KRT86 p.Pro20=
c.60C>G · rs201694571 · VCV1219942
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.11%, 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 -2 | GERP 0.86 |
| Overall | ||
| CADD | 8.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.11%
African / African-American · 832/75,040 alleles
Filtering AF
1.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.02%
Overall
0.312%
5,034/1,613,342 alleles · low-frequency
exomes 4,273/1,460,982 · genomes 761/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.11% | 90 |
| Middle Eastern | 0.726% | 138 |
| Remaining individualsnot grpmax-eligible | 0.357% | 280 |
| European (non-Finnish) | 0.297% | 337 |
| Admixed American | 0.285% | 351 |
| South Asian | 0.17% | 588 |
| East Asian | 0.12% | 831 |
| Finnishnot grpmax-eligible | 0.0691% | 1,448 |
| Ashkenazi Jewishnot grpmax-eligible | 0.044% | 2,274 |
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
- KRT86
- Protein
- p.Pro20=
- Coding
- c.60C>G
- MANE Select
- NM_001320198
- dbSNP
- rs201694571
- Type
- single nucleotide variant
- Location
- chr12:52301976 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.50
- Residue 20
- the 'head' region
Similar variants
- KRT86 p.Ala293Asp Uncertain significance ★★ ⚠ same type
- KRT81 p.Ala359= Benign ★★ same type
- KRT86 c.1027-116G>A Benign ★★ same type
- KRT86 c.1027-15C>T Likely benign ★★ same type
- KRT86 c.1247+36C>A Benign ★★ same type
- KRT86 c.1248-152C>T Likely benign ★★ same type
- KRT86 c.370-9G>A Likely benign ★★ same type
- KRT86 c.578+178G>C 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/krt86-p-pro20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown