ITGA9
Chr 3integrin subunit alpha 9
Also known as: ALPHA-RLC, ITGA4L, RLC
The protein forms an integrin receptor (alpha-9/beta-1) that mediates cell adhesion by binding to VCAM1, cytotactin, and osteopontin, and regulates vascular smooth muscle contraction by inhibiting calcium influx. Mutations cause autosomal recessive muscular dystrophy-limb girdle type 2S, which presents with progressive proximal muscle weakness and elevated creatine kinase levels. The gene is highly constrained against loss-of-function variants (LOEUF 0.42), indicating intolerance to protein-disrupting mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
217 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 | 1 | 0 | 1 |
VUS | 0 | 136 | 12 | 0 | 148 |
Likely Benign | 0 | 7 | 5 | 10 | 22 |
Benign | 0 | 5 | 6 | 8 | 19 |
| Total | 0 | 148 | 35 | 18 | 201 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
ITGA9 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
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