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Intellectual disability

Gene: SLC12A9

Amber List (moderate evidence)
SLC12A9 (solute carrier family 12 member 9)
EnsemblGeneIds (GRCh38): ENSG00000146828
EnsemblGeneIds (GRCh37): ENSG00000146828
OMIM: 616861, Gene2Phenotype
SLC12A9 is in 3 panels

1 review

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

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.
Created: 17 Feb 2026, 11:56 a.m. | Last Modified: 17 Feb 2026, 11:56 a.m.
Panel Version: 9.265
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
Created: 17 Feb 2026, 11:54 a.m. | Last Modified: 17 Feb 2026, 11:56 a.m.
Panel Version: 9.265

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
SLC12A9-related syndromic neurodevelopmental disorder with lysosome defects; neurodevelopmental disorder, MONDO:0700092

Publications

Created: 17 Feb 2026, 11:54 a.m.
Last Modified: 17 Feb 2026, 11:56 a.m.
Panel version: 9.264

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • SLC12A9-related syndromic neurodevelopmental disorder with lysosome defects
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q1_26_promote_green
OMIM
616861
Clinvar variants
Variants in SLC12A9
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Feb 2026, Gel status: 2

Entity classified by Genomics England curator

Ida Ertmanska (Genomics England Curator)

Gene: slc12a9 has been classified as Amber List (Moderate Evidence).

17 Feb 2026, Gel status: 1

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes

Ida Ertmanska (Genomics England Curator)

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