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"count": 221292,
"next": "https://panelapp-aus.org/api/v1/activities/?format=api&page=681",
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"results": [
{
"created": "2022-12-01T15:01:45.476774+11:00",
"panel_name": "Regression",
"panel_id": 206,
"panel_version": "0.509",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "changed review comment from: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported.\r\n\r\nOnly 2 individuals with regression = amber at this stage. \nSources: Literature; to: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported.\r\n\r\nOnly 2 individuals with regression = amber for this panel at this stage. \r\nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T15:01:32.524039+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.515",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Mode of pathogenicity for gene: NUP54 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to None",
"entity_name": "NUP54",
"entity_type": "gene"
},
{
"created": "2022-12-01T15:01:12.882086+11:00",
"panel_name": "Regression",
"panel_id": 206,
"panel_version": "0.509",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "gene: TCEAL1 was added\ngene: TCEAL1 was added to Regression. Sources: Literature\nMode of inheritance for gene: TCEAL1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\nPublications for gene: TCEAL1 were set to PMID: 36368327\nPhenotypes for gene: TCEAL1 were set to hypotonia, abnormal gait, developmental delay, intellectual disability, autism, dysmorphic facial features.\nReview for gene: TCEAL1 was set to AMBER\nAdded comment: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported.\r\n\r\nOnly 2 individuals with regression = amber at this stage. \nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T15:00:56.057272+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.514",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: NUP54 as Amber List (moderate evidence)",
"entity_name": "NUP54",
"entity_type": "gene"
},
{
"created": "2022-12-01T15:00:56.043920+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.514",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: nup54 has been classified as Amber List (Moderate Evidence).",
"entity_name": "NUP54",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:57:11.360934+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5060",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: GABRA3 as ready",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:57:11.348563+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5060",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:56:28.108442+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5060",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Epilepsy, intellectual disability, dysmorphic features, to Epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features, MIM# 301091",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:56:27.324784+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.513",
"user_name": "Hazel Phillimore",
"item_type": "entity",
"text": "gene: NUP54 was added\ngene: NUP54 was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: NUP54 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: NUP54 were set to PMID: 36333996\nPhenotypes for gene: NUP54 were set to Early onset dystonia; progressive neurological deterioration; ataxia; dysarthria; dysphagia; hypotonia\nMode of pathogenicity for gene: NUP54 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments\nReview for gene: NUP54 was set to AMBER\nAdded comment: From PMID: 36333996.; Harrer, P. et al. (2022) Ann Neurol. doi: 10.1002/ana.26544. \r\n\r\nThree patients from unrelated families with dystonia and/or Leigh(-like) syndromes, with biallelic variants in NUP54, in the C-terminal protein region that interacts with NUP62. Onset was between 12 months and 5 years. All had progressive neurological deterioration with dystonia, ataxia, dysarthria, dysphagia, hypotonia. \r\n\r\nPatient / Family A (consanguineous) was homozygous for c.1073T>G p.(Ile358Ser). \r\n\r\nPatient / Family B was compound heterozygous for c.1073T>G p.(Ile358Ser) and c.1126A>G p.(Lys376Glu).\r\n\r\nPatient / Family C was compound heterozygosity for c.1410_1412del p.(Gln471del) and two missense variants c.1414G>A, p.(Glu472Lys); c.1420C>T, p.(Leu474Phe)\r\n\r\nThe phenotypes were similar to those of NUP62 including early-onset dystonia with dysphagic choreoathetosis, and T2-hyperintense lesions in striatum.\r\n\r\nBrain MRIs showed T2/FLAIR hyperintensities in the dorsal putamina. \r\n\r\nWestern blots showing reduced expression of NUP54 and its interaction partners NUP62/NUP58 in patient fibroblasts. \nSources: Literature",
"entity_name": "NUP54",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:55:21.209449+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5059",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: GABRA3 as Green List (high evidence)",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:55:21.194107+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5059",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:55:04.015843+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.513",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: GABRA3 as ready",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:55:03.966729+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.513",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:54:46.645724+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.513",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Epilepsy, intellectual disability, dysmorphic features, to Epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features, MIM# 301091",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:54:32.842249+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.512",
"user_name": "Dean Phelan",
"item_type": "entity",
"text": "reviewed gene: ARF3: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36369169, 34346499; Phenotypes: Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:54:22.588134+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.512",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: GABRA3 as Green List (high evidence)",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:54:22.574485+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.512",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:54:04.371451+11:00",
"panel_name": "Hereditary Neuropathy - complex",
"panel_id": 3070,
"panel_version": "0.137",
"user_name": "Karina Sandoval",
"item_type": "entity",
"text": "changed review comment from: Bi-allelic EMILIN1 loss-of-function variants causative for an entity combining cutis laxa, arterial tortuosity, aneurysm formation, and bone fragility, and transient osteopenia\r\n\r\n4 families - Variants segregated in the all families, carriers\r\nFam 1. 2 affected, homozygous c.831dup consanguineous \r\nFam 2. 2 affected homozygous c.151del consanguineous \r\nFam 3. 1 affected chet\r\nFam 4. 1 affected homozygous c.1606C>T\r\n\r\nMouse models \r\nAll affected individuals presented with generalized arterial tortuosity and fractures; to: Bi-allelic EMILIN1 loss-of-function variants causative for an entity combining cutis laxa, arterial tortuosity, aneurysm formation, and bone fragility, and transient osteopenia\r\n\r\n4 families - Variants segregated in the all families, carriers\r\nFam 1. 2 affected, homozygous c.831dup consanguineous \r\nFam 2. 2 affected homozygous c.151del consanguineous \r\nFam 3. 1 affected chet\r\nFam 4. 1 affected homozygous c.1606C>T\r\n\r\nMouse models \r\nAll affected individuals presented with generalized arterial tortuosity and fractures",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:40.023171+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.511",
"user_name": "Manny Jacobs",
"item_type": "entity",
"text": "reviewed gene: DCLRE1B: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 10699141, 20479256, 35007328; Phenotypes: Dyskeratosis congenita, autosomal recessive 8; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "DCLRE1B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:37.608789+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5058",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: ARF3 as ready",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:37.590569+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5058",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: arf3 has been classified as Green List (High Evidence).",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:31.699844+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5058",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: ARF3 were changed from Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system to Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:29.320456+11:00",
"panel_name": "Aortopathy_Connective Tissue Disorders",
"panel_id": 44,
"panel_version": "1.73",
"user_name": "Karina Sandoval",
"item_type": "entity",
"text": "gene: EMILIN1 was added\ngene: EMILIN1 was added to Aortopathy_Connective Tissue Disorders. Sources: Literature\nMode of inheritance for gene: EMILIN1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal\nPublications for gene: EMILIN1 were set to PMID: 36351433\nPhenotypes for gene: EMILIN1 were set to Neuronopathy, distal hereditary motor, type X, MIM# 620080 Aortic aneurysm, MONDO:0005160, EMILIN2-related\nReview for gene: EMILIN1 was set to GREEN\nAdded comment: Bi-allelic EMILIN1 loss-of-function variants causative for an entity combining cutis laxa, arterial tortuosity, aneurysm formation, and bone fragility, and transient osteopenia\r\n\r\n4 families - Variants segregated in the all families, carriers\r\nFam 1. 2 affected, homozygous c.831dup consanguineous\r\nFam 2. 2 affected homozygous c.151del consanguineous\r\nFam 3. 1 affected chet\r\nFam 4. 1 affected homozygous c.1606C>T\r\n\r\nMouse models\r\nAll affected individuals presented with generalized arterial tortuosity and fractures \nSources: Literature",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:19.771520+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.511",
"user_name": "Naomi Baker",
"item_type": "entity",
"text": "gene: NPC1 was added\ngene: NPC1 was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: NPC1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: NPC1 were set to 36417180\nPhenotypes for gene: NPC1 were set to mitochondrial pyruvate carrier deficiency, MONDO:0013877, MPC2-related\nReview for gene: NPC1 was set to AMBER\nAdded comment: Four patients from two unrelated consanguineous families reported with homozygous variants (missense and stop-loss). Siblings from family 1 were diagnosed prenatally with diffuse subcutaneous oedema, cardiomegaly, corpus callosum agenesis, ventriculomegaly and hypoplasia of the cerebellum. Siblings from family 2 had slightly different presentations, which included anoxo-ischemic encephalopathy, isolated dyspnea, neonatal respiratory distress, neonatal jaundice, hypotonia, visual impairment, microcephaly; both siblings had severe delayed psychomotor development. Immunoblot analysis of protein expression in lysates from patient-derived fibroblasts demonstrated reduced MPC1 and MPC2 protein levels. \nSources: Literature",
"entity_name": "NPC1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:53:06.840444+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1809",
"user_name": "Dean Phelan",
"item_type": "entity",
"text": "reviewed gene: ARF3: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36369169, 34346499; Phenotypes: Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:52:51.649822+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5057",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: ARF3 were changed from Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system to Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:52:30.318839+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5057",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: EPRS as Green List (high evidence)",
"entity_name": "EPRS",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:52:30.303832+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5057",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: eprs has been classified as Green List (High Evidence).",
"entity_name": "EPRS",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:51:59.424829+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5056",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Publications for gene: ARF3 were set to 34346499",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:51:21.826627+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5055",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: ARF3 as Green List (high evidence)",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:51:21.816463+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5055",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: arf3 has been classified as Green List (High Evidence).",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:50:56.638228+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5054",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: ARF3 as Green List (high evidence)",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:50:56.625445+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5054",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: arf3 has been classified as Green List (High Evidence).",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:50:06.478073+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.848",
"user_name": "Naomi Baker",
"item_type": "entity",
"text": "gene: MPC2 was added\ngene: MPC2 was added to Mitochondrial disease. Sources: Literature\nMode of inheritance for gene: MPC2 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: MPC2 were set to 36417180\nPhenotypes for gene: MPC2 were set to mitochondrial pyruvate carrier deficiency, MONDO:0013877, MPC2-related\nReview for gene: MPC2 was set to AMBER\nAdded comment: Four patients from two unrelated consanguineous families reported with homozygous variants (missense and stop-loss). Siblings from family 1 were diagnosed prenatally with diffuse subcutaneous oedema, cardiomegaly, corpus callosum agenesis, ventriculomegaly and hypoplasia of the cerebellum. Siblings from family 2 had slightly different presentations, which included anoxo-ischemic encephalopathy, isolated dyspnea, neonatal respiratory distress, neonatal jaundice, hypotonia, visual impairment, microcephaly; both siblings had severe delayed psychomotor development. Immunoblot analysis of protein expression in lysates from patient-derived fibroblasts demonstrated reduced MPC1 and MPC2 protein levels. \nSources: Literature",
"entity_name": "MPC2",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:48:46.364027+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.511",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Publications for gene: EMILIN1 were set to PMID: 31978608; 26462740.",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:48:21.714091+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.510",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: EMILIN1 were changed from Neuronopathy, distal hereditary motor, type X, MIM# 620080 to Neuronopathy, distal hereditary motor, type X, MIM# 620080; Aortic aneurysm, MONDO:0005160, EMILIN2-related",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:47:39.954320+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.509",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Mode of inheritance for gene: EMILIN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:47:18.723815+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.508",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: EMILIN1 as Green List (high evidence)",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:47:18.710720+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.508",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: emilin1 has been classified as Green List (High Evidence).",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:47:15.270682+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1809",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: SHROOM4 as Green List (high evidence)",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:47:15.259085+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1809",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: shroom4 has been classified as Green List (High Evidence).",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:46:53.239235+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.127",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Marked gene: SHROOM4 as ready",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:46:53.198048+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.127",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: shroom4 has been classified as Green List (High Evidence).",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:46:23.325995+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5053",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "gene: TCEAL1 was added\ngene: TCEAL1 was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: TCEAL1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\nPublications for gene: TCEAL1 were set to PMID: 36368327\nPhenotypes for gene: TCEAL1 were set to hypotonia; abnormal gait; developmental delay; intellectual disability; autism; dysmorphic facial features.\nReview for gene: TCEAL1 was set to GREEN\nAdded comment: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:46:14.516135+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.127",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: SHROOM4 as Green List (high evidence)",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:46:14.499580+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.127",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: shroom4 has been classified as Green List (High Evidence).",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:45:36.382323+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1808",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "gene: SHROOM4 was added\ngene: SHROOM4 was added to Genetic Epilepsy. Sources: Literature\nMode of inheritance for gene: SHROOM4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females\nPublications for gene: SHROOM4 were set to 35663265\nPhenotypes for gene: SHROOM4 were set to epilepsy, idiopathic generalised, SHROOM4-related, MONDO:0005579\nReview for gene: SHROOM4 was set to GREEN\nAdded comment: Six unrelated cases with idiopathic epilepsy without intellectual disability. SHROOM4 variants were all missense variants and were located around the N-terminal PDZ domain and the C-terminal ASD2 domain \nSources: Literature",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:44:29.154816+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.507",
"user_name": "Karina Sandoval",
"item_type": "entity",
"text": "reviewed gene: EMILIN1: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36351433; Phenotypes: Neuronopathy, distal hereditary motor, type X, MIM# 620080, Peripheral neuropathy, aortic aneurysm; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:43:11.107541+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1807",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: GABRA3 as ready",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:43:11.094109+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1807",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:42:51.351303+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1807",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features, MIM#\t301091 to Epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features, MIM#\t301091",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:42:11.634435+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1807",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Neurodevelopmental disorder, MONDO:0700092, GABRA3-related; Epilepsy, intellectual disability, dysmorphic features, to Epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features, MIM#\t301091",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:41:36.954556+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1806",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Neurodevelopmental disorder, MONDO:0700092, GABRA3-related; Epilepsy, intellectual disability, dysmorphic features, to Neurodevelopmental disorder, MONDO:0700092, GABRA3-related; Epilepsy, intellectual disability, dysmorphic features,",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:41:04.828517+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.125",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "gene: SHROOM4 was added\ngene: SHROOM4 was added to Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic. Sources: Literature\nMode of inheritance for gene: SHROOM4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females\nPublications for gene: SHROOM4 were set to 36379543\nPhenotypes for gene: SHROOM4 were set to Congenital anomaly of the kidney and urinary tracy (CAKUT), SHROOM4-related, MONDO:0019719\nReview for gene: SHROOM4 was set to GREEN\nAdded comment: Six individuals from four unrelated families with CAKUT. Embryonic mouse and zebrafish expression studies showed Shroom4 expression in the upper and lower urinary tract, the developing cloaca, the heart and the cerebral CNS. KD studies in zebrafish larvae revealed pronephric cysts, anomalies of the cloaca and the heart, decreased eye-to-head ratio and higher mortality compared with controls. These phenotypes could be rescued by co-injection of human wild-type SHROOM4 mRNA and morpholino. Variants included one missense, one splice variant and two CNVs (deletions). \nSources: Literature",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:40:59.706128+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5053",
"user_name": "Dean Phelan",
"item_type": "entity",
"text": "reviewed gene: ARF3: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36369169, 34346499; Phenotypes: Neurodevelopmental disorder (MONDO:0700092), ARF3-related; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"entity_name": "ARF3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:40:59.256449+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1806",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: GABRA3 were changed from Epilepsy, intellectual disability, dysmorphic features, to Neurodevelopmental disorder, MONDO:0700092, GABRA3-related; Epilepsy, intellectual disability, dysmorphic features,",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:40:44.293170+11:00",
"panel_name": "Hereditary Neuropathy - complex",
"panel_id": 3070,
"panel_version": "0.137",
"user_name": "Karina Sandoval",
"item_type": "entity",
"text": "reviewed gene: EMILIN1: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36351433; Phenotypes: Neuronopathy, distal hereditary motor, type X, MIM# 620080, Peripheral neuropathy, aortic aneurysm; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "EMILIN1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:40:04.961488+11:00",
"panel_name": "Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic",
"panel_id": 63,
"panel_version": "0.125",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "gene: SHROOM4 was added\ngene: SHROOM4 was added to Congenital anomalies of the kidney and urinary tract (CAKUT) Syndromic. Sources: Literature\nMode of inheritance for gene: SHROOM4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females\nPublications for gene: SHROOM4 were set to 36379543\nPhenotypes for gene: SHROOM4 were set to Congenital anomaly of the kidney and urinary tracy (CAKUT), SHROOM4-related, MONDO:0019719\nReview for gene: SHROOM4 was set to GREEN\nAdded comment: Six individuals from four unrelated families with CAKUT. Embryonic mouse and zebrafish expression studies showed Shroom4 expression in the upper and lower urinary tract, the developing cloaca, the heart and the cerebral CNS. KD studies in zebrafish larvae revealed pronephric cysts, anomalies of the cloaca and the heart, decreased eye-to-head ratio and higher mortality compared with controls. These phenotypes could be rescued by co-injection of human wild-type SHROOM4 mRNA and morpholino. Variants included one missense, one splice variant and two CNVs (deletions). \nSources: Literature",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:39:00.828426+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1805",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: GABRA3 as Green List (high evidence)",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:39:00.818041+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1805",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:38:29.686917+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.507",
"user_name": "Sarah Pantaleo",
"item_type": "entity",
"text": "gene: GABRA3 was added\ngene: GABRA3 was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: GABRA3 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\nPublications for gene: GABRA3 were set to PMID: 29053855\nPhenotypes for gene: GABRA3 were set to Epilepsy, intellectual disability, dysmorphic features,\nPenetrance for gene: GABRA3 were set to Incomplete\nReview for gene: GABRA3 was set to GREEN\nAdded comment: Six variants in GABRA3 encoding the alpha3-subunit of the GABA(A) receptor. \r\nFive missense variants and one micro duplication were detected in four families and two sporadic cases presenting with a range of epileptic seizure types, a varying degree of intellectual disability and developmental delay, sometimes with dysmorphic features or nystagmus.\r\nThe variants co-segregated mostly but not completely with the phenotype in the families, indicating in some cases incomplete penetrance, involvement of other genes, or presence of phenocopies.\r\nOverall, males were more severely affected and there were three asymptomatic female mutation carriers compared to only one male without a clinical phenotype. \r\nMechanism suggested - three detected missense variants are localised in the extracellular GABA-binding NH2-terminus, one in the M2-M3 linker and one in the M4 transmembrane segment of the alpha3-subunit. Functional studies in Xenopus leaves oocytes revealed a variable but significant reduction of GABA-evoked anion currents for all mutants compared to wild-type receptors. The degree of current reduction correlated partially with the phenotype.\r\nResults reveal that rare loss-of-function variants in GABRA3 increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay and dysmorphic features, presenting in some pedigrees with an X-linked inheritance pattern. \nSources: Literature",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:38:27.407751+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1804",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: GABRA3 as Green List (high evidence)",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:38:27.396850+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1804",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: gabra3 has been classified as Green List (High Evidence).",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:45.661447+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5053",
"user_name": "Lucy Spencer",
"item_type": "entity",
"text": "gene: EPRS was added\ngene: EPRS was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: EPRS was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: EPRS were set to 29576217, 36411955\nPhenotypes for gene: EPRS were set to Leukodystrophy, hypomyelinating, 15 (MIM#617951)\nReview for gene: EPRS was set to GREEN\nAdded comment: 5 patients across 2 papers, with delayed development (3/5) and/or regression, ataxia, dystonia, hypomyelinating leukodystrophy or periventricular white matter, 2 with epilepsy, 3 with optic atrophy, 2 with deafness, 2 with micrcephaly, 1 noted to have some facial dysmorphism. \nSources: Literature",
"entity_name": "EPRS",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:36.701277+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.79",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Marked gene: KDM2B as ready",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:36.688480+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.79",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Gene: kdm2b has been classified as Green List (High Evidence).",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:35.321383+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5053",
"user_name": "Sarah Pantaleo",
"item_type": "entity",
"text": "gene: GABRA3 was added\ngene: GABRA3 was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: GABRA3 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\nPublications for gene: GABRA3 were set to PMID: 29053855\nPhenotypes for gene: GABRA3 were set to Epilepsy, intellectual disability, dysmorphic features,\nPenetrance for gene: GABRA3 were set to Incomplete\nReview for gene: GABRA3 was set to GREEN\nAdded comment: Six variants in GABRA3 encoding the alpha3-subunit of the GABA(A) receptor. \r\nFive missense variants and one micro duplication were detected in four families and two sporadic cases presenting with a range of epileptic seizure types, a varying degree of intellectual disability and developmental delay, sometimes with dysmorphic features or nystagmus.\r\nThe variants co-segregated mostly but not completely with the phenotype in the families, indicating in some cases incomplete penetrance, involvement of other genes, or presence of phenocopies.\r\nOverall, males were more severely affected and there were three asymptomatic female mutation carriers compared to only one male without a clinical phenotype. \r\nMechanism suggested - three detected missense variants are localised in the extracellular GABA-binding NH2-terminus, one in the M2-M3 linker and one in the M4 transmembrane segment of the alpha3-subunit. Functional studies in Xenopus leaves oocytes revealed a variable but significant reduction of GABA-evoked anion currents for all mutants compared to wild-type receptors. The degree of current reduction correlated partially with the phenotype.\r\nResults reveal that rare loss-of-function variants in GABRA3 increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay and dysmorphic features, presenting in some pedigrees with an X-linked inheritance pattern. \nSources: Literature",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:31.028283+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.79",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Classified gene: KDM2B as Green List (high evidence)",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:31.016042+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.79",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Gene: kdm2b has been classified as Green List (High Evidence).",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:12.256964+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.507",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: TCEAL1 as ready",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:12.232340+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.507",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: tceal1 has been classified as Green List (High Evidence).",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:36:11.429278+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.78",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "gene: KDM2B was added\ngene: KDM2B was added to Fetal anomalies. Sources: Literature\nMode of inheritance for gene: KDM2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted\nPublications for gene: KDM2B were set to 36322151\nPhenotypes for gene: KDM2B were set to neurodevelopmental disorder MONDO#070009, KDM2B-related\nReview for gene: KDM2B was set to GREEN\ngene: KDM2B was marked as current diagnostic\nAdded comment: 27 individuals from 22 families were recruited \r\n13 SNV classified LP/P, all de novo except 2 familial cases\r\n5 variants were classified as VUS if more than 1 het is present in gnomAD or does result in a KDM2B-specific episignature (therefore suggesting normal function) \r\n\r\n14 families with SNVs and a variety of cardiac anomalies including ASD, VSD, MR, PDA, PFO, Atrial septal aneurysm and Mild mitral insufficiency \nSources: Literature",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:35:58.020508+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.507",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Phenotypes for gene: TCEAL1 were changed from hypotonia, abnormal gait, developmental delay, intellectual disability, autism, dysmorphic facial features. to Neurodevelopmental disorder, MONDO:0700092, TCEAL1-related; hypotonia, abnormal gait, developmental delay, intellectual disability, autism, dysmorphic facial features.",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:35:48.267814+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.77",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: SHROOM4 as Green List (high evidence)",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:35:48.248006+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.77",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: shroom4 has been classified as Green List (High Evidence).",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:59.779163+11:00",
"panel_name": "Fetal anomalies",
"panel_id": 3763,
"panel_version": "1.76",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "reviewed gene: SHROOM4: Rating: GREEN; Mode of pathogenicity: None; Publications: 36379543; Phenotypes: Congenital anomaly of the kidney and urinary tracy (CAKUT), SHROOM4-related, MONDO:0019719; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:44.679760+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.506",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: TCEAL1 as Green List (high evidence)",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:44.668490+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.506",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: tceal1 has been classified as Green List (High Evidence).",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:17.689853+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.269",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Classified gene: KDM2B as Green List (high evidence)",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:17.664303+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.269",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Gene: kdm2b has been classified as Green List (High Evidence).",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:34:06.920167+11:00",
"panel_name": "Genetic Epilepsy",
"panel_id": 202,
"panel_version": "0.1803",
"user_name": "Sarah Pantaleo",
"item_type": "entity",
"text": "gene: GABRA3 was added\ngene: GABRA3 was added to Genetic Epilepsy. Sources: Literature\nMode of inheritance for gene: GABRA3 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\nPublications for gene: GABRA3 were set to PMID: 29053855\nPhenotypes for gene: GABRA3 were set to Epilepsy, intellectual disability, dysmorphic features,\nPenetrance for gene: GABRA3 were set to Incomplete\nReview for gene: GABRA3 was set to GREEN\nAdded comment: Six variants in GABRA3 encoding the alpha3-subunit of the GABA(A) receptor. \r\nFive missense variants and one micro duplication were detected in four families and two sporadic cases presenting with a range of epileptic seizure types, a varying degree of intellectual disability and developmental delay, sometimes with dysmorphic features or nystagmus.\r\nThe variants co-segregated mostly but not completely with the phenotype in the families, indicating in some cases incomplete penetrance, involvement of other genes, or presence of phenocopies.\r\nOverall, males were more severely affected and there were three asymptomatic female mutation carriers compared to only one male without a clinical phenotype. \r\nMechanism suggested - three detected missense variants are localised in the extracellular GABA-binding NH2-terminus, one in the M2-M3 linker and one in the M4 transmembrane segment of the alpha3-subunit. Functional studies in Xenopus leaves oocytes revealed a variable but significant reduction of GABA-evoked anion currents for all mutants compared to wild-type receptors. The degree of current reduction correlated partially with the phenotype.\r\nResults reveal that rare loss-of-function variants in GABRA3 increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay and dysmorphic features, presenting in some pedigrees with an X-linked inheritance pattern. \nSources: Literature",
"entity_name": "GABRA3",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:54.255261+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.269",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Classified gene: KDM2B as Green List (high evidence)",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:54.225264+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.269",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Gene: kdm2b has been classified as Green List (High Evidence).",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:25.969778+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.505",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "changed review comment from: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \r\nSources: Literature; to: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \r\nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:24.902872+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.505",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Classified gene: SHROOM4 as Green List (high evidence)",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:24.888100+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.505",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "Gene: shroom4 has been classified as Green List (High Evidence).",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:16.564016+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.504",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "changed review comment from: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \r\nSources: Literature; to: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \r\nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:14.362882+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.268",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Marked gene: KDM2B as ready",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:14.350987+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.268",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "Gene: kdm2b has been classified as Red List (Low Evidence).",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:08.455295+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.504",
"user_name": "Melanie Marty",
"item_type": "entity",
"text": "changed review comment from: 7 individuals (males and females) with de novo variants involving TCEAL1. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \nSources: Literature; to: 7 individuals (males and females) with de novo variants involving TCEAL1 with an X-linked\r\ndominant neurodevelopmental syndrome. Individuals had hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features included strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies.\r\n\r\n1 additional male individual with a maternally inherited missense variant (unaffected mother), which was considered a VUS. This individual had hypertonia and spasticity without syndromic features.\r\n\r\n4 PTCs, 2 CNVs, 2 missense reported. \r\nSources: Literature",
"entity_name": "TCEAL1",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:33:03.947408+11:00",
"panel_name": "Congenital Heart Defect",
"panel_id": 76,
"panel_version": "0.268",
"user_name": "Ain Roesley",
"item_type": "entity",
"text": "gene: KDM2B was added\ngene: KDM2B was added to Congenital Heart Defect. Sources: Literature\nMode of inheritance for gene: KDM2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted\nPublications for gene: KDM2B were set to 36322151\nPhenotypes for gene: KDM2B were set to neurodevelopmental disorder MONDO#070009, KDM2B-related\nReview for gene: KDM2B was set to GREEN\ngene: KDM2B was marked as current diagnostic\nAdded comment: 27 individuals from 22 families were recruited \r\n13 SNV classified LP/P, all de novo except 2 familial cases\r\n5 variants were classified as VUS if more than 1 het is present in gnomAD or does result in a KDM2B-specific episignature (therefore suggesting normal function) \r\n\r\n14 families with SNVs and a variety of cardiac anomalies including ASD, VSD, MR, PDA, PFO, Atrial septal aneurysm and Mild mitral insufficiency \nSources: Literature",
"entity_name": "KDM2B",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:52.708978+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.848",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: UQCRH as Amber List (moderate evidence)",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:52.658746+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.848",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: uqcrh has been classified as Amber List (Moderate Evidence).",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:44.269130+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.847",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: UQCRH as ready",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:44.253258+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.847",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: uqcrh has been classified as Amber List (Moderate Evidence).",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:23.941746+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.504",
"user_name": "Alison Yeung",
"item_type": "entity",
"text": "reviewed gene: SHROOM4: Rating: GREEN; Mode of pathogenicity: None; Publications: 36379543, 35663265; Phenotypes: Congenital anomaly of the kidney and urinary tracy (CAKUT), SHROOM4-related, MONDO:0019719, epilepsy, idiopathic generalised, SHROOM4-related, MONDO:0005579; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females",
"entity_name": "SHROOM4",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:32:20.468279+11:00",
"panel_name": "Mendeliome",
"panel_id": 137,
"panel_version": "1.504",
"user_name": "Chern Lim",
"item_type": "entity",
"text": "gene: UQCRH was added\ngene: UQCRH was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: UQCRH was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: UQCRH were set to 34750991\nPhenotypes for gene: UQCRH were set to Mitochondrial complex III deficiency, nuclear type 11, MIM#620137\nReview for gene: UQCRH was set to AMBER\ngene: UQCRH was marked as current diagnostic\nAdded comment: PMID: 34750991:\r\n- Two affected cousins, presented with recurrent episodes of severe lactic acidosis, hyperammonaemia, hypoglycaemia and encephalopathy.\r\n- Both have a 2.2 kb homozygous deletion of exons 2 and 3 of UQCRH, predicted to culminate in an in-frame deletion exons 2 and 3 of the four-exon UQCRH gene, resulting in a shortened product. \r\n- Mouse model with the equivalent homozygous Uqcrh deletion (Uqcrh-/-) also presented with lactic acidosis and hyperammonaemia, but had a more severe, non-episodic phenotype, resulting in failure to thrive and early death. \r\n- Patient fibroblasts and Uqcrh-/- mouse tissues showed a CIII defect.\r\n- Expression of wild-type UQCRH in patient fibroblasts ameliorates the CIII defect. \nSources: Literature",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:31:56.133734+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.847",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Classified gene: UQCRH as Amber List (moderate evidence)",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:31:56.119233+11:00",
"panel_name": "Mitochondrial disease",
"panel_id": 203,
"panel_version": "0.847",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Gene: uqcrh has been classified as Amber List (Moderate Evidence).",
"entity_name": "UQCRH",
"entity_type": "gene"
},
{
"created": "2022-12-01T14:29:36.037364+11:00",
"panel_name": "Intellectual disability syndromic and non-syndromic",
"panel_id": 250,
"panel_version": "0.5053",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "Marked gene: FEM1C as ready",
"entity_name": "FEM1C",
"entity_type": "gene"
}
]
}