COL6A3 p.Val256=
c.768C>T · rs79606264 · VCV94995
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 11 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.98%, mid)
Conditions
2
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 6.4 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 9.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.98%
Middle Eastern · 241/6,062 alleles
Filtering AF
3.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.4%
Overall
1.45%
23,408/1,614,168 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.98% | 25 |
| South Asian | 3.33% | 30 |
| Ashkenazi Jewishnot grpmax-eligible | 2.77% | 36 |
| Remaining individualsnot grpmax-eligible | 1.72% | 58 |
| Amishnot grpmax-eligible | 1.64% | 61 |
| European (non-Finnish) | 1.4% | 71 |
| Finnishnot grpmax-eligible | 0.908% | 110 |
| Admixed American | 0.896% | 112 |
| African / African-American | 0.711% | 141 |
| East Asian | 0.02% | 4,988 |
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
- COL6A3
- Protein
- p.Val256=
- Coding
- c.768C>T
- MANE Select
- NM_004369
- dbSNP
- rs79606264
- Type
- single nucleotide variant
- Location
- chr2:237388126 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Residue 256
- the 'nonhelical region' region; the vwfa 2 domain
Similar variants
- COL6A3 c.5838+1G>T Pathogenic/Likely pathogenic ★★ same condition
- COL6A3 c.6156+1G>A Pathogenic ★★ same condition
- COL6A3 c.6157-2A>C Pathogenic ★★ same condition
- COL6A3 c.6210+1G>A Pathogenic ★★ same condition
- COL6A3 c.6282+1G>A Pathogenic ★★ same condition
- COL6A3 c.6282+1G>C Pathogenic/Likely pathogenic ★★ same condition
- COL6A3 c.6309+1G>A Pathogenic ★★ same condition
- COL6A3 c.6309+1G>T Pathogenic/Likely pathogenic ★★ 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/col6a3-p-val256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown