KRT6C p.Val159=
c.477G>A · rs372187804 · VCV2643022
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00301%, 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 -14 | GERP -0.18 |
| Overall | ||
| CADD | 1.763 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00301%
European (non-Finnish) · 34/1,130,014 alleles
Filtering AF
0.00217%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.0022%
34/1,548,550 alleles · very rare
exomes 34/1,414,598 · genomes 0/133,952 · joint denominator
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
- KRT6C
- Protein
- p.Val159=
- Coding
- c.477G>A
- MANE Select
- NM_173086
- dbSNP
- rs372187804
- Type
- single nucleotide variant
- Location
- chr12:52473261 (GRCh38)
- Gene constraint
- LOEUF 1.34 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.63
- Residue 159
- the 'head' region
Similar variants
- KRT6C p.Glu472Lys Pathogenic/Likely pathogenic ★★ same type
- KRT6C p.Arg260Cys Uncertain significance ★★ ⚠ same type
- KRT6C p.Arg349Trp Uncertain significance ★★ ⚠ same type
- KRT6C p.Arg466Cys Uncertain significance ★★ ⚠ same type
- KRT6C p.Asp331His Uncertain significance ★★ ⚠ same type
- KRT6C p.Glu479Lys Uncertain significance ★★ same type
- KRT6C p.Gly504Ser Uncertain significance ★★ ⚠ same type
- KRT6C p.Gly525Ser Uncertain significance ★★ ⚠ 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/krt6c-p-val159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown