COL6A2 p.Glu887=
c.2661G>A · rs148249892 · VCV284815
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.101%, amr)
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 3.8 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 6.217 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
Admixed American · 54/53,230 alleles
Filtering AF
0.0798%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0721%
Overall
0.031%
486/1,569,366 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.101% | 986 |
| Finnishnot grpmax-eligible | 0.0805% | 1,242 |
| European (non-Finnish) | 0.0317% | 3,158 |
| Remaining individualsnot grpmax-eligible | 0.0247% | 4,056 |
| Middle Eastern | 0.0166% | 6,038 |
| African / African-American | 0.00271% | 36,847 |
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.Glu887=
- Coding
- c.2661G>A
- MANE Select
- NM_001849
- dbSNP
- rs148249892
- Type
- single nucleotide variant
- Location
- chr21:46132153 (GRCh38)
- Gene constraint
- LOEUF 0.895 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.58 · 1 PDB
- Residue 887
- the vwfa 3 domain; a β-strand; the 'nonhelical region' region
Similar variants
- COL6A2 p.Glu887Lys 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-glu887 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown