KRT5 p.Phe83=
c.249C>T · rs780670406 · VCV884175
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00373%, nfe)
Conditions
1
epidermolysis bullosa simplex
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 3.9 | phastCons 1 |
| Overall | ||
| CADD | 10.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00373%
European (non-Finnish) · 44/1,180,016 alleles
Filtering AF
0.00283%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00252%
Overall
0.00273%
44/1,613,954 alleles · very rare
exomes 43/1,461,876 · genomes 1/152,078 · 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
- KRT5
- Protein
- p.Phe83=
- Coding
- c.249C>T
- MANE Select
- NM_000424
- dbSNP
- rs780670406
- Type
- single nucleotide variant
- Location
- chr12:52520048 (GRCh38)
- Gene constraint
- LOEUF 0.538 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 68.86 · 2 PDB
- Residue 83
- the 'head' region; a UniProt-annotated variant site (in ddd1)
Similar variants
- KRT5 p.Phe83Leu Uncertain significance ★★ ⚠ same residue
- KRT5 p.Ala428Thr Pathogenic/Likely pathogenic ★★ same condition
- KRT5 p.Ala428Val Pathogenic/Likely pathogenic ★★ same condition
- KRT5 p.Glu170Lys Pathogenic ★★ same condition
- KRT5 p.Glu466Gln Pathogenic/Likely pathogenic ★★ same condition
- KRT5 p.Glu477Lys Pathogenic ★★ same condition
- KRT5 p.Leu196Pro Pathogenic/Likely pathogenic ★★ same condition
- KRT5 p.Leu463Pro Pathogenic ★★ same condition
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-phe83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown