KRT2 p.Val382=
c.1146C>T · rs138774076 · VCV2060908
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.176%, afr)
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 -6 | GERP -3.7 |
| Overall | ||
| CADD | 3.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.176%
African / African-American · 132/75,006 alleles
Filtering AF
0.152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.142%
Overall
0.00991%
160/1,614,050 alleles · rare
exomes 69/1,461,802 · genomes 91/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.176% | 568 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| European (non-Finnish) | 0.00195% | 51,305 |
| South Asian | 0.0011% | 91,044 |
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.Val382=
- Coding
- c.1146C>T
- MANE Select
- NM_000423
- dbSNP
- rs138774076
- Type
- single nucleotide variant
- Location
- chr12:52647832 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.38
- Residue 382
- the if rod domain; the 'coil 2' 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-val382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown