0000282", @@ -367,29 +334,24 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0008058", - "label": "Aplasia/Hypoplasia of the optic nerve", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0002194", - "label": "Delayed gross motor development", "observed": "yes" }, { "id": "HP:0002281", - "label": "Gray matter heterotopias", "observed": "yes" } ], @@ -403,26 +365,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.588+2T>G", + "end": 7050691, + "referenceBases": "A", "referenceName": "18", - "start": 7050691 - } - }, - { - "gene": { - "id": "LAMA1" - }, - "type": { - "id": "SO:0001630", - "label": "SPLICING" + "start": 7050690 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.588+2T>G", - "referenceName": "18", - "start": 7050691 - } + "zygosity": 2 } ], "id": "P0000333", @@ -439,32 +389,26 @@ "features": [ { "id": "HP:0001644", - "label": "Dilated cardiomyopathy", "observed": "yes" }, { "id": "HP:0003325", - "label": "Limb-girdle muscle weakness", "observed": "yes" }, { "id": "HP:0000158", - "label": "Macroglossia", "observed": "yes" }, { "id": "HP:0002093", - "label": "Respiratory insufficiency", "observed": "yes" }, { "id": "HP:0002273", - "label": "Tetraparesis", "observed": "yes" }, { "id": "HP:0030284", - "label": "Triangular tongue", "observed": "yes" } ], @@ -478,11 +422,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.342C>G", + "end": 128412081, + "referenceBases": "G", "referenceName": "2", - "start": 128412081 - } + "start": 128412080 + }, + "zygosity": 1 }, { "gene": { @@ -493,11 +440,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.356C>T", + "end": 128412067, + "referenceBases": "G", "referenceName": "2", - "start": 128412067 - } + "start": 128412066 + }, + "zygosity": 1 }, { "gene": { @@ -508,11 +458,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.1034T>C", + "end": 128396914, + "referenceBases": "A", "referenceName": "2", - "start": 128396914 - } + "start": 128396913 + }, + "zygosity": 1 } ], "id": "P0001009", @@ -529,27 +482,22 @@ "features": [ { "id": "HP:0008981", - "label": "Calf muscle hypertrophy", "observed": "yes" }, { "id": "HP:0001644", - "label": "Dilated cardiomyopathy", "observed": "yes" }, { "id": "HP:0000158", - "label": "Macroglossia", "observed": "yes" }, { "id": "HP:0003701", - "label": "Proximal muscle weakness", "observed": "yes" }, { "id": "HP:0030284", - "label": "Triangular tongue", "observed": "yes" } ], @@ -563,11 +511,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.342C>G", + "end": 128412081, + "referenceBases": "G", "referenceName": "2", - "start": 128412081 - } + "start": 128412080 + }, + "zygosity": 1 }, { "gene": { @@ -578,11 +529,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.356C>T", + "end": 128412067, + "referenceBases": "G", "referenceName": "2", - "start": 128412067 - } + "start": 128412066 + }, + "zygosity": 1 }, { "gene": { @@ -593,11 +547,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_001136037.2(LIMS2):c.1034T>C", + "end": 128396914, + "referenceBases": "A", "referenceName": "2", - "start": 128396914 - } + "start": 128396913 + }, + "zygosity": 1 } ], "id": "P0001010", @@ -612,19 +569,16 @@ }, "disorders": [ { - "id": "MIM:614665", - "label": "#614665 MECONIUM ILEUS" + "id": "MIM:614665" } ], "features": [ { "id": "HP:0010943", - "label": "Echogenic fetal bowel", "observed": "yes" }, { "id": "HP:0004401", - "label": "Meconium ileus", "observed": "yes" } ], @@ -638,26 +592,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_004963.3(GUCY2C):c.2008G>A", + "end": 14794076, + "referenceBases": "C", "referenceName": "12", - "start": 14794076 - } - }, - { - "gene": { - "id": "GUCY2C" + "start": 14794075 }, - "type": { - "id": "SO:0001583", - "label": "MISSENSE" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_004963.3(GUCY2C):c.2008G>A", - "referenceName": "12", - "start": 14794076 - } + "zygosity": 2 } ], "id": "P0001011", @@ -672,19 +614,16 @@ }, "disorders": [ { - "id": "MIM:614665", - "label": "#614665 MECONIUM ILEUS" + "id": "MIM:614665" } ], "features": [ { "id": "HP:0010943", - "label": "Echogenic fetal bowel", "observed": "yes" }, { "id": "HP:0004401", - "label": "Meconium ileus", "observed": "yes" } ], @@ -698,11 +637,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_004963.3(GUCY2C):c.2008G>A", + "end": 14794076, + "referenceBases": "C", "referenceName": "12", - "start": 14794076 - } + "start": 14794075 + }, + "zygosity": 1 }, { "gene": { @@ -713,11 +655,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_004963.3(GUCY2C):c.2008G>A", + "end": 14772238, + "referenceBases": "A", "referenceName": "12", - "start": 14794076 - } + "start": 14772237 + }, + "zygosity": 1 } ], "id": "P0001012", @@ -734,57 +679,46 @@ "features": [ { "id": "HP:0007965", - "label": "Absence of visual evoked potentials", "observed": "yes" }, { "id": "HP:0012430", - "label": "Cerebral white matter hypoplasia", "observed": "yes" }, { "id": "HP:0011185", - "label": "EEG with focal epileptiform discharges", "observed": "yes" }, { "id": "HP:0011198", - "label": "EEG with generalized epileptiform discharges", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002079", - "label": "Hypoplasia of the corpus callosum", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0012043", - "label": "Pendular nystagmus", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0000572", - "label": "Visual loss", "observed": "yes" } ], @@ -798,11 +732,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_005548.2(KARS):c.1312C>T", + "end": 75665092, + "referenceBases": "G", "referenceName": "16", - "start": 75665092 - } + "start": 75665091 + }, + "zygosity": 1 }, { "gene": { @@ -813,11 +750,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_005548.2(KARS):c.1573G>A", + "end": 75662589, + "referenceBases": "C", "referenceName": "16", - "start": 75662589 - } + "start": 75662588 + }, + "zygosity": 1 } ], "id": "P0001013", @@ -834,42 +774,34 @@ "features": [ { "id": "HP:0001344", - "label": "Absent speech", "observed": "yes" }, { "id": "HP:0012430", - "label": "Cerebral white matter hypoplasia", "observed": "yes" }, { "id": "HP:0011198", - "label": "EEG with generalized epileptiform discharges", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002079", - "label": "Hypoplasia of the corpus callosum", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0000505", - "label": "Visual impairment", "observed": "yes" } ], @@ -883,11 +815,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_005548.2(KARS):c.1312C>T", + "end": 75665092, + "referenceBases": "G", "referenceName": "16", - "start": 75665092 - } + "start": 75665091 + }, + "zygosity": 1 }, { "gene": { @@ -898,11 +833,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_005548.2(KARS):c.1573G>A", + "end": 75662589, + "referenceBases": "C", "referenceName": "16", - "start": 75662589 - } + "start": 75662588 + }, + "zygosity": 1 } ], "id": "P0001014", @@ -919,42 +857,34 @@ "features": [ { "id": "HP:0002059", - "label": "Cerebral atrophy", "observed": "yes" }, { "id": "HP:0100704", - "label": "Cortical visual impairment", "observed": "yes" }, { "id": "HP:0011968", - "label": "Feeding difficulties", "observed": "yes" }, { "id": "HP:0001290", - "label": "Generalized hypotonia", "observed": "yes" }, { "id": "HP:0002069", - "label": "Generalized tonic-clonic seizures", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002180", - "label": "Neurodegeneration", "observed": "yes" }, { "id": "HP:0002878", - "label": "Respiratory failure", "observed": "yes" } ], @@ -968,26 +898,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_003895.3(SYNJ1):c.406C>T", + "end": 34072338, + "referenceBases": "G", "referenceName": "21", - "start": 34072338 - } - }, - { - "gene": { - "id": "SYNJ1" - }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" + "start": 34072337 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_003895.3(SYNJ1):c.406C>T", - "referenceName": "21", - "start": 34072338 - } + "zygosity": 2 } ], "id": "P0001015", @@ -1002,69 +920,56 @@ }, "disorders": [ { - "id": "MIM:616007", - "label": "#616007 CATARACTS, GROWTH HORMONE DEFICIENCY, SENSORY NEUROPATHY, SENSORINEURAL HEARING LOSS, AND SKELETAL DYSPLASIA; CAGSSS" + "id": "MIM:616007" } ], "features": [ { "id": "HP:0008619", - "label": "Bilateral sensorineural hearing impairment", "observed": "yes" }, { "id": "HP:0000518", - "label": "Cataract", "observed": "yes" }, { "id": "HP:0002194", - "label": "Delayed gross motor development", "observed": "yes" }, { "id": "HP:0007067", - "label": "Distal peripheral sensory neuropathy", "observed": "yes" }, { "id": "HP:0002857", - "label": "Genu valgum", "observed": "yes" }, { "id": "HP:0000824", - "label": "Growth hormone deficiency", "observed": "yes" }, { "id": "HP:0005775", - "label": "Multiple skeletal anomalies", "observed": "yes" }, { "id": "HP:0000160", - "label": "Narrow mouth", "observed": "yes" }, { "id": "HP:0011220", - "label": "Prominent forehead", "observed": "yes" }, { "id": "HP:0003510", - "label": "Severe short stature", "observed": "yes" }, { "id": "HP:0000574", - "label": "Thick eyebrow", "observed": "yes" }, { "id": "HP:0002943", - "label": "Thoracic scoliosis", "observed": "yes" } ], @@ -1078,26 +983,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_018060.3(IARS2):c.2726C>T", + "end": 220316451, + "referenceBases": "C", "referenceName": "1", - "start": 220316451 - } - }, - { - "gene": { - "id": "IARS2" + "start": 220316450 }, - "type": { - "id": "SO:0001583", - "label": "MISSENSE" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018060.3(IARS2):c.2726C>T", - "referenceName": "1", - "start": 220316451 - } + "zygosity": 2 } ], "id": "P0001016", @@ -1112,84 +1005,68 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0002418", - "label": "Abnormality of midbrain morphology", "observed": "yes" }, { "id": "HP:0011932", - "label": "Abnormality of the superior cerebellar peduncle", "observed": "yes" }, { "id": "HP:0001274", - "label": "Agenesis of corpus callosum", "observed": "yes" }, { "id": "HP:0002350", - "label": "Cerebellar cyst", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0001320", - "label": "Cerebellar vermis hypoplasia", "observed": "yes" }, { "id": "HP:0000750", - "label": "Delayed speech and language development", "observed": "yes" }, { "id": "HP:0002198", - "label": "Dilated fourth ventricle", "observed": "yes" }, { "id": "HP:0001090", - "label": "Large eyes", "observed": "yes" }, { "id": "HP:0001270", - "label": "Motor delay", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0030283", - "label": "Partial absence of the septum pellucidum", "observed": "yes" }, { "id": "HP:0011003", - "label": "Severe Myopia", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" }, { "id": "HP:0002119", - "label": "Ventriculomegaly", "observed": "yes" } ], @@ -1203,11 +1080,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.6345+3G>C", + "end": 6977723, + "referenceBases": "C", "referenceName": "18", - "start": 6977723 - } + "start": 6977722 + }, + "zygosity": 1 }, { "gene": { @@ -1219,10 +1099,9 @@ }, "variant": { "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.exon4-11del", - "referenceName": "18", - "start": 7038809 - } + "referenceName": "18" + }, + "zygosity": 1 } ], "id": "P0001017", @@ -1237,59 +1116,48 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0007980", - "label": "Absent retinal pigment epithelium", "observed": "yes" }, { "id": "HP:0002350", - "label": "Cerebellar cyst", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0001320", - "label": "Cerebellar vermis hypoplasia", "observed": "yes" }, { "id": "HP:0002198", - "label": "Dilated fourth ventricle", "observed": "yes" }, { "id": "HP:0001090", - "label": "Large eyes", "observed": "yes" }, { "id": "HP:0001270", - "label": "Motor delay", "observed": "yes" }, { "id": "HP:0000545", - "label": "Myopia", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -1304,10 +1172,9 @@ }, "variant": { "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.7965-15_7965-3del", - "referenceName": "18", - "start": 6956767 - } + "referenceName": "18" + }, + "zygosity": 1 }, { "gene": { @@ -1318,11 +1185,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.2988_2989delA", + "end": 7016493, + "referenceBases": "GT", "referenceName": "18", - "start": 7016490 - } + "start": 7016491 + }, + "zygosity": 1 } ], "id": "P0001018", @@ -1337,94 +1207,76 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0004691", - "label": "2-3 toe syndactyly", "observed": "yes" }, { "id": "HP:0002418", - "label": "Abnormality of midbrain morphology", "observed": "yes" }, { "id": "HP:0007980", - "label": "Absent retinal pigment epithelium", "observed": "yes" }, { "id": "HP:0000646", - "label": "Amblyopia", "observed": "yes" }, { "id": "HP:0000729", - "label": "Autistic behavior", "observed": "yes" }, { "id": "HP:0000518", - "label": "Cataract", "observed": "yes" }, { "id": "HP:0002350", - "label": "Cerebellar cyst", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0001320", - "label": "Cerebellar vermis hypoplasia", "observed": "yes" }, { "id": "HP:0000750", - "label": "Delayed speech and language development", "observed": "yes" }, { "id": "HP:0002198", - "label": "Dilated fourth ventricle", "observed": "yes" }, { "id": "HP:0001090", - "label": "Large eyes", "observed": "yes" }, { "id": "HP:0001270", - "label": "Motor delay", "observed": "yes" }, { "id": "HP:0001105", - "label": "Retinal atrophy", "observed": "yes" }, { "id": "HP:0011003", - "label": "Severe Myopia", "observed": "yes" }, { "id": "HP:0030285", - "label": "Splayed superior cerebellar peduncle", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -1438,11 +1290,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "AGGG", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.6701delC", + "end": 6973132, + "referenceBases": "AGGGG", "referenceName": "18", - "start": 6973129 - } + "start": 6973127 + }, + "zygosity": 1 }, { "gene": { @@ -1453,11 +1308,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.8557-1G>C", + "end": 6948556, + "referenceBases": "C", "referenceName": "18", - "start": 6948556 - } + "start": 6948555 + }, + "zygosity": 1 }, { "gene": { @@ -1468,11 +1326,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.768+1G>A", + "end": 7049076, + "referenceBases": "C", "referenceName": "18", - "start": 7049076 - } + "start": 7049075 + }, + "zygosity": 1 } ], "id": "P0001019", @@ -1487,59 +1348,48 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0000479", - "label": "Abnormality of the retina", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0001320", - "label": "Cerebellar vermis hypoplasia", "observed": "yes" }, { "id": "HP:0000750", - "label": "Delayed speech and language development", "observed": "yes" }, { "id": "HP:0002198", - "label": "Dilated fourth ventricle", "observed": "yes" }, { "id": "HP:0001290", - "label": "Generalized hypotonia", "observed": "yes" }, { "id": "HP:0007068", - "label": "Inferior vermis hypoplasia", "observed": "yes" }, { "id": "HP:0001270", - "label": "Motor delay", "observed": "yes" }, { "id": "HP:0000545", - "label": "Myopia", "observed": "yes" }, { "id": "HP:0000657", - "label": "Oculomotor apraxia", "observed": "yes" } ], @@ -1553,11 +1403,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.2816_2817delAT", + "end": 7016663, + "referenceBases": "AAT", "referenceName": "18", - "start": 7016662 - } + "start": 7016660 + }, + "zygosity": 1 }, { "gene": { @@ -1568,11 +1421,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.555T>G", + "end": 7050726, + "referenceBases": "A", "referenceName": "18", - "start": 7050726 - } + "start": 7050725 + }, + "zygosity": 1 } ], "id": "P0001022", @@ -1587,69 +1443,56 @@ }, "disorders": [ { - "id": "MIM:615960", - "label": "#615960 PORETTI-BOLTSHAUSER SYNDROME; PTBHS" + "id": "MIM:615960" } ], "features": [ { "id": "HP:0000479", - "label": "Abnormality of the retina", "observed": "yes" }, { "id": "HP:0007033", - "label": "Cerebellar dysplasia", "observed": "yes" }, { "id": "HP:0000533", - "label": "Chorioretinal atrophy", "observed": "yes" }, { "id": "HP:0000750", - "label": "Delayed speech and language development", "observed": "yes" }, { "id": "HP:0001290", - "label": "Generalized hypotonia", "observed": "yes" }, { "id": "HP:0007068", - "label": "Inferior vermis hypoplasia", "observed": "yes" }, { "id": "HP:0001090", - "label": "Large eyes", "observed": "yes" }, { "id": "HP:0001270", - "label": "Motor delay", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0000657", - "label": "Oculomotor apraxia", "observed": "yes" }, { "id": "HP:0011003", - "label": "Severe Myopia", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -1663,11 +1506,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.2816_2817delAT", + "end": 7016663, + "referenceBases": "AAT", "referenceName": "18", - "start": 7016662 - } + "start": 7016660 + }, + "zygosity": 1 }, { "gene": { @@ -1678,11 +1524,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_005559.3(LAMA1):c.555T>G", + "end": 7050726, + "referenceBases": "A", "referenceName": "18", - "start": 7050726 - } + "start": 7050725 + }, + "zygosity": 1 } ], "id": "P0001023", @@ -1697,19 +1546,16 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0003002", - "label": "Breast carcinoma", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" } ], @@ -1723,11 +1569,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001024", @@ -1742,39 +1591,32 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0011968", - "label": "Feeding difficulties", "observed": "yes" }, { "id": "HP:0012418", - "label": "Hypoxemia", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0001328", - "label": "Specific learning disability", "observed": "yes" } ], @@ -1788,11 +1630,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001025", @@ -1807,54 +1652,44 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000878", - "label": "11 pairs of ribs", "observed": "yes" }, { "id": "HP:0000670", - "label": "Carious teeth", "observed": "yes" }, { "id": "HP:0000494", - "label": "Downslanted palpebral fissures", "observed": "yes" }, { "id": "HP:0011968", - "label": "Feeding difficulties", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" }, { "id": "HP:0030279", - "label": "Hypoplastic L5 vertebral pedicle", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0001328", - "label": "Specific learning disability", "observed": "yes" } ], @@ -1868,11 +1703,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001026", @@ -1887,54 +1725,44 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0002072", - "label": "Chorea", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0000494", - "label": "Downslanted palpebral fissures", "observed": "yes" }, { "id": "HP:0000316", - "label": "Hypertelorism", "observed": "yes" }, { "id": "HP:0002011", - "label": "Morphological abnormality of the central nervous system", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002091", - "label": "Restrictive lung disease", "observed": "yes" }, { "id": "HP:0001257", - "label": "Spasticity", "observed": "yes" } ], @@ -1948,11 +1776,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+406C>A", + "end": 2447847, + "referenceBases": "G", "referenceName": "20", - "start": 2447847 - } + "start": 2447846 + }, + "zygosity": 1 } ], "id": "P0001027", @@ -1967,54 +1798,44 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0012306", - "label": "Abnormal rib ossification", "observed": "yes" }, { "id": "HP:0000453", - "label": "Choanal atresia", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0000476", - "label": "Cystic hygroma", "observed": "yes" }, { "id": "HP:0001631", - "label": "Defect in the atrial septum", "observed": "yes" }, { "id": "HP:0001040", - "label": "Multiple pterygia", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0000465", - "label": "Webbed neck", "observed": "yes" } ], @@ -2028,11 +1849,14 @@ "label": "3'UTR" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.-72G>A", + "end": 2451408, + "referenceBases": "G", "referenceName": "20", - "start": 2451408 - } + "start": 2451407 + }, + "zygosity": 1 } ], "id": "P0001029", @@ -2047,24 +1871,20 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000765", - "label": "Abnormality of the thorax", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" } ], @@ -2078,11 +1898,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001030", @@ -2097,39 +1920,32 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0000405", - "label": "Conductive hearing impairment", "observed": "yes" }, { "id": "HP:0000824", - "label": "Growth hormone deficiency", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" } ], @@ -2143,11 +1959,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001049", @@ -2162,39 +1981,32 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0002025", - "label": "Anal stenosis", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0100543", - "label": "Cognitive impairment", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0000883", - "label": "Thin ribs", "observed": "yes" } ], @@ -2208,11 +2020,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+300G>C", + "end": 2447953, + "referenceBases": "C", "referenceName": "20", - "start": 2447953 - } + "start": 2447952 + }, + "zygosity": 1 } ], "id": "P0001052", @@ -2227,49 +2042,40 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0030300", - "label": "10 pairs of ribs", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0001631", - "label": "Defect in the atrial septum", "observed": "yes" }, { "id": "HP:0011968", - "label": "Feeding difficulties", "observed": "yes" }, { "id": "HP:0004719", - "label": "Hyperechogenic kidneys", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002093", - "label": "Respiratory insufficiency", "observed": "yes" } ], @@ -2283,11 +2089,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+300G>C", + "end": 2447953, + "referenceBases": "C", "referenceName": "20", - "start": 2447953 - } + "start": 2447952 + }, + "zygosity": 1 } ], "id": "P0001053", @@ -2302,44 +2111,36 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0030300", - "label": "10 pairs of ribs", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0000204", - "label": "Cleft upper lip", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002880", - "label": "Respiratory difficulties", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" } ], @@ -2353,11 +2154,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+301G>C", + "end": 2447952, + "referenceBases": "C", "referenceName": "20", - "start": 2447952 - } + "start": 2447951 + }, + "zygosity": 1 } ], "id": "P0001054", @@ -2372,54 +2176,44 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000405", - "label": "Conductive hearing impairment", "observed": "yes" }, { "id": "HP:0001631", - "label": "Defect in the atrial septum", "observed": "yes" }, { "id": "HP:0011968", - "label": "Feeding difficulties", "observed": "yes" }, { "id": "HP:0000540", - "label": "Hypermetropia", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002880", - "label": "Respiratory difficulties", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -2433,11 +2227,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+300G>C", + "end": 2447953, + "referenceBases": "C", "referenceName": "20", - "start": 2447953 - } + "start": 2447952 + }, + "zygosity": 1 } ], "id": "P0001055", @@ -2452,44 +2249,36 @@ }, "disorders": [ { - "id": "MIM:117650", - "label": "117650 CEREBROCOSTOMANDIBULAR SYNDROME ;;CCM SYNDROME; CCMS;; RIB GAP DEFECTS WITH MICROGNATHIA" + "id": "MIM:117650" } ], "features": [ { "id": "HP:0000878", - "label": "11 pairs of ribs", "observed": "yes" }, { "id": "HP:0000175", - "label": "Cleft palate", "observed": "yes" }, { "id": "HP:0000405", - "label": "Conductive hearing impairment", "observed": "yes" }, { "id": "HP:0000201", - "label": "Pierre-Robin sequence", "observed": "yes" }, { "id": "HP:0030282", - "label": "Posterior rib gap", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0000883", - "label": "Thin ribs", "observed": "yes" } ], @@ -2503,11 +2292,14 @@ "label": "INTRONIC" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_003091.3(SNRPB):c.155+407C>T", + "end": 2447846, + "referenceBases": "G", "referenceName": "20", - "start": 2447846 - } + "start": 2447845 + }, + "zygosity": 1 } ], "id": "P0001056", @@ -2522,59 +2314,48 @@ }, "disorders": [ { - "id": "MIM:245570", - "label": "#245570 EPILEPSY, FOCAL, WITH SPEECH DISORDER AND WITH OR WITHOUT MENTAL RETARDATION; FESD ;;APHASIA, ACQUIRED, WITH EPILEPSY LANDAU-KLEFFNER SYNDROME, INCLUDED; LKS, INCLUDED;; CONTINUOUS SPIKE AND WAVES DURING SLOW-WAVE SLEEP SYNDROME, INCLUDED; CSWS, INCLUDED; CSWSS, INCLUDED;; ROLANDIC EPILEPSY, MENTAL RETARDATION, AND SPEECH DYSPRAXIA, AUTOSOMAL DOMINANT, INCLUDED; RESDAD, INCLUDED; ADRESD, INCLUDED;; BENIGN EPILEPSY OF CHILDHOOD WITH CENTROTEMPORAL SPIKES, INCLUDED; BECTS, INCLUDED" + "id": "MIM:245570" } ], "features": [ { "id": "HP:0011347", - "label": "Abnormality of ocular abduction", "observed": "yes" }, { "id": "HP:0000337", - "label": "Broad forehead", "observed": "yes" }, { "id": "HP:0009765", - "label": "Low hanging columella", "observed": "yes" }, { "id": "HP:0000272", - "label": "Malar flattening", "observed": "yes" }, { "id": "HP:0000160", - "label": "Narrow mouth", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0007930", - "label": "Prominent epicanthal folds", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0011344", - "label": "Severe global developmental delay", "observed": "yes" }, { "id": "HP:0003196", - "label": "Short nose", "observed": "yes" } ], @@ -2588,11 +2369,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_001134407.1(GRIN2A):c.2449A>G", + "end": 9862854, + "referenceBases": "T", "referenceName": "16", - "start": 9862854 - } + "start": 9862853 + }, + "zygosity": 1 } ], "id": "P0001057", @@ -2607,79 +2391,64 @@ }, "disorders": [ { - "id": "MIM:250220", - "label": "#250220 SPONDYLOMETAPHYSEAL DYSPLASIA, SEDAGHATIAN TYPE; SMDS ;;SEDAGHATIAN CHONDRODYSPLASIA;; METAPHYSEAL CHONDRODYSPLASIA, CONGENITAL LETHAL" + "id": "MIM:250220" } ], "features": [ { "id": "HP:0030306", - "label": "11 thoracic vertebrae", "observed": "yes" }, { "id": "HP:0001999", - "label": "Abnormal facial shape", "observed": "yes" }, { "id": "HP:0002104", - "label": "Apnea", "observed": "yes" }, { "id": "HP:0011675", - "label": "Arrhythmia", "observed": "yes" }, { "id": "HP:0001230", - "label": "Broad metacarpals", "observed": "yes" }, { "id": "HP:0006009", - "label": "Broad phalanx", "observed": "yes" }, { "id": "HP:0003180", - "label": "Flat acetabular roof", "observed": "yes" }, { "id": "HP:0002866", - "label": "Hypoplastic iliac wing", "observed": "yes" }, { "id": "HP:0003025", - "label": "Metaphyseal irregularity", "observed": "yes" }, { "id": "HP:0000926", - "label": "Platyspondyly", "observed": "yes" }, { "id": "HP:0008905", - "label": "Rhizomelia", "observed": "yes" }, { "id": "HP:0010049", - "label": "Short metacarpal", "observed": "yes" }, { "id": "HP:0008416", - "label": "Six lumbar vertebrae", "observed": "yes" }, { "id": "HP:0005257", - "label": "Thoracic hypoplasia", "observed": "yes" } ], @@ -2693,11 +2462,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_001039848.1(GPX4):c.587+5G>A", + "end": 1105813, + "referenceBases": "G", "referenceName": "19", - "start": 1105813 - } + "start": 1105812 + }, + "zygosity": 1 }, { "gene": { @@ -2708,11 +2480,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_001039848.1(GPX4):c.588-8_588-4del", + "end": 1106237, + "referenceBases": "CTTTTC", "referenceName": "19", - "start": 1106233 - } + "start": 1106231 + }, + "zygosity": 1 } ], "id": "P0001058", @@ -2727,84 +2502,68 @@ }, "disorders": [ { - "id": "MIM:250220", - "label": "#250220 SPONDYLOMETAPHYSEAL DYSPLASIA, SEDAGHATIAN TYPE; SMDS ;;SEDAGHATIAN CHONDRODYSPLASIA;; METAPHYSEAL CHONDRODYSPLASIA, CONGENITAL LETHAL" + "id": "MIM:250220" } ], "features": [ { "id": "HP:0005108", - "label": "Abnormality of the intervertebral disk", "observed": "yes" }, { "id": "HP:0001678", - "label": "Atrioventricular block", "observed": "yes" }, { "id": "HP:0001321", - "label": "Cerebellar hypoplasia", "observed": "yes" }, { "id": "HP:0009879", - "label": "Cortical gyral simplification", "observed": "yes" }, { "id": "HP:0004273", - "label": "Cupped metaphyses of hand bones", "observed": "yes" }, { "id": "HP:0003180", - "label": "Flat acetabular roof", "observed": "yes" }, { "id": "HP:0001290", - "label": "Generalized hypotonia", "observed": "yes" }, { "id": "HP:0002123", - "label": "Generalized myoclonic seizures", "observed": "yes" }, { "id": "HP:0002079", - "label": "Hypoplasia of the corpus callosum", "observed": "yes" }, { "id": "HP:0000946", - "label": "Hypoplastic ilia", "observed": "yes" }, { "id": "HP:0100255", - "label": "Metaphyseal dysplasia", "observed": "yes" }, { "id": "HP:0003375", - "label": "Narrow greater sacrosciatic notches", "observed": "yes" }, { "id": "HP:0000926", - "label": "Platyspondyly", "observed": "yes" }, { "id": "HP:0002880", - "label": "Respiratory difficulties", "observed": "yes" }, { "id": "HP:0001248", - "label": "Short tubular bones (hand)", "observed": "yes" } ], @@ -2818,26 +2577,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_001039848.1(GPX4):c.381C>A", + "end": 1105455, + "referenceBases": "C", "referenceName": "19", - "start": 1105455 - } - }, - { - "gene": { - "id": "GPX4" - }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" + "start": 1105454 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_001039848.1(GPX4):c.381C>A", - "referenceName": "19", - "start": 1105455 - } + "zygosity": 2 } ], "id": "P0001059", @@ -2854,37 +2601,30 @@ "features": [ { "id": "HP:0200128", - "label": "Biventricular hypertrophy", "observed": "yes" }, { "id": "HP:0003546", - "label": "Exercise intolerance", "observed": "yes" }, { "id": "HP:0003738", - "label": "Exercise-induced myalgia", "observed": "yes" }, { "id": "HP:0003348", - "label": "Hyperalaninemia", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0011664", - "label": "Left ventricular noncompaction cardiomyopathy", "observed": "yes" }, { "id": "HP:0006970", - "label": "Periventricular leukomalacia", "observed": "yes" } ], @@ -2898,11 +2638,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_002047.2(GARS):c.1904C>T", + "end": 30671863, + "referenceBases": "C", "referenceName": "7", - "start": 30671863 - } + "start": 30671862 + }, + "zygosity": 1 }, { "gene": { @@ -2913,11 +2656,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_002047.2(GARS):c.1787G>A", + "end": 30668263, + "referenceBases": "G", "referenceName": "7", - "start": 30668263 - } + "start": 30668262 + }, + "zygosity": 1 } ], "id": "P0001060", @@ -2932,104 +2678,84 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0010605", - "label": "Chalazion", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0006254", - "label": "Elevated alpha-fetoprotein", "observed": "yes" }, { "id": "HP:0002910", - "label": "Elevated hepatic transaminases", "observed": "yes" }, { "id": "HP:0002171", - "label": "Gliosis", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0001395", - "label": "Hepatic fibrosis", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0009830", - "label": "Peripheral neuropathy", "observed": "yes" }, { "id": "HP:0012520", - "label": "Perivascular spaces", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0000495", - "label": "Recurrent corneal erosions", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0001773", - "label": "Short foot", "observed": "yes" }, { "id": "HP:0200055", - "label": "Small hand", "observed": "yes" } ], @@ -3043,11 +2769,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "TGG", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1891delC", + "end": 25761027, + "referenceBases": "TGGG", "referenceName": "3", - "start": 25761025 - } + "start": 25761023 + }, + "zygosity": 1 }, { "gene": { @@ -3058,11 +2787,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } + "start": 25775421 + }, + "zygosity": 1 } ], "id": "P0001069", @@ -3077,79 +2809,64 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0002910", - "label": "Elevated hepatic transaminases", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0001511", - "label": "Intrauterine growth retardation", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0009830", - "label": "Peripheral neuropathy", "observed": "yes" }, { "id": "HP:0000495", - "label": "Recurrent corneal erosions", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" } ], @@ -3163,26 +2880,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "TCCCCCC", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1370dupG", + "end": 25773869, + "referenceBases": "TCCCCC", "referenceName": "3", - "start": 25773865 - } - }, - { - "gene": { - "id": "NGLY1" + "start": 25773863 }, - "type": { - "id": "SO:0001589", - "label": "FRAMESHIFT" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1370dupG", - "referenceName": "3", - "start": 25773865 - } + "zygosity": 2 } ], "id": "P0001070", @@ -3197,129 +2902,104 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0006958", - "label": "Abnormal auditory evoked potentials", "observed": "yes" }, { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0010605", - "label": "Chalazion", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0012448", - "label": "Delayed myelination", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0006254", - "label": "Elevated alpha-fetoprotein", "observed": "yes" }, { "id": "HP:0002910", - "label": "Elevated hepatic transaminases", "observed": "yes" }, { "id": "HP:0002171", - "label": "Gliosis", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0001395", - "label": "Hepatic fibrosis", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0001511", - "label": "Intrauterine growth retardation", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0012520", - "label": "Perivascular spaces", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0000495", - "label": "Recurrent corneal erosions", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0001773", - "label": "Short foot", "observed": "yes" }, { "id": "HP:0200055", - "label": "Small hand", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -3333,26 +3013,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } - }, - { - "gene": { - "id": "NGLY1" + "start": 25775421 }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", - "referenceName": "3", - "start": 25775422 - } + "zygosity": 2 } ], "id": "P0001071", @@ -3367,139 +3035,112 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0002418", - "label": "Abnormality of midbrain morphology", "observed": "yes" }, { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0009085", - "label": "Alveolar ridge overgrowth", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0006254", - "label": "Elevated alpha-fetoprotein", "observed": "yes" }, { "id": "HP:0000286", - "label": "Epicanthus", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0001511", - "label": "Intrauterine growth retardation", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0000347", - "label": "Micrognathia", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0009830", - "label": "Peripheral neuropathy", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0000508", - "label": "Ptosis", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0001773", - "label": "Short foot", "observed": "yes" }, { "id": "HP:0003196", - "label": "Short nose", "observed": "yes" }, { "id": "HP:0200055", - "label": "Small hand", "observed": "yes" }, { "id": "HP:0009891", - "label": "Underdeveloped supraorbital ridges", "observed": "yes" }, { "id": "HP:0002119", - "label": "Ventriculomegaly", "observed": "yes" } ], @@ -3513,26 +3154,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } - }, - { - "gene": { - "id": "NGLY1" - }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" + "start": 25775421 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", - "referenceName": "3", - "start": 25775422 - } + "zygosity": 2 } ], "id": "P0001076", @@ -3547,64 +3176,52 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0006956", - "label": "Dilation of lateral ventricles", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0000286", - "label": "Epicanthus", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0001395", - "label": "Hepatic fibrosis", "observed": "yes" }, { "id": "HP:0001511", - "label": "Intrauterine growth retardation", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0003196", - "label": "Short nose", "observed": "yes" } ], @@ -3618,26 +3235,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } - }, - { - "gene": { - "id": "NGLY1" + "start": 25775421 }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", - "referenceName": "3", - "start": 25775422 - } + "zygosity": 2 } ], "id": "P0001078", @@ -3652,109 +3257,88 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0010605", - "label": "Chalazion", "observed": "yes" }, { "id": "HP:0011918", - "label": "Clinodactyly of the 4th toe", "observed": "yes" }, { "id": "HP:0001864", - "label": "Clinodactyly of the 5th toe", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0002910", - "label": "Elevated hepatic transaminases", "observed": "yes" }, { "id": "HP:0000286", - "label": "Epicanthus", "observed": "yes" }, { "id": "HP:0002007", - "label": "Frontal bossing", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002557", - "label": "Hypoplastic nipples", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0000657", - "label": "Oculomotor apraxia", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0005487", - "label": "Prominent metopic ridge", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" }, { "id": "HP:0001182", - "label": "Tapered finger", "observed": "yes" }, { "id": "HP:0010804", - "label": "Tented upper lip vermilion", "observed": "yes" } ], @@ -3768,26 +3352,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } - }, - { - "gene": { - "id": "NGLY1" + "start": 25775421 }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", - "referenceName": "3", - "start": 25775422 - } + "zygosity": 2 } ], "id": "P0001079", @@ -3802,114 +3374,92 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0000678", - "label": "Dental crowding", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002553", - "label": "Highly arched eyebrow", "observed": "yes" }, { "id": "HP:0001511", - "label": "Intrauterine growth retardation", "observed": "yes" }, { "id": "HP:0005320", - "label": "Lack of facial subcutaneous fat", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0000657", - "label": "Oculomotor apraxia", "observed": "yes" }, { "id": "HP:0000520", - "label": "Proptosis", "observed": "yes" }, { "id": "HP:0000495", - "label": "Recurrent corneal erosions", "observed": "yes" }, { "id": "HP:0001315", - "label": "Reduced tendon reflexes", "observed": "yes" }, { "id": "HP:0002650", - "label": "Scoliosis", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" }, { "id": "HP:0001773", - "label": "Short foot", "observed": "yes" }, { "id": "HP:0200055", - "label": "Small hand", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" }, { "id": "HP:0000431", - "label": "Wide nasal bridge", "observed": "yes" } ], @@ -3923,26 +3473,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", + "end": 25775422, + "referenceBases": "T", "referenceName": "3", - "start": 25775422 - } - }, - { - "gene": { - "id": "NGLY1" + "start": 25775421 }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1201A>T", - "referenceName": "3", - "start": 25775422 - } + "zygosity": 2 } ], "id": "P0001080", @@ -3957,29 +3495,24 @@ }, "disorders": [ { - "id": "MIM:604317", - "label": "#604317 MICROCEPHALY 2, PRIMARY, AUTOSOMAL RECESSIVE, WITH OR WITHOUT CORTICAL MALFORMATIONS; MCPH2" + "id": "MIM:604317" } ], "features": [ { "id": "HP:0000718", - "label": "Aggressive behavior", "observed": "yes" }, { "id": "HP:0010864", - "label": "Intellectual disability, severe", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001250", - "label": "Seizures", "observed": "yes" } ], @@ -3993,26 +3526,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "CTTTT", "assembly": "GRCh37", - "hgvs": "NM_001083961.1(WDR62):c.1821dupT", + "end": 36579992, + "referenceBases": "CTTT", "referenceName": "19", - "start": 36579992 - } - }, - { - "gene": { - "id": "WDR62" - }, - "type": { - "id": "SO:0001589", - "label": "FRAMESHIFT" + "start": 36579988 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_001083961.1(WDR62):c.1821dupT", - "referenceName": "19", - "start": 36579992 - } + "zygosity": 2 } ], "id": "P0001081", @@ -4027,59 +3548,48 @@ }, "disorders": [ { - "id": "MIM:601338", - "label": "#601338 CEREBELLAR ATAXIA, AREFLEXIA, PES CAVUS, OPTIC ATROPHY, AND SENSORINEURAL HEARING LOSS; CAPOS" + "id": "MIM:601338" } ], "features": [ { "id": "HP:0007965", - "label": "Absence of visual evoked potentials", "observed": "yes" }, { "id": "HP:0001251", - "label": "Ataxia", "observed": "yes" }, { "id": "HP:0008619", - "label": "Bilateral sensorineural hearing impairment", "observed": "yes" }, { "id": "HP:0001260", - "label": "Dysarthria", "observed": "yes" }, { "id": "HP:0002066", - "label": "Gait ataxia", "observed": "yes" }, { "id": "HP:0001254", - "label": "Lethargy", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0000639", - "label": "Nystagmus", "observed": "yes" }, { "id": "HP:0000648", - "label": "Optic atrophy", "observed": "yes" }, { "id": "HP:0002370", - "label": "Poor coordination", "observed": "yes" } ], @@ -4093,11 +3603,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_152296(ATP1A3):c.2452G>A", + "end": 42474427, + "referenceBases": "C", "referenceName": "19", - "start": 42474427 - } + "start": 42474426 + }, + "zygosity": 1 } ], "id": "P0001084", @@ -4112,144 +3625,116 @@ }, "disorders": [ { - "id": "MIM:182212", - "label": "#182212 SHPRINTZEN-GOLDBERG CRANIOSYNOSTOSIS SYNDROME; SGS ;;CRANIOSYNOSTOSIS WITH ARACHNODACTYLY AND ABDOMINAL HERNIAS;; MARFANOID DISORDER WITH CRANIOSYNOSTOSIS, TYPE I;; MARFANOID CRANIOSYNOSTOSIS SYNDROME" + "id": "MIM:182212" } ], "features": [ { "id": "HP:0002410", - "label": "Aqueductal stenosis", "observed": "yes" }, { "id": "HP:0001166", - "label": "Arachnodactyly", "observed": "yes" }, { "id": "HP:0010665", - "label": "Bilateral coxa valga", "observed": "yes" }, { "id": "HP:0001363", - "label": "Craniosynostosis", "observed": "yes" }, { "id": "HP:0001631", - "label": "Defect in the atrial septum", "observed": "yes" }, { "id": "HP:0000494", - "label": "Downslanted palpebral fissures", "observed": "yes" }, { "id": "HP:0002474", - "label": "Expressive language delay", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" }, { "id": "HP:0006801", - "label": "Hyperactive deep tendon reflexes", "observed": "yes" }, { "id": "HP:0000316", - "label": "Hypertelorism", "observed": "yes" }, { "id": "HP:0001265", - "label": "Hyporeflexia", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0006889", - "label": "Intellectual disability, borderline", "observed": "yes" }, { "id": "HP:0001388", - "label": "Joint laxity", "observed": "yes" }, { "id": "HP:0000369", - "label": "Low-set ears", "observed": "yes" }, { "id": "HP:0000347", - "label": "Micrognathia", "observed": "yes" }, { "id": "HP:0002868", - "label": "Narrow iliac wings", "observed": "yes" }, { "id": "HP:0001655", - "label": "Patent foramen ovale", "observed": "yes" }, { "id": "HP:0000768", - "label": "Pectus carinatum", "observed": "yes" }, { "id": "HP:0001763", - "label": "Pes planus", "observed": "yes" }, { "id": "HP:0011220", - "label": "Prominent forehead", "observed": "yes" }, { "id": "HP:0000278", - "label": "Retrognathia", "observed": "yes" }, { "id": "HP:0000319", - "label": "Smooth philtrum", "observed": "yes" }, { "id": "HP:0003298", - "label": "Spina bifida occulta", "observed": "yes" }, { "id": "HP:0003396", - "label": "Syringomyelia", "observed": "yes" }, { "id": "HP:0001762", - "label": "Talipes equinovarus", "observed": "yes" }, { "id": "HP:0001537", - "label": "Umbilical hernia", "observed": "yes" } ], @@ -4263,11 +3748,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_003036.3(SKI):c.347G>A", + "end": 2160552, + "referenceBases": "G", "referenceName": "1", - "start": 2160552 - } + "start": 2160551 + }, + "zygosity": 1 } ], "id": "P0001085", @@ -4282,129 +3770,104 @@ }, "disorders": [ { - "id": "MIM:614105", - "label": "#614105 METHYLMALONATE SEMIALDEHYDE DEHYDROGENASE DEFICIENCY; MMSDHD ;;MMSDH DEFICIENCY" + "id": "MIM:614105" } ], "features": [ { "id": "HP:0001344", - "label": "Absent speech", "observed": "yes" }, { "id": "HP:0000463", - "label": "Anteverted nares", "observed": "yes" }, { "id": "HP:0010055", - "label": "Broad hallux", "observed": "yes" }, { "id": "HP:0012448", - "label": "Delayed myelination", "observed": "yes" }, { "id": "HP:0006956", - "label": "Dilation of lateral ventricles", "observed": "yes" }, { "id": "HP:0040155", - "label": "Elevated urinary 3-hydroxybutyric acid", "observed": "yes" }, { "id": "HP:0045034", - "label": "Elevated urinary aminoisobutyric acid", "observed": "yes" }, { "id": "HP:0000286", - "label": "Epicanthus", "observed": "yes" }, { "id": "HP:0002007", - "label": "Frontal bossing", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0002281", - "label": "Gray matter heterotopias", "observed": "yes" }, { "id": "HP:0000348", - "label": "High forehead", "observed": "yes" }, { "id": "HP:0000218", - "label": "High palate", "observed": "yes" }, { "id": "HP:0000316", - "label": "Hypertelorism", "observed": "yes" }, { "id": "HP:0002079", - "label": "Hypoplasia of the corpus callosum", "observed": "yes" }, { "id": "HP:0007793", - "label": "Macular retinal pigment epithelial mottling", "observed": "yes" }, { "id": "HP:0002912", - "label": "Methylmalonic acidemia", "observed": "yes" }, { "id": "HP:0012120", - "label": "Methylmalonic aciduria", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0003196", - "label": "Short nose", "observed": "yes" }, { "id": "HP:0000322", - "label": "Short philtrum", "observed": "yes" }, { "id": "HP:0000954", - "label": "Single transverse palmar crease", "observed": "yes" }, { "id": "HP:0008070", - "label": "Sparse hair", "observed": "yes" }, { "id": "HP:0010804", - "label": "Tented upper lip vermilion", "observed": "yes" } ], @@ -4418,11 +3881,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_005589(ALDH6A1):c.514T>C", + "end": 74538114, + "referenceBases": "A", "referenceName": "14", - "start": 74538114 - } + "start": 74538113 + }, + "zygosity": 1 }, { "gene": { @@ -4433,11 +3899,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_005589(ALDH6A1):c.1603C>T", + "end": 74527350, + "referenceBases": "G", "referenceName": "14", - "start": 74527350 - } + "start": 74527349 + }, + "zygosity": 1 } ], "id": "P0001086", @@ -4452,49 +3921,40 @@ }, "disorders": [ { - "id": "MIM:269880", - "label": "#269880 SHORT SYNDROME ;;SHORT STATURE, HYPEREXTENSIBILITY, HERNIA, OCULAR DEPRESSION, RIEGER ANOMALY, AND TEETHING DELAY;; LIPODYSTROPHY, PARTIAL, WITH RIEGER ANOMALY AND SHORT STATURE" + "id": "MIM:269880" } ], "features": [ { "id": "HP:0000490", - "label": "Deeply set eye", "observed": "yes" }, { "id": "HP:0000684", - "label": "Delayed eruption of teeth", "observed": "yes" }, { "id": "HP:0009125", - "label": "Lipodystrophy", "observed": "yes" }, { "id": "HP:0007495", - "label": "Prematurely aged appearance", "observed": "yes" }, { "id": "HP:0000558", - "label": "Rieger anomaly", "observed": "yes" }, { "id": "HP:0004322", - "label": "Short stature", "observed": "yes" }, { "id": "HP:0000325", - "label": "Triangular face", "observed": "yes" }, { "id": "HP:0000430", - "label": "Underdeveloped nasal alae", "observed": "yes" } ], @@ -4508,11 +3968,14 @@ "label": "FRAMESHIFT" }, "variant": { + "alternateBases": "AC", "assembly": "GRCh37", - "hgvs": "NM_181523.2(PIK3R1):c.1906_1907insC", + "end": 67592090, + "referenceBases": "A", "referenceName": "5", - "start": 67592090 - } + "start": 67592089 + }, + "zygosity": 1 } ], "id": "P0001091", @@ -4527,89 +3990,72 @@ }, "disorders": [ { - "id": "MIM:613680", - "label": "#613680 BEAULIEU-BOYCOTT-INNES SYNDROME; BBIS ;;MICROCEPHALY, MENTAL RETARDATION, AND DISTINCTIVE FACIES, WITH CARDIAC AND GENITOURINARY MALFORMATIONS" + "id": "MIM:613680" } ], "features": [ { "id": "HP:0000670", - "label": "Carious teeth", "observed": "yes" }, { "id": "HP:0000490", - "label": "Deeply set eye", "observed": "yes" }, { "id": "HP:0000689", - "label": "Dental malocclusion", "observed": "yes" }, { "id": "HP:0009890", - "label": "High anterior hairline", "observed": "yes" }, { "id": "HP:0000348", - "label": "High forehead", "observed": "yes" }, { "id": "HP:0000085", - "label": "Horseshoe kidney", "observed": "yes" }, { "id": "HP:0002342", - "label": "Intellectual disability, moderate", "observed": "yes" }, { "id": "HP:0003189", - "label": "Long nose", "observed": "yes" }, { "id": "HP:0009765", - "label": "Low hanging columella", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0000545", - "label": "Myopia", "observed": "yes" }, { "id": "HP:0001643", - "label": "Patent ductus arteriosus", "observed": "yes" }, { "id": "HP:0012745", - "label": "Short palpebral fissure", "observed": "yes" }, { "id": "HP:0000179", - "label": "Thick lower lip vermilion", "observed": "yes" }, { "id": "HP:0000215", - "label": "Thick upper lip vermilion", "observed": "yes" }, { "id": "HP:0000582", - "label": "Upslanted palpebral fissure", "observed": "yes" } ], @@ -4623,26 +4069,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_024339.3(THOC6):c.136G>A", + "end": 3075805, + "referenceBases": "G", "referenceName": "16", - "start": 3075805 - } - }, - { - "gene": { - "id": "THOC6" - }, - "type": { - "id": "SO:0001583", - "label": "MISSENSE" + "start": 3075804 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_024339.3(THOC6):c.136G>A", - "referenceName": "16", - "start": 3075805 - } + "zygosity": 2 } ], "id": "P0001105", @@ -4657,59 +4091,48 @@ }, "disorders": [ { - "id": "MIM:612541", - "label": "#612541 NEUTROPENIA, SEVERE CONGENITAL, 4, AUTOSOMAL RECESSIVE; SCN4 DURSUN SYNDROME, INCLUDED;; PULMONARY ARTERIAL HYPERTENSION, LEUKOPENIA, AND ATRIAL SEPTAL DEFECT, INCLUDED" + "id": "MIM:612541" } ], "features": [ { "id": "HP:0000230", - "label": "Gingivitis", "observed": "yes" }, { "id": "HP:0012138", - "label": "Granulocytic hyperplasia", "observed": "yes" }, { "id": "HP:0004866", - "label": "Impaired ADP-induced platelet aggregation", "observed": "yes" }, { "id": "HP:0004854", - "label": "Intermittent thrombocytopenia", "observed": "yes" }, { "id": "HP:0001888", - "label": "Lymphopenia", "observed": "yes" }, { "id": "HP:0001875", - "label": "Neutropenia", "observed": "yes" }, { "id": "HP:0005401", - "label": "Recurrent candida infections", "observed": "yes" }, { "id": "HP:0000403", - "label": "Recurrent otitis media", "observed": "yes" }, { "id": "HP:0000010", - "label": "Recurrent urinary tract infections", "observed": "yes" }, { "id": "HP:0001744", - "label": "Splenomegaly", "observed": "yes" } ], @@ -4723,26 +4146,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_138387.3(G6PC3):c.829C>T", + "end": 42153199, + "referenceBases": "C", "referenceName": "17", - "start": 42153199 - } - }, - { - "gene": { - "id": "G6PC3" - }, - "type": { - "id": "SO:0001587", - "label": "STOPGAIN" + "start": 42153198 }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_138387.3(G6PC3):c.829C>T", - "referenceName": "17", - "start": 42153199 - } + "zygosity": 2 } ], "id": "P0001106", @@ -4757,24 +4168,20 @@ }, "disorders": [ { - "id": "MIM:243150", - "label": "#243150 INTESTINAL ATRESIA, MULTIPLE; MINAT ;;FAMILIAL INTESTINAL POLYATRESIA SYNDROME; FIPA" + "id": "MIM:243150" } ], "features": [ { "id": "HP:0011100", - "label": "Intestinal atresia", "observed": "yes" }, { "id": "HP:0005214", - "label": "Intestinal obstruction", "observed": "yes" }, { "id": "HP:0001539", - "label": "Omphalocele", "observed": "yes" } ], @@ -4788,26 +4195,14 @@ "label": "SPLICING" }, "variant": { + "alternateBases": "T", "assembly": "GRCh37", - "hgvs": "NM_020458.2(TTC7A):c.1001+3_1001+6del", + "end": 47221659, + "referenceBases": "TAAGT", "referenceName": "2", - "start": 47221656 - } - }, - { - "gene": { - "id": "TTC7A" + "start": 47221654 }, - "type": { - "id": "SO:0001630", - "label": "SPLICING" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_020458.2(TTC7A):c.1001+3_1001+6del", - "referenceName": "2", - "start": 47221656 - } + "zygosity": 2 } ], "id": "P0001107", @@ -4824,22 +4219,18 @@ "features": [ { "id": "HP:0001662", - "label": "Bradycardia", "observed": "yes" }, { "id": "HP:0001508", - "label": "Failure to thrive", "observed": "yes" }, { "id": "HP:0005214", - "label": "Intestinal obstruction", "observed": "yes" }, { "id": "HP:0001649", - "label": "Tachycardia", "observed": "yes" } ], @@ -4853,26 +4244,14 @@ "label": "MISSENSE" }, "variant": { + "alternateBases": "C", "assembly": "GRCh37", - "hgvs": "NM_001012410.3(SGOL1):c.67A>G", + "end": 20225453, + "referenceBases": "T", "referenceName": "3", - "start": 20225453 - } - }, - { - "gene": { - "id": "SGOL1" + "start": 20225452 }, - "type": { - "id": "SO:0001583", - "label": "MISSENSE" - }, - "variant": { - "assembly": "GRCh37", - "hgvs": "NM_001012410.3(SGOL1):c.67A>G", - "referenceName": "3", - "start": 20225453 - } + "zygosity": 2 } ], "id": "P0001108", @@ -4887,114 +4266,92 @@ }, "disorders": [ { - "id": "MIM:615273", - "label": "#615273 CONGENITAL DISORDER OF DEGLYCOSYLATION; CDDG ;;CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Iv; CDG1V;; CDG Iv; CDGIv" + "id": "MIM:615273" } ], "features": [ { "id": "HP:0006958", - "label": "Abnormal auditory evoked potentials", "observed": "yes" }, { "id": "HP:0100022", - "label": "Abnormality of movement", "observed": "yes" }, { "id": "HP:0000522", - "label": "Alacrima", "observed": "yes" }, { "id": "HP:0002059", - "label": "Cerebral atrophy", "observed": "yes" }, { "id": "HP:0010605", - "label": "Chalazion", "observed": "yes" }, { "id": "HP:0002019", - "label": "Constipation", "observed": "yes" }, { "id": "HP:0002353", - "label": "EEG abnormality", "observed": "yes" }, { "id": "HP:0002910", - "label": "Elevated hepatic transaminases", "observed": "yes" }, { "id": "HP:0001263", - "label": "Global developmental delay", "observed": "yes" }, { "id": "HP:0001395", - "label": "Hepatic fibrosis", "observed": "yes" }, { "id": "HP:0002079", - "label": "Hypoplasia of the corpus callosum", "observed": "yes" }, { "id": "HP:0030303", - "label": "Hypoplastic anterior commissure", "observed": "yes" }, { "id": "HP:0002151", - "label": "Increased serum lactate", "observed": "yes" }, { "id": "HP:0000252", - "label": "Microcephaly", "observed": "yes" }, { "id": "HP:0001252", - "label": "Muscular hypotonia", "observed": "yes" }, { "id": "HP:0000657", - "label": "Oculomotor apraxia", "observed": "yes" }, { "id": "HP:0006579", - "label": "Prolonged neonatal jaundice", "observed": "yes" }, { "id": "HP:0001773", - "label": "Short foot", "observed": "yes" }, { "id": "HP:0002472", - "label": "Small cerebral cortex", "observed": "yes" }, { "id": "HP:0200055", - "label": "Small hand", "observed": "yes" }, { "id": "HP:0000486", - "label": "Strabismus", "observed": "yes" } ], @@ -5008,11 +4365,14 @@ "label": "INFRAME-DELETION" }, "variant": { + "alternateBases": "G", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1205_1207del", + "end": 25775418, + "referenceBases": "GTTC", "referenceName": "3", - "start": 25775416 - } + "start": 25775414 + }, + "zygosity": 1 }, { "gene": { @@ -5023,11 +4383,14 @@ "label": "STOPGAIN" }, "variant": { + "alternateBases": "A", "assembly": "GRCh37", - "hgvs": "NM_018297.3(NGLY1):c.1570C>T", + "end": 25761670, + "referenceBases": "G", "referenceName": "3", - "start": 25770665 - } + "start": 25761669 + }, + "zygosity": 1 } ], "id": "P0001135", diff --git a/testing/fhs.json b/testing/fhs.json deleted file mode 100644 index 71b007e..0000000 --- a/testing/fhs.json +++ /dev/null @@ -1,652 +0,0 @@ -[ - 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