KRT6A p.Pro131=
c.393C>A · rs184577522 · VCV731839
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.299%, eas)
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 -20 | GERP -1.5 |
| Overall | ||
| CADD | 6.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.299%
East Asian · 134/44,852 alleles
Filtering AF
0.258%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.242%
Overall
0.012%
193/1,613,300 alleles · rare
exomes 173/1,461,562 · genomes 20/151,738 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.299% | 335 |
| South Asian | 0.0253% | 3,955 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,941 |
| European (non-Finnish) | 0.00212% | 47,190 |
| Finnishnot grpmax-eligible | 0.00156% | 63,988 |
| African / African-American | 0.00134% | 74,850 |
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
- KRT6A
- Protein
- p.Pro131=
- Coding
- c.393C>A
- MANE Select
- NM_005554
- dbSNP
- rs184577522
- Type
- single nucleotide variant
- Location
- chr12:52492796 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.16 · 1 PDB
- Residue 131
- the 'head' region
Similar variants
- KRT6A p.Pro131Thr Uncertain significance ★ same residue
- KRT6A c.1460-1G>C Pathogenic/Likely pathogenic ★★ same type
- KRT6A p.Arg164Cys Pathogenic/Likely pathogenic ★★ same type
- KRT6A p.Asn171Lys Pathogenic ★★ same type
- KRT6A p.Asn171Ser Pathogenic ★★ same type
- KRT6A p.Glu163Lys Pathogenic ★★ same type
- KRT6A p.Glu472Lys Pathogenic/Likely pathogenic ★★ same type
- KRT6A p.Ile462Asn 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/krt6a-p-pro131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown