KRT6C p.Ser98=
c.294T>C · rs1387932030 · VCV2643024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00604%, sas)
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 -16 | GERP -0.47 |
| Overall | ||
| CADD | 4.687 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00604%
South Asian · 5/82,770 alleles
Filtering AF
0.00236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00148%
Overall
0.000365%
5/1,369,534 alleles · very rare
exomes 5/1,245,712 · genomes 0/123,822 · 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.Ser98=
- Coding
- c.294T>C
- MANE Select
- NM_173086
- dbSNP
- rs1387932030
- Type
- single nucleotide variant
- Location
- chr12:52473444 (GRCh38)
- Gene constraint
- LOEUF 1.34 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.63
- Residue 98
- the 'head' region
Similar variants
- KRT6C p.Ser98Asn Uncertain significance ★ ⚠ same residue
- 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
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-ser98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown