COL6A5 p.Lys620=
c.1860A>G · rs10212372 · VCV1244282
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 55.2%, eas) — too common for a highly-penetrant pathogenic allele
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 6.1 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 14.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
55.2%
East Asian · 22,570/40,874 alleles
Filtering AF
54.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 54.4%
Overall
24.3%
376,688/1,547,888 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 55.2% | 2 |
| African / African-American | 44.8% | 2 |
| Admixed American | 42% | 2 |
| South Asian | 30.9% | 3 |
| Remaining individualsnot grpmax-eligible | 26.1% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.8% | 4 |
| Middle Eastern | 21.9% | 5 |
| European (non-Finnish) | 21.1% | 5 |
| Amishnot grpmax-eligible | 20.9% | 5 |
| Finnishnot grpmax-eligible | 14.9% | 7 |
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.Lys620=
- Coding
- c.1860A>G
- MANE Select
- NM_001278298
- dbSNP
- rs10212372
- Type
- single nucleotide variant
- Location
- chr3:130385363 (GRCh38)
- Gene constraint
- LOEUF 0.913 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
- Structure
- AlphaFold pLDDT 70.94
- Residue 620
- the 'nonhelical region' region
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.Ser1539Thr Benign ★★ same type
- COL6A5 p.Thr572= Benign ★★ same type
- COL6A5 p.Val2425Ile Benign ★★ same type
- COL6A5 p.Val669Gly 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/col6a5-p-lys620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown