KRT6C p.Phe297=
c.891C>T · rs148330805 · VCV741017
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.426%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP 1.8, phastCons 0.99 |
| Overall | ||
| CADD | 11.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.426%
East Asian · 191/44,886 alleles
Filtering AF
0.376%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.357%
Overall
0.0151%
244/1,613,902 alleles · rare
exomes 217/1,461,716 · genomes 27/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.426% | 235 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,404 |
| South Asian | 0.022% | 4,553 |
| African / African-American | 0.00534% | 18,744 |
| Admixed American | 0.00167% | 60,016 |
| European (non-Finnish) | 0.00017% | 589,946 |
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.Phe297=
- Coding
- c.891C>T
- MANE Select
- NM_173086
- dbSNP
- rs148330805
- Type
- single nucleotide variant
- Location
- chr12:52471442 (GRCh38)
- Gene constraint
- LOEUF 1.34 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.63
- Residue 297
- the if rod domain; the 'coil 1b' 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-phe297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown