KRT6A p.Ala442=
c.1326C>T · rs555046513 · VCV3040393
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0691%, eas)
Conditions
1
KRT6A-related disorder
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 -3.8 |
| Overall | ||
| CADD | 6.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0691%
East Asian · 31/44,862 alleles
Filtering AF
0.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0435%
Overall
0.00204%
33/1,614,110 alleles · ultra-rare
exomes 26/1,461,892 · genomes 7/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0691% | 1,447 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
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.Ala442=
- Coding
- c.1326C>T
- MANE Select
- NM_005554
- dbSNP
- rs555046513
- Type
- single nucleotide variant
- Location
- chr12:52488426 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.16 · 1 PDB
- Residue 442
- the if rod domain; the 'coil 2' region
Disease context
KRT6A-related disorder
Similar variants
- KRT6A p.Arg164Cys Pathogenic/Likely pathogenic ★★ same condition
- KRT6A p.Asn171Lys Pathogenic ★★ same condition
- KRT6A p.Ala106= Likely benign same condition
- KRT6A p.Arg15His Likely benign ⚠ same condition
- KRT6A p.Arg443Gln Benign ⚠ same condition
- KRT6A p.Gly95= Likely benign same condition
- KRT6A p.Leu112= Likely benign same condition
- KRT6A p.Leu198= Likely benign same condition
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-ala442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown