ITGA6 p.Ala2=
c.6C>T · rs774450070 · VCV743028
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00695%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 16.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00695%
Admixed American · 4/57,544 alleles
Filtering AF
0.00232%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00139%
Overall
0.000628%
10/1,593,460 alleles · very rare
exomes 6/1,441,522 · genomes 4/151,938 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00695% | 14,386 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,548 |
| African / African-American | 0.00137% | 73,128 |
| South Asian | 0.00113% | 88,500 |
| European (non-Finnish) | 8.54e-05% | 1,171,646 |
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.Ala2=
- Coding
- c.6C>T
- MANE Select
- NM_000210
- dbSNP
- rs774450070
- Type
- single nucleotide variant
- Location
- chr2:172427794 (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-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown