KRT6A p.Ile313=
c.939C>A · rs374415163 · VCV2914614
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0382%, 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 -1.1 | GERP 0.88 |
| Overall | ||
| CADD | 12.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0382%
European (non-Finnish) · 451/1,180,050 alleles
Filtering AF
0.0353%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0341%
Overall
0.0289%
466/1,614,130 alleles · ultra-rare
exomes 446/1,461,894 · genomes 20/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0382% | 2,617 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| African / African-American | 0.00534% | 18,737 |
| Admixed American | 0.00333% | 30,007 |
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.Ile313=
- Coding
- c.939C>A
- MANE Select
- NM_005554
- dbSNP
- rs374415163
- Type
- single nucleotide variant
- Location
- chr12:52490707 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.16 · 1 PDB
- Residue 313
- the if rod domain; the 'linker 12' region
Similar variants
- KRT6A p.Ile313Val 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-ile313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown