{"count":221304,"next":"https://panelapp-aus.org/api/v1/activities/?format=json&page=636","previous":"https://panelapp-aus.org/api/v1/activities/?format=json&page=634","results":[{"created":"2023-03-02T14:40:09.918347+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.695","user_name":"Seb Lunke","item_type":"entity","text":"Gene: amotl1 has been classified as Green List (High Evidence).","entity_name":"AMOTL1","entity_type":"gene"},{"created":"2023-03-02T14:38:59.718606+11:00","panel_name":"Hereditary Neuropathy - complex","panel_id":3070,"panel_version":"0.142","user_name":"Zornitza Stark","item_type":"entity","text":"Publications for gene: COQ7 were set to PMID: 36454683","entity_name":"COQ7","entity_type":"gene"},{"created":"2023-03-02T14:38:46.150855+11:00","panel_name":"Hyperammonaemia","panel_id":3470,"panel_version":"0.9","user_name":"Krithika Murali","item_type":"entity","text":"gene: SLC25A36 was added\ngene: SLC25A36 was added to Hyperammonaemia. Sources: Literature\nMode of inheritance for gene: SLC25A36 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: SLC25A36 were set to 34971397; 34576089; 31036718\nPhenotypes for gene: SLC25A36 were set to Hyperinsulinemic hypoglycemia, familial, 8 - MIM#620211\nReview for gene: SLC25A36 was set to GREEN\nAdded comment: Solute carrier family 25 members 33 (SLC25A33) and 36 (SLC25A36) are the only known mitochondrial pyrimidine nucleotide carriers in humans\r\n\r\nPMID: 34971397 Sharoor et al 2022 report 2 siblings with hyperinsulinism, hypoglycemia and hyperammonemia from early infancy with homozygous SLC25A36 c.284 + 3 A > T variant identified through WES. Functional studies support LoF.\r\n\r\nPMID: 34576089 report a 12-year-old patient with hypothyroidism, hyperinsulinism, hyperammonemia, chronical obstipation, short stature, along with language and general developmental delay. WES identified SLC25A36 gene homozygous c.803dupT, p.Ser269llefs*35 variant. Functional analysis of mutant SLC25A36 protein in proteoliposomes showed a virtually abolished transport activity. Immunoblotting results suggest that the mutant SLC25A36 protein in the patient undergoes fast degradation. Supplementation with uridine lead to some improvement in clinical course.\r\n\r\nPMID: 31036718 deficiencies in SLC25A36 in mouse embryonic stem cells have been associated with mtDNA depletion as well as mitochondrial dysfunction \nSources: Literature","entity_name":"SLC25A36","entity_type":"gene"},{"created":"2023-03-02T14:38:34.956281+11:00","panel_name":"Hereditary Neuropathy - complex","panel_id":3070,"panel_version":"0.141","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: COQ7 as Green List (high evidence)","entity_name":"COQ7","entity_type":"gene"},{"created":"2023-03-02T14:38:34.947950+11:00","panel_name":"Hereditary Neuropathy - complex","panel_id":3070,"panel_version":"0.141","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: coq7 has been classified as Green List (High Evidence).","entity_name":"COQ7","entity_type":"gene"},{"created":"2023-03-02T14:38:22.156992+11:00","panel_name":"Clefting disorders","panel_id":3368,"panel_version":"0.190","user_name":"Lucy Spencer","item_type":"entity","text":"reviewed gene: AMOTL1: Rating: GREEN; Mode of pathogenicity: None; Publications: 33026150; Phenotypes: Orofacial clefting syndrome, MONDO:0015335, AMOTL1-related; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted","entity_name":"AMOTL1","entity_type":"gene"},{"created":"2023-03-02T14:37:25.912592+11:00","panel_name":"Mitochondrial disease","panel_id":203,"panel_version":"0.856","user_name":"Ee Ming Wong","item_type":"entity","text":"gene: TEFM was added\ngene: TEFM was added to Mitochondrial disease. Sources: Literature\nMode of inheritance for gene: TEFM was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: TEFM were set to 36823193\nPhenotypes for gene: TEFM were set to Mitochondrial disease (MONDO#0044970), TEFM-related\nReview for gene: TEFM was set to GREEN\ngene: TEFM was marked as current diagnostic\nAdded comment: - Seven TEFM variants (4 missense, 2 fs, 1 in-frame del) in seven individuals across five unrelated families\r\n- Muscle and primary fibroblast from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts\r\n- TEFM knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function \nSources: Literature","entity_name":"TEFM","entity_type":"gene"},{"created":"2023-03-02T14:37:13.220429+11:00","panel_name":"Hyperinsulinism","panel_id":118,"panel_version":"1.7","user_name":"Krithika Murali","item_type":"entity","text":"gene: SLC25A36 was added\ngene: SLC25A36 was added to Hyperinsulinism. Sources: Literature\nMode of inheritance for gene: SLC25A36 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: SLC25A36 were set to 34971397; 34576089; 31036718\nPhenotypes for gene: SLC25A36 were set to Hyperinsulinemic hypoglycemia, familial, 8 - MIM#620211\nReview for gene: SLC25A36 was set to GREEN\nAdded comment: Solute carrier family 25 members 33 (SLC25A33) and 36 (SLC25A36) are the only known mitochondrial pyrimidine nucleotide carriers in humans\r\n\r\nPMID: 34971397 Sharoor et al 2022 report 2 siblings with hyperinsulinism, hypoglycemia and hyperammonemia from early infancy with homozygous SLC25A36 c.284 + 3 A > T variant identified through WES. Functional studies support LoF. \r\n\r\nPMID: 34576089 report a 12-year-old patient with hypothyroidism, hyperinsulinism, hyperammonemia, chronical obstipation, short stature, along with language and general developmental delay. WES identified SLC25A36 gene homozygous c.803dupT, p.Ser269llefs*35 variant. Functional analysis of mutant SLC25A36 protein in proteoliposomes showed a virtually abolished transport activity. Immunoblotting results suggest that the mutant SLC25A36 protein in the patient undergoes fast degradation. Supplementation with uridine lead to some improvement in clinical course.\r\n\r\nPMID: 31036718 deficiencies in SLC25A36 in mouse embryonic stem cells have been associated with mtDNA depletion as well as mitochondrial dysfunction \nSources: Literature","entity_name":"SLC25A36","entity_type":"gene"},{"created":"2023-03-02T14:32:40.051064+11:00","panel_name":"Hereditary Neuropathy - complex","panel_id":3070,"panel_version":"0.140","user_name":"Chern Lim","item_type":"entity","text":"reviewed gene: COQ7: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID:36758993, 36759155; Phenotypes: Distal hereditary motor neuropathy (MONDO#0018894), COQ7-related; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes","entity_name":"COQ7","entity_type":"gene"},{"created":"2023-03-02T14:32:28.289625+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.694","user_name":"Lucy Spencer","item_type":"entity","text":"reviewed gene: AMOTL1: Rating: GREEN; Mode of pathogenicity: None; Publications: 36751037; Phenotypes: Orofacial clefting syndrome, MONDO:0015335, AMOTL1 -related; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted","entity_name":"AMOTL1","entity_type":"gene"},{"created":"2023-03-02T14:31:36.446980+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.266","user_name":"Ain Roesley","item_type":"entity","text":"Phenotypes for gene: HMGB1 were changed from brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905 to brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:31:04.314586+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.265","user_name":"Ain Roesley","item_type":"entity","text":"Phenotypes for gene: HMGB1 were changed from Mirror image foot polydactyly to brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:30:42.623377+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.265","user_name":"Ain Roesley","item_type":"entity","text":"Publications for gene: HMGB1 were set to 34159400","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:30:37.295221+11:00","panel_name":"Fetal anomalies","panel_id":3763,"panel_version":"1.89","user_name":"Ain Roesley","item_type":"entity","text":"Phenotypes for gene: HMGB1 were changed from Neurodevelopmental disorder MONDO:0700092, HMGB1-related; microcephaly; intellectual disability to Neurodevelopmental disorder MONDO:0700092, HMGB1-related; microcephaly; intellectual disability; brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:30:34.838243+11:00","panel_name":"Fetal anomalies","panel_id":3763,"panel_version":"1.89","user_name":"Ain Roesley","item_type":"entity","text":"Publications for gene: HMGB1 were set to 34164801","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:30:20.023481+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.694","user_name":"Ain Roesley","item_type":"entity","text":"Phenotypes for gene: HMGB1 were changed from Mirror image foot polydactyly; Neurodevelopmental disorder MONDO:0700092, HMGB1-related to brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905; Neurodevelopmental disorder MONDO:0700092, HMGB1-related","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:30:19.748316+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.694","user_name":"Ain Roesley","item_type":"entity","text":"Publications for gene: HMGB1 were set to 34159400; 34164801","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:29:58.862424+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.693","user_name":"Elena Savva","item_type":"entity","text":"Phenotypes for gene: LGR4 were changed from {Bone mineral density, low, susceptibility to} MIM#615311; Delayed puberty, self-limited MIM#619613; Syndromic disease, LGR4-related (MONDO#0002254) to {Bone mineral density, low, susceptibility to} MIM#615311; Delayed puberty, self-limited MIM#619613; Syndromic disease, LGR4-related (MONDO#0002254)","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:29:57.633275+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.265","user_name":"Ain Roesley","item_type":"entity","text":"Classified gene: HMGB1 as Green List (high evidence)","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:29:57.619803+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.265","user_name":"Ain Roesley","item_type":"entity","text":"Gene: hmgb1 has been classified as Green List (High Evidence).","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:29:46.405599+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.692","user_name":"Elena Savva","item_type":"entity","text":"Phenotypes for gene: LGR4 were changed from Delayed puberty to {Bone mineral density, low, susceptibility to} MIM#615311; Delayed puberty, self-limited MIM#619613; Syndromic disease, LGR4-related (MONDO#0002254)","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:29:24.178263+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.691","user_name":"Ain Roesley","item_type":"entity","text":"edited their review of gene: HMGB1: Added comment: PMID:36755093\r\n4 new families with de novo protein truncating variants.\r\n\r\nIn addition with PMID 34159400 ( all de novos) \r\n\r\nc.556_559delGAAG;p.(Glu186Argfs*42) - 1 family\r\nc.551_554delAGAA;p.(Lys184Argfs*44) - 4 families; Changed rating: GREEN; Changed publications: 34159400, 36755093; Changed phenotypes: brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905; Set current diagnostic: yes","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:28:43.084911+11:00","panel_name":"Fetal anomalies","panel_id":3763,"panel_version":"1.88","user_name":"Ain Roesley","item_type":"entity","text":"reviewed gene: HMGB1: Rating: GREEN; Mode of pathogenicity: None; Publications: 36755093, 34159400; Phenotypes: brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905; Mode of inheritance: None; Current diagnostic: yes","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:28:14.153013+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.691","user_name":"Elena Savva","item_type":"entity","text":"Publications for gene: LGR4 were set to 32493844","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:27:57.326670+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.690","user_name":"Elena Savva","item_type":"entity","text":"Mode of inheritance for gene: LGR4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:27:55.244491+11:00","panel_name":"Polydactyly","panel_id":159,"panel_version":"0.264","user_name":"Ain Roesley","item_type":"entity","text":"edited their review of gene: HMGB1: Added comment: PMID:36755093\r\n4 new families with de novo protein truncating variants.\r\n\r\nIn addition with PMID 34159400,\r\n\r\nc.556_559delGAAG;p.(Glu186Argfs*42) - 1 family\r\nc.551_554delAGAA;p.(Lys184Argfs*44) - 4 families; Changed rating: GREEN; Changed publications: 34159400, 36755093; Changed phenotypes: brachyphalangy, polydactyly, and tibial aplasia/hypoplasia MIM#163905","entity_name":"HMGB1","entity_type":"gene"},{"created":"2023-03-02T14:27:53.849713+11:00","panel_name":"Neuroferritinopathies","panel_id":3438,"panel_version":"0.9","user_name":"Paul De Fazio","item_type":"entity","text":"gene: FTH1 was added\ngene: FTH1 was added to Neuroferritinopathies. Sources: Literature\nMode of inheritance for gene: FTH1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown\nPublications for gene: FTH1 were set to 36778397\nPhenotypes for gene: FTH1 were set to Neuroferritinopathy (MONDO:0011638)\nMode of pathogenicity for gene: FTH1 was set to Other\nReview for gene: FTH1 was set to AMBER\ngene: FTH1 was marked as current diagnostic\nAdded comment: Note paper is pre-print hence Amber rating.\r\n\r\n5 unrelated paediatric patients presented with developmental delay, epilepsy, and progressive neurologic decline. Heterozygous nonsense FTH1 variants were identified by WES in all patients, 4 of which were confirmed de novo. All variants are predicted to escape NMD and appear to act by a dominant toxic gain-of-function mechanism. p.F171* was recurrent in three unrelated individuals.\r\n\r\nPatient fibroblasts show elevated ferritin protein levels, markers of oxidative stress, and increased susceptibility to iron accumulation. Targeted knock-down of mutant FTH1 transcript with rescues cellular phenotypes.\r\n\r\nNote NMD-escape variants in gnomAD exist, upstream of the variants in patients. \nSources: Literature","entity_name":"FTH1","entity_type":"gene"},{"created":"2023-03-02T14:27:48.391751+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.34","user_name":"Zornitza Stark","item_type":"entity","text":"Marked gene: TRPV1 as ready","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T14:27:48.374475+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.34","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: trpv1 has been classified as Red List (Low Evidence).","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T14:27:42.226787+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.34","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: TRPV1 as Red List (low evidence)","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T14:27:42.217567+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.34","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: trpv1 has been classified as Red List (Low Evidence).","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T14:27:30.950838+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Elena Savva","item_type":"entity","text":"changed review comment from: PMID: 36538378 - hom canonical splice variant in an infant with failure to thrive, severe salt-wasting crises associated with isolated hypoaldosteronism, nail anomalies, short stature, and deafness. Multiple affected siblings but all deceased, two normal siblings found to be het or wildtype. Functional studies proved INFRAME exon 6 skipping, patients cell shad minimal protein.\r\nConditional K/O mouse model showed reduced expression of Wnt target genes, adrenal hypoplasia and aberrant zonal differentiation\r\n\r\ngnomAD: no hom PTCs\r\n\r\nPMID: 32493844 - 6 patients with delayed puberty, supported by functional studies on mice displaying impaired Wnt/β-catenin signaling. Recurring missense p.G363C present in 4/6 families, but super common in the population (67 homozygotes).; to: PMID: 36538378 - hom canonical splice variant in an infant with failure to thrive, severe salt-wasting crises associated with isolated hypoaldosteronism, nail anomalies, short stature, and deafness. Multiple affected siblings but all deceased, two normal siblings found to be het or wildtype. Functional studies proved INFRAME exon 6 skipping, patients cell shad minimal protein.\r\nConditional K/O mouse model showed reduced expression of Wnt target genes, adrenal hypoplasia and aberrant zonal differentiation\r\n\r\ngnomAD: no hom PTCs\r\n\r\nPMID: 32493844 - 6 patients with delayed puberty, supported by functional studies on mice displaying impaired Wnt/β-catenin signaling. Recurring missense p.G363C present in 4/6 families, but super common in the population (67 homozygotes).","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:22:03.374599+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Elena Savva","item_type":"entity","text":"edited their review of gene: LGR4: Added comment: PMID: 36538378 - hom canonical splice variant in an infant with failure to thrive, severe salt-wasting crises associated with isolated hypoaldosteronism, nail anomalies, short stature, and deafness. Multiple affected siblings but all deceased, two normal siblings found to be het or wildtype. Functional studies proved INFRAME exon 6 skipping, patients cell shad minimal protein.\r\nConditional K/O mouse model showed reduced expression of Wnt target genes, adrenal hypoplasia and aberrant zonal differentiation\r\n\r\ngnomAD: no hom PTCs\r\n\r\nPMID: 32493844 - 6 patients with delayed puberty, supported by functional studies on mice displaying impaired Wnt/β-catenin signaling. Recurring missense p.G363C present in 4/6 families, but super common in the population (67 homozygotes).; Changed publications: PMID: 32493844, 36538378; Changed phenotypes: {Bone mineral density, low, susceptibility to} MIM#615311; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal","entity_name":"LGR4","entity_type":"gene"},{"created":"2023-03-02T14:19:11.944622+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.33","user_name":"Krithika Murali","item_type":"entity","text":"changed review comment from: PMID: 36454632 Katz et al 2023 describe two individuals from a consanguineous Palestinian Arab family with elevated heat pain and cold pain threshold with insensitivity to application of capsaicin to mouth and skin. No obvious associated health issues reported in this 11 year old and 1 year old individual secondary to this. Homozygous TPRV1 c.993C>G; p.N331K variant identified in both individuals (absent from gnomAD, highly conserved). Variant cell lines demonstrated loss of channel function with normal expression. In addition, homozygous PROKR1 variant identified in both affected individuals with potential for contribution to phenotype. \r\n\r\nPMID: 36472910 - knockin mouse models with missense TRPV1 variant (K710N) also showed reduced capsaicin-induced calcium influx in dorsal root ganglion neurons. \nSources: Literature; to: PMID: 36454632 Katz et al 2023 describe two individuals from a consanguineous Palestinian Arab family with elevated heat pain and cold pain threshold with insensitivity to application of capsaicin to mouth and skin. No obvious associated health issues reported in this 11 year old and 1 year old individual secondary to this. Homozygous TPRV1 c.993C>G; p.N331K variant identified in both individuals (absent from gnomAD, highly conserved). Variant cell lines demonstrated loss of channel function with normal expression. In addition, homozygous PROKR1 gene variant identified in both affected individuals with potential for contribution to phenotype. \r\n\r\nPMID: 36472910 - knockin mouse models with missense TRPV1 variant (K710N) also showed reduced capsaicin-induced calcium influx in dorsal root ganglion neurons. \r\nSources: Literature","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T14:17:37.474417+11:00","panel_name":"Pain syndromes","panel_id":3126,"panel_version":"0.33","user_name":"Krithika Murali","item_type":"entity","text":"gene: TRPV1 was added\ngene: TRPV1 was added to Pain syndromes. Sources: Literature\nMode of inheritance for gene: TRPV1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: TRPV1 were set to PMID: 36454632; PMID: 36472910\nPhenotypes for gene: TRPV1 were set to Channelopathy-associated congenital insensitivity to pain, autosomal recessive - MONDO:0009459\nReview for gene: TRPV1 was set to RED\nAdded comment: PMID: 36454632 Katz et al 2023 describe two individuals from a consanguineous Palestinian Arab family with elevated heat pain and cold pain threshold with insensitivity to application of capsaicin to mouth and skin. No obvious associated health issues reported in this 11 year old and 1 year old individual secondary to this. Homozygous TPRV1 c.993C>G; p.N331K variant identified in both individuals (absent from gnomAD, highly conserved). Variant cell lines demonstrated loss of channel function with normal expression. In addition, homozygous PROKR1 variant identified in both affected individuals with potential for contribution to phenotype. \r\n\r\nPMID: 36472910 - knockin mouse models with missense TRPV1 variant (K710N) also showed reduced capsaicin-induced calcium influx in dorsal root ganglion neurons. \nSources: Literature","entity_name":"TRPV1","entity_type":"gene"},{"created":"2023-03-02T12:52:01.265302+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Bryony Thompson","item_type":"entity","text":"Marked gene: USMG5 as ready","entity_name":"USMG5","entity_type":"gene"},{"created":"2023-03-02T12:52:01.232976+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Bryony Thompson","item_type":"entity","text":"Gene: usmg5 has been classified as Amber List (Moderate Evidence).","entity_name":"USMG5","entity_type":"gene"},{"created":"2023-03-02T12:51:42.915917+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Bryony Thompson","item_type":"entity","text":"Classified gene: USMG5 as Amber List (moderate evidence)","entity_name":"USMG5","entity_type":"gene"},{"created":"2023-03-02T12:51:42.906542+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.689","user_name":"Bryony Thompson","item_type":"entity","text":"Gene: usmg5 has been classified as Amber List (Moderate Evidence).","entity_name":"USMG5","entity_type":"gene"},{"created":"2023-03-02T10:29:14.553984+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.688","user_name":"Bryony Thompson","item_type":"entity","text":"gene: USMG5 was added\ngene: USMG5 was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: USMG5 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: USMG5 were set to 29917077; 30240627\nPhenotypes for gene: USMG5 were set to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 6 MIM#618683\nReview for gene: USMG5 was set to AMBER\nAdded comment: A homozygous splice site mutation in 4 patients from 3 unrelated families of Ashkenazi Jewish descent. Experimental analyses demonstrated that the splice variant leads to loss of protein expression and haplotype analysis suggested a founder effect. In situ cryo-ET analysis of the mitochondria of a homozygous affected case showed profound disturbances of mitochondrial crista ultrastructure. \nSources: Literature","entity_name":"USMG5","entity_type":"gene"},{"created":"2023-03-02T06:58:23.517303+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5181","user_name":"Zornitza Stark","item_type":"entity","text":"Marked gene: SLC35B2 as ready","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:58:23.509373+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5181","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: slc35b2 has been classified as Amber List (Moderate Evidence).","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:58:15.968796+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5181","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: SLC35B2 as Amber List (moderate evidence)","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:58:15.959601+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5181","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: slc35b2 has been classified as Amber List (Moderate Evidence).","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:57:43.371516+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5180","user_name":"Zornitza Stark","item_type":"entity","text":"gene: SLC35B2 was added\ngene: SLC35B2 was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: SLC35B2 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: SLC35B2 were set to 35325049\nPhenotypes for gene: SLC35B2 were set to Leukodystrophy, hypomyelinating, 26, with chondrodysplasia, MIM# 620269\nReview for gene: SLC35B2 was set to AMBER\nAdded comment: 2 x individuals with homozygous variants (c.1218_1220del and c.1224_1225del) in SLC35B2. Phenotypes included pre- and postnatal growth retardation, scoliosis, severe motor and intellectual disabilities and hypomyelinating leukodystrophy. Functional analysis on patient cells showed that the variants result in a decreased expression of mRNA and affect protein subcellular localization leading to functional impairment of the protein. \nSources: Literature","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:55:54.597209+11:00","panel_name":"Leukodystrophy - paediatric","panel_id":298,"panel_version":"0.282","user_name":"Zornitza Stark","item_type":"entity","text":"edited their review of gene: SLC35B2: Changed phenotypes: Leukodystrophy, hypomyelinating, 26, with chondrodysplasia, MIM# 620269","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:55:36.266219+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.687","user_name":"Zornitza Stark","item_type":"entity","text":"Phenotypes for gene: SLC35B2 were changed from Leukodystrophy, MONDO:0019046, SLC35B2-related to Leukodystrophy, hypomyelinating, 26, with chondrodysplasia, MIM# 620269","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T06:55:14.763723+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.686","user_name":"Zornitza Stark","item_type":"entity","text":"reviewed gene: SLC35B2: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: Leukodystrophy, hypomyelinating, 26, with chondrodysplasia, MIM# 620269; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"SLC35B2","entity_type":"gene"},{"created":"2023-03-02T01:35:47.465299+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5179","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"reviewed gene: EMC1: Rating: GREEN; Mode of pathogenicity: None; Publications: 35234901; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal","entity_name":"EMC1","entity_type":"gene"},{"created":"2023-03-01T19:58:15.288573+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5179","user_name":"Zornitza Stark","item_type":"entity","text":"Marked gene: ATG4D as ready","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:58:15.278955+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5179","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: atg4d has been classified as Green List (High Evidence).","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:58:09.975089+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5179","user_name":"Zornitza Stark","item_type":"entity","text":"Phenotypes for gene: ATG4D were changed from neurodevelopmental disorder; Abnormal facial shape to Neurodevelopmental disorder, MONDO:0700092, ATG4D-related","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:57:36.062668+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5178","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: ATG4D as Green List (high evidence)","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:57:36.050595+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5178","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: atg4d has been classified as Green List (High Evidence).","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:57:03.631627+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5177","user_name":"Zornitza Stark","item_type":"entity","text":"reviewed gene: ATG4D: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Neurodevelopmental disorder, MONDO:0700092, ATG4D-related; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:56:45.567679+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.686","user_name":"Zornitza Stark","item_type":"entity","text":"Marked gene: ATG4D as ready","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:56:45.553979+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.686","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: atg4d has been classified as Green List (High Evidence).","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:56:36.594222+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.686","user_name":"Zornitza Stark","item_type":"entity","text":"Phenotypes for gene: ATG4D were changed from neurodevelopmental disorder; Abnormal facial shape to Neurodevelopmental disorder, MONDO:0700092, ATG4D-related","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:56:14.913017+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.685","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: ATG4D as Green List (high evidence)","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:56:14.902969+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.685","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: atg4d has been classified as Green List (High Evidence).","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T19:55:56.173303+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Zornitza Stark","item_type":"entity","text":"reviewed gene: ATG4D: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Neurodevelopmental disorder, MONDO:0700092, ATG4D-related; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-03-01T16:29:47.185547+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Elena Savva","item_type":"entity","text":"reviewed gene: NLGN4X: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 36747195; Phenotypes: Intellectual developmental disorder, X-linked MIM#300495; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)","entity_name":"NLGN4X","entity_type":"gene"},{"created":"2023-03-01T15:20:12.552715+11:00","panel_name":"Proteinuria","panel_id":144,"panel_version":"0.215","user_name":"Ain Roesley","item_type":"entity","text":"Phenotypes for gene: GLA were changed from Fairy disease, MIM#\t301500 to Fabry disease, MIM#\t301500","entity_name":"GLA","entity_type":"gene"},{"created":"2023-02-28T16:24:43.758553+11:00","panel_name":"Disorders of immune dysregulation","panel_id":229,"panel_version":"0.166","user_name":"Peter McNaughton","item_type":"entity","text":"gene: DOCK2 was added\ngene: DOCK2 was added to Disorders of immune dysregulation. Sources: Literature\nMode of inheritance for gene: DOCK2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted\nPublications for gene: DOCK2 were set to PMID: 36836791\nPhenotypes for gene: DOCK2 were set to HLH\nReview for gene: DOCK2 was set to AMBER\nAdded comment: Patient with recurrent HLH.  Heterozygous c.1334A>G (p.Asn445Ser) variant.  Functional studies showing lower CD107a expression and diminished NK degranulation and cytotoxicity.  ? partial dominant negative. \nSources: Literature","entity_name":"DOCK2","entity_type":"gene"},{"created":"2023-02-28T11:28:54.177624+11:00","panel_name":"Hyperammonaemia","panel_id":3470,"panel_version":"0.9","user_name":"Bryony Thompson","item_type":"panel","text":"Panel types changed to Victorian Clinical Genetics Services; Royal Melbourne Hospital; Rare Disease","entity_name":null,"entity_type":null},{"created":"2023-02-27T12:48:18.211482+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: MAT1A: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Methionine adenosyltransferase deficiency MIM#250850; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal","entity_name":"MAT1A","entity_type":"gene"},{"created":"2023-02-27T12:45:22.979002+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"gene: LIAS was added\ngene: LIAS was added to gNBS. Sources: Expert list\nMode of inheritance for gene: LIAS was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: LIAS were set to PMID: 24334290, 24777537,\nPhenotypes for gene: LIAS were set to Hyperglycinemia, lactic acidosis, and seizures MIM#614462\nReview for gene: LIAS was set to RED\nAdded comment: pyruvate dehydrogenase lipoic acid synthetase deficiency (PDHLD)\r\nincreased serum glycine and lactate in the first days of life, hypotonia, seizures, early death\r\nNo treatment \nSources: Expert list","entity_name":"LIAS","entity_type":"gene"},{"created":"2023-02-27T12:35:52.023927+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: HPD: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 9343288, PMID: 11916315, PMID: 32520295; Phenotypes: Tyrosinemia, type III MIM#276710; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal","entity_name":"HPD","entity_type":"gene"},{"created":"2023-02-27T12:27:19.087066+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"gene: HMGCS2 was added\ngene: HMGCS2 was added to gNBS. Sources: Expert list\nMode of inheritance for gene: HMGCS2 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: HMGCS2 were set to PMID: 32259399, 32470406\nPhenotypes for gene: HMGCS2 were set to HMG-CoA synthase-2 deficiency MIM#605911\nPenetrance for gene: HMGCS2 were set to Incomplete\nReview for gene: HMGCS2 was set to AMBER\nAdded comment: Metabolic disorder; patients present with hypoketotic hypoglycemia, encephalopathy, and hepatomegaly, usually precipitated by an intercurrent infection or prolonged fasting. Recover completely between illnesses, do develop fatty liver. \r\n?incomplete penetrance or variable age of onset \r\nOn GUARDIAN and Rx Genes \r\nRx IV glucose during acute episodes, avoid prolonged fasting\r\nMetabolic parameters are normal in between episodes, so no ability to do a confirmatory biochemical test. \r\nPros: readily treatable if child has an episode Cons: unncessary worry as child may never have episode \r\nSuper rare ?30 cases \r\nDiscuss with JC? \nSources: Expert list","entity_name":"HMGCS2","entity_type":"gene"},{"created":"2023-02-27T12:15:42.757521+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: HIBCH: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 32642440, PMID: 17160907, PMID: 27400804; Phenotypes: 3-hydroxyisobutryl-CoA hydrolase deficiency MIM#250620; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"HIBCH","entity_type":"gene"},{"created":"2023-02-25T06:22:30.149638+11:00","panel_name":"Skeletal dysplasia","panel_id":258,"panel_version":"0.229","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"gene: DDRGK1 was added\ngene: DDRGK1 was added to Skeletal dysplasia. Sources: Literature\nMode of inheritance for gene: DDRGK1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: DDRGK1 were set to 28263186; 35377455; 35670300; 36243336\nPhenotypes for gene: DDRGK1 were set to Spondyloepimetaphyseal dysplasia, Shohat type, OMIM:602557\nReview for gene: DDRGK1 was set to GREEN\nAdded comment: Comment on gene classification: This gene should be rated GREEN as it has been associated with Spondyloepimetaphyseal dysplasia, Shohat type from seven unrelated cases from multiple ethnicities and supported by functional studies. \r\n\r\nPMID:28263186 reported six individuals from three different families of Iraqi Jewish descent (three patients from family 1 and one individual each from families 2-4) identified with homozygous c.408+1G>A donor splice site loss-of-function mutation in DDRGK1 and presented with Shohat-type spondyloepimetaphyseal dysplasia (SEMD). It is a skeletal dysplasia that affects cartilage development.\r\n\r\nPMID: 35670300 reported two unrelated cases of Moroccan descent identified with homozygous missense variant c.406G>A and presented with SEMD. PMID:36243336 reported an Omani female patient identified with the same homozygous variant as the Iraqi cases and was reported with SEMD.\r\n\r\nIn addition, studies on both zebrafish and mouse models confirms the physiological role of DDRGK1 in the development and maintenance of the growth plate cartilage and deficiency of DDRGK1 recapitulate the clinical phenotype of short stature and joint abnormalities observed in patients with Shohat type SEMD (PMID:28263186; PMID:35377455).\r\n\r\nThis gene has been associated with relevant phenotype in OMIM (MIM #602557), but not in Gene2Phenotype. \nSources: Literature","entity_name":"DDRGK1","entity_type":"gene"},{"created":"2023-02-24T21:41:57.154722+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: GLIS3: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 29406006, 29992946, 27899417, PMID: 26259131; Phenotypes: Diabetes mellitus, neonatal, with congenital hypothyroidism MIM#610199; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"GLIS3","entity_type":"gene"},{"created":"2023-02-24T21:30:33.199679+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"gene: GATM was added\ngene: GATM was added to gNBS. Sources: Expert list\nMode of inheritance for gene: GATM was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: GATM were set to PMID: 20301745, 34972654\nPhenotypes for gene: GATM were set to Cerebral creatine deficiency syndrome 3 MIM#612718\nReview for gene: GATM was set to GREEN\nAdded comment: GUARDIAN gene list (not on babyseq or rxgenes)\r\nID and myopathy, early onset \r\nRx creatine\r\nSeems like a good fit? I'm not clear from the literature how effective the treatment is. check with JC \nSources: Expert list","entity_name":"GATM","entity_type":"gene"},{"created":"2023-02-24T21:22:43.137515+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: FOXE1: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 33272083, 2918525,  20453517, 35963604; Phenotypes: Bamforth-Lazarus syndrome MIM# 241850; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"FOXE1","entity_type":"gene"},{"created":"2023-02-24T21:02:38.673144+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: ALDH4A1: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 31884946, 34037900, 30930802,  34302426; Phenotypes: Hyperprolinemia, type II MIM#239510; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ALDH4A1","entity_type":"gene"},{"created":"2023-02-24T20:29:03.740495+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: ACADSB: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: 2-methylbutyrylglycinuria MIM#610006; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ACADSB","entity_type":"gene"},{"created":"2023-02-23T14:49:11.946729+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Suliman Khan","item_type":"entity","text":"reviewed gene: CRIPT: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36630262; Phenotypes: Short stature with microcephaly and distinctive facies; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"CRIPT","entity_type":"gene"},{"created":"2023-02-23T14:48:10.135856+11:00","panel_name":"Fetal anomalies","panel_id":3763,"panel_version":"1.88","user_name":"Suliman Khan","item_type":"entity","text":"reviewed gene: CRIPT: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36630262; Phenotypes: Short stature with microcephaly and distinctive facies; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"CRIPT","entity_type":"gene"},{"created":"2023-02-23T14:46:32.138632+11:00","panel_name":"Growth failure","panel_id":3631,"panel_version":"1.59","user_name":"Suliman Khan","item_type":"entity","text":"reviewed gene: CRIPT: Rating: ; Mode of pathogenicity: None; Publications: PMID: 36630262; Phenotypes: Short stature with microcephaly and distinctive facies; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"CRIPT","entity_type":"gene"},{"created":"2023-02-23T14:44:07.416152+11:00","panel_name":"Microcephaly","panel_id":138,"panel_version":"1.194","user_name":"Suliman Khan","item_type":"entity","text":"changed review comment from: PMID: 36630262 reported a patient with profound prenatal/postnatal growth restriction, developmental delay, dysmorphic facial features, and skin lesions along with the findings of bicytopenia and extensive retinal pigmentation defect. A novel truncating homozygous variant c.7_8delTG; p.(Cys3Argfs*4) was detected in CRIPT gene.; to: PMID: 36630262 reported a patient with profound prenatal/postnatal growth restriction, developmental delay, dysmorphic facial features, and skin lesions along with the findings of bicytopenia and extensive retinal pigmentation defect. A novel truncating homozygous variant was detected in CRIPT gene.","entity_name":"CRIPT","entity_type":"gene"},{"created":"2023-02-23T14:43:32.465307+11:00","panel_name":"Microcephaly","panel_id":138,"panel_version":"1.194","user_name":"Suliman Khan","item_type":"entity","text":"reviewed gene: CRIPT: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 36630262; Phenotypes: short stature, microcephaly, distinctive facies; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"CRIPT","entity_type":"gene"},{"created":"2023-02-23T14:40:04.838490+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: ACADS: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Acyl-CoA dehydrogenase, short-chain, deficiency of MIM#201470; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ACADS","entity_type":"gene"},{"created":"2023-02-23T14:33:03.857113+11:00","panel_name":"gNBS","panel_id":3931,"panel_version":"0.1872","user_name":"Lilian Downie","item_type":"entity","text":"reviewed gene: ABCD4: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 22922874, PMID: 33729671; Phenotypes: Methylmalonic aciduria and homocystinuria, cblJ type MIM#614857; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal","entity_name":"ABCD4","entity_type":"gene"},{"created":"2023-02-23T04:17:00.368636+11:00","panel_name":"Congenital nystagmus","panel_id":3762,"panel_version":"1.17","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"gene: ROBO1 was added\ngene: ROBO1 was added to Congenital nystagmus. Sources: Literature\nMode of inheritance for gene: ROBO1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: ROBO1 were set to 35348658\nPhenotypes for gene: ROBO1 were set to nystagmus, congenital, autosomal recessive, MONDO:0009762\nReview for gene: ROBO1 was set to RED\nAdded comment: Comment on classification of gene: This gene should be rated RED as this gene has been associated with nystagmus from only one family.\r\n\r\nPMID:35348658 reported three male siblings from the same family with nystagmus and they were identified with a homozygous missense variant p.Ser1522Leu.\r\n\r\nThis gene has not yet been associated with any phenotypes either in OMIM or Gene2Phenotype. \nSources: Literature","entity_name":"ROBO1","entity_type":"gene"},{"created":"2023-02-23T03:42:48.693110+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5177","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"gene: ROBO1 was added\ngene: ROBO1 was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: ROBO1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: ROBO1 were set to 28286008; 30692597; 35227688; 35348658\nPhenotypes for gene: ROBO1 were set to intellectual disability, MONDO:0001071\nReview for gene: ROBO1 was set to GREEN\nAdded comment: Comment on gene classification: This gene should be rated green as this gene has been associated with intellectual disability from six unrelated cases. However, the MOI should be set as \"BIALLELIC, autosomal or pseudoautosomal\"  as five of these cases were reported with biallelic variants and only one case was reported with monoallelic variant.\r\n\r\nPMID:28286008 reported a boy with compound heterozygous variants that was presented with developmental delay in 13 months and had severe intellectual disability and hyperactivity at nine years of age. He was nonverbal and wheelchair dependent because of spastic diplegia and ataxia.\r\n\r\nPMID:30692597 reported a five year old boy identified with a homozygous ROBO1 variant who had combined pituitary hormone deficiency, psychomotor developmental delay, severe intellectual disability, sensorineural hearing loss, strabismus and characteristic facial features.\r\n\r\nPMID:35227688 reported eight patients including the boy reported in PMID:30692597. Of the other seven patients, three were presented with intellectual disability. Of these three patients, two harboured compound heterozygous and one harboured homozygous variants.\r\n\r\nPMID:35348658 reported a patient identified with monoallelic de novo variant (p.D422G) who presented with early-onset epileptic encephalopathy and had severe developmental delay.\r\n\r\nThis gene has not yet been associated with any phenotypes in OMIM or Gene2Phenotype. \nSources: Literature","entity_name":"ROBO1","entity_type":"gene"},{"created":"2023-02-23T01:51:36.632839+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"gene: ELOC was added\ngene: ELOC was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: ELOC was set to Unknown\nPublications for gene: ELOC were set to 35323939\nPhenotypes for gene: ELOC were set to von Hippel-Lindau disease, MONDO:0008667; renal cell carcinoma, MONDO:0005086; retinal hemangioblastoma, MONDO:0003343\nReview for gene: ELOC was set to RED\nAdded comment: Comment on gene classification: This gene should be rated red as there is only one case with germline variant found so far.\r\n\r\nA female patient was identified with a germline de novo missense variant in ELOC gene (c.236A>G/ p.Tyr79Cys) and satisfied the clinical diagnostic criteria for von Hippel-Lindau (VHL) disease. The patient had left retinal haemangioblastomas, renal cell carcinomas, cyst of the right kidney, spinal haemangioblastoma, a haemangioblastoma at the cervicomedullary junction and Henoch-Schonlein purpura (PMID:35323939). \r\n\r\nThis is the only germline variant detected in ELOC gene and was associated with VHL so far. However, ~20 somatic ELOC variants have been reported to be associated with renal cell carcinomas so far.\r\n\r\nThis gene has not yet been associated with relevant phenotypes in OMIM or Gene2Phenotype. \nSources: Literature","entity_name":"ELOC","entity_type":"gene"},{"created":"2023-02-22T00:56:54.831630+11:00","panel_name":"Ectodermal Dysplasia","panel_id":3089,"panel_version":"0.80","user_name":"Achchuthan Shanmugasundram","item_type":"entity","text":"gene: RIPK4 was added\ngene: RIPK4 was added to Ectodermal Dysplasia. Sources: Literature\nMode of inheritance for gene: RIPK4 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: RIPK4 were set to 26129644; 28940926; 33713555; 35220430\nPhenotypes for gene: RIPK4 were set to CHAND syndrome, OMIM:214350; Popliteal pterygium syndrome, Bartsocas-Papas type 1, OMIM:263650; ectodermal dysplasia syndrome, MONDO:0019287\nReview for gene: RIPK4 was set to GREEN\nAdded comment: Comment on classification of gene: RIPK4 should be rated green as biallelic variants in this gene has been implicated in ectodermal dysplasias (ED) of varying severity in multiple (>3) unrelated patients and supported by functional studies.\r\n\r\nThis gene has already been associated with relevant phenotypes in both OMIM and Gene2Phenotype.\r\n\r\nThe clinically distinct ED syndromes reported with RIPK4 variants include early lethal BPS (MIM #263650) and milder forms such as PPS and CHAND syndrome (MIM #214350). BPS1 is characterized by multiple popliteal pterygia, ankyloblepharon, filiform bands between the jaws, cleft lip and palate, and syndactyly and CHAND is characterized by ankyloblepharon, sparse, curly, and woolly hair, nail dysplasia, and oral frenula.\r\n\r\nPMID:35220430 reported two siblings with novel biallelic (compound heterozygous) variants presented with cutaneous syndactyly associated to hair defects, alopecia, nail dysplasia and hyperkeratosis. This phenotype expands the clinical spectrum of the disorder further and is intermediary between BPS and CHAND syndrome. \nSources: Literature","entity_name":"RIPK4","entity_type":"gene"},{"created":"2023-02-21T17:32:41.564662+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Suliman Khan","item_type":"entity","text":"gene: ATG4D was added\ngene: ATG4D was added to Mendeliome. Sources: Literature\nMode of inheritance for gene: ATG4D was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: ATG4D were set to PMID: 36765070\nPhenotypes for gene: ATG4D were set to neurodevelopmental disorder; Abnormal facial shape\nPenetrance for gene: ATG4D were set to unknown\nReview for gene: ATG4D was set to GREEN\nAdded comment: PMID: 36765070 reported three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment with a similar facial gestalt comprising almond-shaped eyes, depressed nasal bridge, and a prominent Cupid’s bow with variable disease severity and progression. NGS analysis revealed bi-allelic loss-of-function variants in ATG4D gene. Based on the clinical, bioinformatic, and functional data, the author concluded that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of syndromic neurodevelopmental disorder. \nSources: Literature","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-02-21T16:45:26.180381+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5177","user_name":"Suliman Khan","item_type":"entity","text":"gene: ATG4D was added\ngene: ATG4D was added to Intellectual disability syndromic and non-syndromic. Sources: Literature\nMode of inheritance for gene: ATG4D was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: ATG4D were set to PMID: 36765070\nPhenotypes for gene: ATG4D were set to neurodevelopmental disorder; Abnormal facial shape\nPenetrance for gene: ATG4D were set to unknown\nReview for gene: ATG4D was set to GREEN\nAdded comment: PMID: 36765070 reported three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment with a similar facial gestalt comprising almond-shaped eyes, depressed nasal bridge, and a prominent Cupid’s bow with variable disease severity and progression. NGS analysis revealed bi-allelic loss-of-function variants in ATG4D gene. Based on the clinical, bioinformatic, and functional data, the author concluded that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of syndromic neurodevelopmental disorder. \nSources: Literature","entity_name":"ATG4D","entity_type":"gene"},{"created":"2023-02-20T15:34:59.053178+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.684","user_name":"Zornitza Stark","item_type":"entity","text":"Phenotypes for gene: TRPM3 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures, MIM# 620224 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures, MIM# 620224; Cataract 50 with or without glaucoma, MIM#620253","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:34:31.048145+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.683","user_name":"Zornitza Stark","item_type":"entity","text":"Publications for gene: TRPM3 were set to 31278393","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:34:06.917181+11:00","panel_name":"Mendeliome","panel_id":137,"panel_version":"1.682","user_name":"Zornitza Stark","item_type":"entity","text":"edited their review of gene: TRPM3: Added comment: Publications 25090642; 33484482: Single multi-generational family reported with a missense variant in this gene and cataract. Mouse model of same variant supports association. Amber for this association.; Changed publications: 31278393, 25090642, 33484482; Changed phenotypes: Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures, MIM# 620224, Cataract 50 with or without glaucoma, MIM#620253","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:33:38.968363+11:00","panel_name":"Cataract","panel_id":66,"panel_version":"0.350","user_name":"Zornitza Stark","item_type":"entity","text":"Marked gene: TRPM3 as ready","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:33:38.953572+11:00","panel_name":"Cataract","panel_id":66,"panel_version":"0.350","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: trpm3 has been classified as Amber List (Moderate Evidence).","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:32:55.672369+11:00","panel_name":"Cataract","panel_id":66,"panel_version":"0.350","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: TRPM3 as Amber List (moderate evidence)","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:32:55.665445+11:00","panel_name":"Cataract","panel_id":66,"panel_version":"0.350","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: trpm3 has been classified as Amber List (Moderate Evidence).","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-20T15:32:27.658888+11:00","panel_name":"Cataract","panel_id":66,"panel_version":"0.349","user_name":"Zornitza Stark","item_type":"entity","text":"gene: TRPM3 was added\ngene: TRPM3 was added to Cataract. Sources: Expert list\nMode of inheritance for gene: TRPM3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted\nPublications for gene: TRPM3 were set to 25090642; 33484482\nPhenotypes for gene: TRPM3 were set to Cataract 50 with or without glaucoma, MIM#620253\nReview for gene: TRPM3 was set to AMBER\nAdded comment: Single multi-generational family reported with a missense variant in this gene and cataract. Mouse model of same variant. \nSources: Expert list","entity_name":"TRPM3","entity_type":"gene"},{"created":"2023-02-18T17:36:27.942294+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5177","user_name":"Zornitza Stark","item_type":"entity","text":"Publications for gene: PPM1K were set to 23086801","entity_name":"PPM1K","entity_type":"gene"},{"created":"2023-02-18T17:35:06.423271+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5176","user_name":"Zornitza Stark","item_type":"entity","text":"Classified gene: PPM1K as Amber List (moderate evidence)","entity_name":"PPM1K","entity_type":"gene"},{"created":"2023-02-18T17:35:06.385880+11:00","panel_name":"Intellectual disability syndromic and non-syndromic","panel_id":250,"panel_version":"0.5176","user_name":"Zornitza Stark","item_type":"entity","text":"Gene: ppm1k has been classified as Amber List (Moderate Evidence).","entity_name":"PPM1K","entity_type":"gene"}]}