KRT5 p.Ser34=
c.102C>T · rs377261145 · VCV764103
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -5 | |
| Overall | ||
| CADD | 7.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
European (non-Finnish) · 63/1,179,976 alleles
Filtering AF
0.00426%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00388%
Overall
0.00415%
67/1,613,950 alleles · very rare
exomes 60/1,461,748 · genomes 7/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00534% | 18,730 |
| Admixed American | 0.005% | 20,004 |
| East Asian | 0.00223% | 44,890 |
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
- KRT5
- Protein
- p.Ser34=
- Coding
- c.102C>T
- MANE Select
- NM_000424
- dbSNP
- rs377261145
- Type
- single nucleotide variant
- Location
- chr12:52520195 (GRCh38)
- Gene constraint
- LOEUF 0.538 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 68.86 · 2 PDB
- Residue 34
- the 'head' region; a UniProt-annotated variant site (in ddd1)
Similar variants
- KRT5 c.555+1G>A Pathogenic ★★ same type
- KRT5 p.Ala428Thr Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Ala428Val Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Arg165Ser Pathogenic ★★ same type
- KRT5 p.Arg331Cys Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Arg331His Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Asn176Ser Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Asn177Ser 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/krt5-p-ser34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown