KRT12 p.Leu222=
c.664C>T · rs200506470 · VCV731529
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.178%, amr)
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 2.4 | GERP -1.1, phastCons 0.42 |
| Overall | ||
| CADD | 6.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.178%
Admixed American · 107/60,026 alleles
Filtering AF
0.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.157%
Overall
0.134%
2,171/1,614,224 alleles · rare
exomes 2,027/1,461,866 · genomes 144/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.178% | 561 |
| European (non-Finnish) | 0.166% | 603 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| African / African-American | 0.0226% | 4,416 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- KRT12
- Protein
- p.Leu222=
- Coding
- c.664C>T
- MANE Select
- NM_000223
- dbSNP
- rs200506470
- Type
- single nucleotide variant
- Location
- chr17:40864949 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57
- Residue 222
- the if rod domain; the 'coil 1b' region
Similar variants
- KRT12 p.Leu222Arg Uncertain significance ★ ⚠ same residue
- KRT12 p.Met129Val Pathogenic/Likely pathogenic ★★ same type
- KRT12 p.Asp213Tyr Uncertain significance ★★ ⚠ same type
- KRT12 p.Gln486Glu Uncertain significance ★★ ⚠ same type
- KRT12 p.Ile195Phe Uncertain significance ★★ ⚠ same type
- KRT12 p.Val228Ile Uncertain significance ★★ ⚠ same type
- KRT12 c.808-17T>A Benign/Likely benign ★★ same type
- KRT12 p.Arg20Trp 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/krt12-p-leu222 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown