KRT12 p.Arg20=
c.60G>C · rs761086617 · VCV2647750
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 -0.56 | GERP -1.1 |
| Overall | ||
| CADD | 1.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,004 alleles
Filtering AF
0.000953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000787%
Overall
0.00136%
22/1,612,994 alleles · very rare
exomes 20/1,460,800 · genomes 2/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.00153% | 65,558 |
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.Arg20=
- Coding
- c.60G>C
- MANE Select
- NM_000223
- dbSNP
- rs761086617
- Type
- single nucleotide variant
- Location
- chr17:40867127 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57
- Residue 20
- a UniProt-annotated variant site (in); the 'head' region; the 'disordered' region
Similar variants
- KRT12 p.Arg20Trp Benign ★★ ⚠ 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.Gln475Arg Likely 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-arg20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown