COL6A1 p.Ala962=
c.2886C>T · rs754524630 · VCV898862
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, sas)
Conditions
1
collagen 6-related myopathy
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 -2.5 | GERP -3.2 |
| Overall | ||
| CADD | 6.313 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
South Asian · 16/90,990 alleles
Filtering AF
0.011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00899%
Overall
0.00106%
17/1,606,756 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0176% | 5,687 |
| East Asian | 0.00224% | 44,704 |
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
- COL6A1
- Protein
- p.Ala962=
- Coding
- c.2886C>T
- MANE Select
- NM_001848
- dbSNP
- rs754524630
- Type
- single nucleotide variant
- Location
- chr21:46003812 (GRCh38)
- Gene constraint
- LOEUF 0.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.28 · 1 PDB
- Residue 962
- the vwfa 3 domain; the 'c-terminal globular domain' region
Similar variants
- COL6A1 p.Ala962Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL6A1 p.Ala962Val Uncertain significance ★ ⚠ same residue
- COL6A1 p.Gly263Val Pathogenic/Likely pathogenic ★★ same condition
- COL6A1 p.Gly275Glu Pathogenic/Likely pathogenic ★★ same condition
- COL6A1 p.Gly284Arg Pathogenic/Likely pathogenic ★★ same condition
- COL6A1 c.1002+6T>C Uncertain significance ★★ same condition
- COL6A1 c.228-7C>T Uncertain significance ★★ same condition
- COL6A1 p.Ala448Thr Uncertain significance ★★ ⚠ same condition
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/col6a1-p-ala962 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown