COL6A1 p.Arg76=
c.226A>C · rs886043954 · VCV288618
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
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 8.8 | GERP 0.43, phastCons 1 |
| Overall | ||
| CADD | 19.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,864 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,612,024 alleles · very rare
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.Arg76=
- Coding
- c.226A>C
- MANE Select
- NM_001848
- dbSNP
- rs886043954
- Type
- single nucleotide variant
- Location
- chr21:45982762 (GRCh38)
- Gene constraint
- LOEUF 0.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.28 · 1 PDB
- Residue 76
- the vwfa 1 domain; the 'n-terminal globular domain' region
Similar variants
- COL6A1 c.1002+1G>A Pathogenic ★★ same type
- COL6A1 c.1003-1G>A Pathogenic ★★ same type
- COL6A1 c.1003-2A>C Pathogenic ★★ same type
- COL6A1 c.1003-2A>G Pathogenic ★★ same type
- COL6A1 c.1056+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL6A1 c.1056+1G>C Pathogenic ★★ same type
- COL6A1 c.1056+2T>A Pathogenic/Likely pathogenic ★★ same type
- COL6A1 c.1056+5G>A Pathogenic/Likely pathogenic ★★ 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/col6a1-p-arg76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown