COL6A5 p.Val31=
c.93C>T · VCV3388395
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0805%, 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 -4 | GERP -3.6 |
| Overall | ||
| CADD | 1.884 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0805%
European (non-Finnish) · 948/1,176,962 alleles
Filtering AF
0.0763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0746%
Overall
0.0631%
1,014/1,607,912 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0805% | 1,242 |
| Remaining individualsnot grpmax-eligible | 0.0531% | 1,884 |
| Finnishnot grpmax-eligible | 0.0283% | 3,535 |
| African / African-American | 0.0134% | 7,475 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00688% | 14,540 |
| Admixed American | 0.00506% | 19,773 |
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
- COL6A5
- Protein
- p.Val31=
- Coding
- c.93C>T
- MANE Select
- NM_001278298
- Type
- single nucleotide variant
- Location
- chr3:130376262 (GRCh38)
- Gene constraint
- LOEUF 0.913 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
- Structure
- AlphaFold pLDDT 70.94
- Residue 31
- the 'nonhelical region' region; the vwfa 1 domain
Similar variants
- COL6A5 p.Ala2589Thr Benign ★★ same type
- COL6A5 p.Asn641His Benign ★★ same type
- COL6A5 p.Asp160= Benign ★★ same type
- COL6A5 p.Glu2272Ter Benign ★★ same type
- COL6A5 p.Lys620= Benign ★★ same type
- COL6A5 p.Ser1539Thr Benign ★★ same type
- COL6A5 p.Thr572= Benign ★★ same type
- COL6A5 p.Val2425Ile 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/col6a5-p-val31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown