COL6A2 p.Ser27=
c.81G>A · rs111639540 · VCV290722
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.695%, afr)
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 -6.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.854 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.695%
African / African-American · 521/74,998 alleles
Filtering AF
0.645%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.626%
Overall
0.0365%
588/1,612,856 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.695% | 144 |
| Middle Eastern | 0.066% | 1,514 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,838 |
| Admixed American | 0.0267% | 3,751 |
| South Asian | 0.00329% | 30,355 |
| East Asian | 0.00223% | 44,864 |
| European (non-Finnish) | 0.000763% | 131,102 |
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
- COL6A2
- Protein
- p.Ser27=
- Coding
- c.81G>A
- MANE Select
- NM_001849
- dbSNP
- rs111639540
- Type
- single nucleotide variant
- Location
- chr21:46111557 (GRCh38)
- Gene constraint
- LOEUF 0.895 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.58 · 1 PDB
- Residue 27
- the 'nonhelical region' region
Similar variants
- COL6A2 p.Ser27Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL6A2 c.1000-1G>T Pathogenic ★★ same condition
- COL6A2 c.1000-2A>C Pathogenic ★★ same condition
- COL6A2 c.1053+1G>A Pathogenic ★★ same condition
- COL6A2 c.1053+1G>C Pathogenic/Likely pathogenic ★★ same condition
- COL6A2 c.1053+2T>C Pathogenic/Likely pathogenic ★★ same condition
- COL6A2 c.1054-2A>G Pathogenic/Likely pathogenic ★★ same condition
- COL6A2 c.115+2T>C 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/col6a2-p-ser27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown