TM9SF4
Chr 20transmembrane 9 superfamily member 4
Also known as: dJ836N17.2
TM9SF4 encodes a transmembrane protein that regulates protein localization to the cell surface and controls V-ATPase complex assembly for intracellular pH regulation in the Golgi apparatus and endosomes. Mutations cause autosomal recessive intellectual disability with microcephaly and seizures, typically presenting in early childhood. This gene is highly constrained against loss-of-function variants in the general population.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Moderately missense-constrained (top ~2.5%)
ClinVar Variant Classifications
96 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 11 | 0 | 11 |
Likely Pathogenic | 0 | 0 | 4 | 0 | 4 |
VUS | 0 | 47 | 5 | 0 | 52 |
Likely Benign | 0 | 3 | 1 | 2 | 6 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 50 | 21 | 2 | 73 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
TM9SF4 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools