COL6A6 p.Asp157=
c.471C>T · rs748065583 · VCV2654137
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.148%, mid)
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 -16 | GERP -6.6 |
| Overall | ||
| CADD | 0.425 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.148%
Middle Eastern · 9/6,084 alleles
Filtering AF
0.0772%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0576%
Overall
0.00948%
153/1,613,878 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.148% | 676 |
| Admixed American | 0.0383% | 2,609 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,470 |
| South Asian | 0.0176% | 5,693 |
| African / African-American | 0.00801% | 12,487 |
| European (non-Finnish) | 0.00678% | 14,749 |
| East Asian | 0.00223% | 44,896 |
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
- COL6A6
- Protein
- p.Asp157=
- Coding
- c.471C>T
- MANE Select
- NM_001102608
- dbSNP
- rs748065583
- Type
- single nucleotide variant
- Location
- chr3:130563474 (GRCh38)
- Gene constraint
- LOEUF 1.043 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.61
- Residue 157
- the 'nonhelical region' region; the vwfa 1 domain
Similar variants
- COL6A6 p.Asp157Val Uncertain significance ★ same residue
- COL6A6 p.Arg1295Ter Uncertain significance ★★ same type
- COL6A6 p.Arg1864Thr Uncertain significance ★★ same type
- COL6A6 p.Arg906His Uncertain significance ★★ ⚠ same type
- COL6A6 p.Arg937Trp Uncertain significance ★★ ⚠ same type
- COL6A6 p.Tyr1805Cys Uncertain significance ★★ ⚠ same type
- COL6A6 c.2977+4A>T Benign ★★ same type
- COL6A6 c.4273-3C>T Likely benign ★★ 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/col6a6-p-asp157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown