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| Intellectual disability v9.265 | SLC12A9 |
Ida Ertmanska changed review comment from: PMID: 38334070 Accogli et al., 2024 3 unrelated patients with biallelic LoF variants. Common features included intellectual disability/GDD, skeletal defects (fusion and segmentation vertebral defects) and brain structural abnormalities (thin corpus callosum, hypoplasia of the pons and inferior cerebellar vermis), congenital heart defects, and hypopigmented hair. Patient 1 was homozygous for SLC12A9 nonsense variant p.(Arg615∗), patient 2 was compound heterozygous for SLC12A9 p.(Ser109Lysfs∗20) and a de novo large deletion, and proband 3 was compound heterozygous for SLC12A9 p.(Glu290Glyfs∗36) and p.(Asn552Lys). Method: trio exome / genome seq + Sanger seq segregation confirmation. Functional evidence (rescue): Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wild-type SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect. This gene is not yet associated with a phenotype in OMIM (accessed 17th Feb 2026). Sources: Literature; to: PMID: 38334070 Accogli et al., 2024 3 unrelated patients with biallelic LoF variants. Common features included intellectual disability/GDD, skeletal defects (fusion and segmentation vertebral defects) and brain structural abnormalities (thin corpus callosum, hypoplasia of the pons and inferior cerebellar vermis), congenital heart defects, and hypopigmented hair. Patient 1 was homozygous for SLC12A9 nonsense variant p.(Arg615∗), patient 2 was compound heterozygous for SLC12A9 p.(Ser109Lysfs∗20) and a de novo large deletion 2.1 Mb ((98,261,637-100,363,719)x1 [GRCh37]) on chromosome 7q22.1 that fully encompasses SLC12A9, and proband 3 was compound heterozygous for SLC12A9 p.(Glu290Glyfs∗36) and p.(Asn552Lys). Method: trio exome / genome seq + Sanger seq segregation confirmation. Functional evidence (rescue): Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wild-type SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect. This gene is not yet associated with a phenotype in OMIM (accessed 17th Feb 2026). Sources: Literature |
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| Intellectual disability v9.265 | SLC12A9 | Ida Ertmanska Classified gene: SLC12A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v9.265 | SLC12A9 | Ida Ertmanska Added comment: Comment on list classification: There are 3 unrelated individuals reported in PMID:38334070 with biallelic SLC12A9 variants and a syndromic neurodevelopmental disorder with lysosome defects. ID/GDD was present in all 3 individuals. Hence, this gene should be promoted to Green for Intellectual disability. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v9.265 | SLC12A9 | Ida Ertmanska Gene: slc12a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v9.264 | SLC12A9 |
Ida Ertmanska gene: SLC12A9 was added gene: SLC12A9 was added to Intellectual disability. Sources: Literature Q1_26_promote_green tags were added to gene: SLC12A9. Mode of inheritance for gene: SLC12A9 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC12A9 were set to 38334070 Phenotypes for gene: SLC12A9 were set to SLC12A9-related syndromic neurodevelopmental disorder with lysosome defects; neurodevelopmental disorder, MONDO:0700092 Review for gene: SLC12A9 was set to GREEN Added comment: PMID: 38334070 Accogli et al., 2024 3 unrelated patients with biallelic LoF variants. Common features included intellectual disability/GDD, skeletal defects (fusion and segmentation vertebral defects) and brain structural abnormalities (thin corpus callosum, hypoplasia of the pons and inferior cerebellar vermis), congenital heart defects, and hypopigmented hair. Patient 1 was homozygous for SLC12A9 nonsense variant p.(Arg615∗), patient 2 was compound heterozygous for SLC12A9 p.(Ser109Lysfs∗20) and a de novo large deletion, and proband 3 was compound heterozygous for SLC12A9 p.(Glu290Glyfs∗36) and p.(Asn552Lys). Method: trio exome / genome seq + Sanger seq segregation confirmation. Functional evidence (rescue): Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wild-type SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect. This gene is not yet associated with a phenotype in OMIM (accessed 17th Feb 2026). Sources: Literature |
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