KRT2 p.Thr37=
c.111T>A · VCV4917019
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, 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 0.49 | GERP -4.3 |
| Overall | ||
| CADD | 5.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,954 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,608,036 alleles · very rare
exomes 2/1,455,788 · genomes 0/152,248 · 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.Thr37=
- Coding
- c.111T>A
- MANE Select
- NM_000423
- Type
- single nucleotide variant
- Location
- chr12:52652032 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.38
- Residue 37
- the 'head' region
Similar variants
- 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
- KRT2 c.1249-7G>T 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-thr37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown