COL6A3 p.Pro1407=
c.4221C>G · rs565366400 · VCV894958
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 0.58 | GERP -0.58, phastCons 1 |
| Overall | ||
| CADD | 3.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,874 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000372%
6/1,613,876 alleles · ultra-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
- COL6A3
- Protein
- p.Pro1407=
- Coding
- c.4221C>G
- MANE Select
- NM_004369
- dbSNP
- rs565366400
- Type
- single nucleotide variant
- Location
- chr2:237371796 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Residue 1407
- the 'nonhelical region' region
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-pro1407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown