KRT17 p.Glu413=
c.1239A>G · rs767866536 · VCV798837
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00102%, 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 -0.5 | GERP -3.7, phastCons 0.09 |
| Overall | ||
| CADD | 7.972 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,180,016 alleles
Filtering AF
0.000542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000428%
Overall
0.000744%
12/1,612,080 alleles · very rare
exomes 10/1,459,912 · genomes 2/152,168 · 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
- KRT17
- Protein
- p.Glu413=
- Coding
- c.1239A>G
- MANE Select
- NM_000422
- dbSNP
- rs767866536
- Type
- single nucleotide variant
- Location
- chr17:41619654 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.28
- Residue 413
- the 'tail' region; a UniProt-annotated variant site (found in a patient with a keratinization disorder with associated thrombocytopenia; uncertain significance)
Similar variants
- KRT17 p.Arg94Cys Pathogenic ★★ same type
- KRT17 p.Arg94His Pathogenic/Likely pathogenic ★★ same type
- KRT17 p.Arg94Leu Likely pathogenic ★★ same type
- KRT17 p.Asn92Asp Pathogenic ★★ same type
- KRT17 p.Asn92Ser Pathogenic ★★ same type
- KRT17 p.Leu99Pro Pathogenic/Likely pathogenic ★★ same type
- KRT17 p.Arg406Cys Uncertain significance ★★ ⚠ same type
- KRT17 p.Pro125Arg 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/krt17-p-glu413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown