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Prepair 1000+ v1.2080 SLC30A10 Zornitza Stark Phenotypes for gene: SLC30A10 were changed from Hypermanganesemia with dystonia, polycythemia, and cirrhosis, 613280 (3) to Hypermanganesemia with dystonia 1, MIM#613280
Prepair 1000+ v1.1924 GM2A Zornitza Stark Phenotypes for gene: GM2A were changed from GM2-gangliosidosis, AB variant, 272750 (3) to GM2-gangliosidosis, AB variant MIM #272750
Prepair 1000+ v1.1822 SLC30A10 Crystle Lee reviewed gene: SLC30A10: Rating: GREEN; Mode of pathogenicity: None; Publications: 38283630, 34877518, 22341971; Phenotypes: Hypermanganesemia with dystonia 1, MIM#613280; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1811 SCO1 Andrew Coventry changed review comment from: Four unrelated families reported, typically presenting with lactatic acidosis and encephalopathy in infancy. SCO1 pathogenic variants were first described in an infant with respiratory distress, metabolic acidosis, hepatic failure, and encephalopathy in the setting of profound complex IV deficiency in muscle and liver. Further reports have shown phenotypic spectrum to include cardiomyopathy, encephalopathy, and lactic acidosis without cardiac or hepatic involvement. Many cases are fatal in the first few months of life.
Functional studies and model organisms also present.

ClinGen: While various names have been given to the constellation of features seen in those with SCO1-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the SCO1 phenotype has been lumped into one disease entity.
Sources: Literature; to: Six unrelated families reported.
Typically presenting with lactatic acidosis and encephalopathy in infancy. SCO1 pathogenic variants were first described in an infant with respiratory distress, metabolic acidosis, hepatic failure, and encephalopathy in the setting of profound complex IV deficiency in muscle and liver. Further reports have shown phenotypic spectrum to include cardiomyopathy, encephalopathy, and lactic acidosis without cardiac or hepatic involvement. Many cases are fatal in the first few months of life.
Functional studies and model organisms also present.

ClinGen: While various names have been given to the constellation of features seen in those with SCO1-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the SCO1 phenotype has been lumped into one disease entity.

PMID: 39214134: 3 cases from 2 unrelated families, with developmental and epileptic encephalopathy, hypopituitarism.
Prepair 1000+ v1.1811 SCO1 Andrew Coventry gene: SCO1 was added
gene: SCO1 was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: SCO1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SCO1 were set to 11013136; 19295170; 31352446; 23878101
Phenotypes for gene: SCO1 were set to Mitochondrial disease MONDO:0044970; Mitochondrial complex IV deficiency, nuclear type 4 MIM#619048
Review for gene: SCO1 was set to GREEN
Added comment: Four unrelated families reported, typically presenting with lactatic acidosis and encephalopathy in infancy. SCO1 pathogenic variants were first described in an infant with respiratory distress, metabolic acidosis, hepatic failure, and encephalopathy in the setting of profound complex IV deficiency in muscle and liver. Further reports have shown phenotypic spectrum to include cardiomyopathy, encephalopathy, and lactic acidosis without cardiac or hepatic involvement. Many cases are fatal in the first few months of life.
Functional studies and model organisms also present.

ClinGen: While various names have been given to the constellation of features seen in those with SCO1-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the SCO1 phenotype has been lumped into one disease entity.
Sources: Literature
Prepair 1000+ v1.1568 HEXA Karina Sandoval reviewed gene: HEXA: Rating: GREEN; Mode of pathogenicity: None; Publications: 31388111, 20301397; Phenotypes: Tay-Sachs disease, GM2-gangliosidosis, several forms, [Hex A pseudodeficiency], MIM#272800; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1460 PKD1L1 Lilian Downie gene: PKD1L1 was added
gene: PKD1L1 was added to Prepair 1000+. Sources: Expert list
Mode of inheritance for gene: PKD1L1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PKD1L1 were set to PMID: 33655537; PMID: 27616478
Phenotypes for gene: PKD1L1 were set to Heterotaxy, visceral, 8, autosomal MIM#617205
Review for gene: PKD1L1 was set to AMBER
Added comment: Variable penetrance but can cause major organ malformation, particularly cardiac, intestinal malformation, ciliary dyskinesia, hydrops.
Sources: Expert list
Prepair 1000+ v1.1436 SLC39A14 Zornitza Stark Phenotypes for gene: SLC39A14 were changed from Hypermanganesemia with dystonia 2, 617013 (3), Autosomal recessive to Hypermanganesaemia with dystonia 2, MIM# 617013
Prepair 1000+ v1.1397 SLC39A14 Clare Hunt reviewed gene: SLC39A14: Rating: GREEN; Mode of pathogenicity: None; Publications: 27431290, 29498153, 27231142, 30232769; Phenotypes: Hypermanganesemia with dystonia 2, MIM# 617013; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.608 GM2A Kate Scarff reviewed gene: GM2A: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 28417072, 28192816, 27402091, 33819415; Phenotypes: GM2-gangliosidosis, AB variant MIM #272750; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.545 GLB1 Zornitza Stark Phenotypes for gene: GLB1 were changed from Mucopolysaccharidosis type IVB (Morquio), 253010 (3) to GM1-gangliosidosis, type I MIM#230500; GM1-gangliosidosis, type II MIM#230600; GM1-gangliosidosis, type III MIM#230650; Mucopolysaccharidosis type IVB (Morquio) MIM#253010
Prepair 1000+ v1.521 GLB1 Andrew Coventry reviewed gene: GLB1: Rating: GREEN; Mode of pathogenicity: None; Publications: 34539759 24156116 16941474 17309651 25936995 32219518 1928092 33558080 10841810; Phenotypes: GM1-gangliosidosis, type I MIM#230500, GM1-gangliosidosis, type II MIM#230600, GM1-gangliosidosis, type III MIM#230650, Mucopolysaccharidosis type IVB (Morquio) MIM#253010; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.354 GAN Lilian Downie Marked gene: GAN as ready
Prepair 1000+ v1.354 GAN Lilian Downie Gene: gan has been classified as Green List (High Evidence).
Prepair 1000+ v1.354 GAN Lilian Downie Publications for gene: GAN were set to
Prepair 1000+ v1.322 GAN Marta Cifuentes Ochoa reviewed gene: GAN: Rating: GREEN; Mode of pathogenicity: None; Publications: 30532362, 11062483; Phenotypes: Giant axonal neuropathy-1, MIM# 256850, MONDO:0009749; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.272 FANCC Lilian Downie Added comment: Comment when marking as ready: Characteristic clinical features include developmental abnormalities in major organ systems, early-onset bone marrow failure, and a high predisposition to cancer. The cellular hallmark of FA is hypersensitivity to DNA crosslinking agents and high frequency of chromosomal aberrations pointing to a defect in DNA repair
Prepair 1000+ v1.143 CSMD1 Krithika Murali gene: CSMD1 was added
gene: CSMD1 was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: CSMD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSMD1 were set to PMID:38816421
Phenotypes for gene: CSMD1 were set to complex neurodevelopmental disorder MONDO:0100038
Review for gene: CSMD1 was set to GREEN
Added comment: PMID 38816421 Werren et al 2024 report 8 individuals from 6 families with biallelic missense CSMD1 variants identified through exome sequencing and subsequent gene-sharing efforts. Shared phenotypic features included: GDD, ID, microcephaly and polymicrogyria. Other features included dysmorphism, IUGR, hypotonia, arthrogryposis, seizures, opthalmological anomalies and other brain white matter anomalies Heterozygous parents were unaffected.

Loss of function is the postulated mechanism based on experimental data involving early-stage forebrain organoids differentiated from CSMD1 knockout human embryonic stem cells. ClinGen haploinsufficiency score of 1, however, this curation was last reviewed in 2018. This gene is within the scope of review for the ClinGen Autism and ID GCEP.
Sources: Literature
Prepair 1000+ v1.98 ADAMTS2 Zornitza Stark changed review comment from: Congenital onset, severe CTD.; to: Congenital onset, marked joint hyper mobility, skin abnormalities, risk of organ rupture.
Prepair 1000+ v0.0 SLC39A14 Zornitza Stark gene: SLC39A14 was added
gene: SLC39A14 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SLC39A14 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC39A14 were set to Hypermanganesemia with dystonia 2, 617013 (3), Autosomal recessive
Prepair 1000+ v0.0 SLC30A10 Zornitza Stark gene: SLC30A10 was added
gene: SLC30A10 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SLC30A10 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC30A10 were set to Hypermanganesemia with dystonia, polycythemia, and cirrhosis, 613280 (3)
Prepair 1000+ v0.0 GM2A Zornitza Stark gene: GM2A was added
gene: GM2A was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: GM2A was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: GM2A were set to GM2-gangliosidosis, AB variant, 272750 (3)
Prepair 1000+ v0.0 GAN Zornitza Stark gene: GAN was added
gene: GAN was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: GAN was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: GAN were set to Giant axonal neuropathy-1, 256850 (3)