ITGA6 p.Leu796=
c.2388T>G · rs765244353 · VCV2901810
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0847%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 10.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0847%
East Asian · 38/44,876 alleles
Filtering AF
0.0634%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.056%
Overall
0.00254%
41/1,613,818 alleles · ultra-rare
exomes 38/1,461,634 · genomes 3/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0847% | 1,181 |
| Admixed American | 0.00167% | 60,008 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 8.48e-05% | 1,179,846 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ITGA6
- Protein
- p.Leu796=
- Coding
- c.2388T>G
- MANE Select
- NM_000210
- dbSNP
- rs765244353
- Type
- single nucleotide variant
- Location
- chr2:172488024 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.69 (gnomAD)
- Structure
- AlphaFold pLDDT 80.05 · 2 PDB
Similar variants
- ITGA6 p.Arg148Ter Pathogenic/Likely pathogenic ★★ same type
- ITGA6 p.Arg976Ter Pathogenic/Likely pathogenic ★★ same type
- ITGA6 c.986+3G>A Uncertain significance ★★ same type
- ITGA6 c.*2124T>A Uncertain significance ★★ same type
- ITGA6 c.*65C>G Uncertain significance ★★ ⚠ same type
- ITGA6 p.Ala1024Thr Uncertain significance ★★ ⚠ same type
- ITGA6 p.Ala321Val Uncertain significance ★★ ⚠ same type
- ITGA6 p.Ala491Val Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/itga6-p-leu796 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown