KRT2 p.Pro138=
c.414T>C · rs375808782 · VCV1933686
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
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 0.1 | GERP -3, phastCons 0.23 |
| Overall | ||
| CADD | 5.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,990 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,613,904 alleles · very rare
exomes 3/1,461,882 · genomes 1/152,022 · 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
- KRT2
- Protein
- p.Pro138=
- Coding
- c.414T>C
- MANE Select
- NM_000423
- dbSNP
- rs375808782
- Type
- single nucleotide variant
- Location
- chr12:52651729 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.38
- Residue 138
- the 'head' region
Similar variants
- KRT2 p.Pro138Ser Uncertain significance ★ ⚠ same residue
- KRT2 p.Glu487Lys Pathogenic ★★ same type
- KRT2 p.Glu488Lys Likely pathogenic ★★ same type
- KRT2 p.Arg544Gln Uncertain significance ★★ ⚠ same type
- KRT2 p.Asn498Ile Uncertain significance ★★ ⚠ same type
- KRT2 c.1122+16G>A Benign ★★ same type
- KRT2 c.1248+22C>T Benign ★★ same type
- KRT2 c.1249-4A>G Benign ★★ 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/krt2-p-pro138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown