KRT17 p.Ala124=
c.372C>T · rs200866964 · VCV3047810
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, sas)
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 -0.075 | GERP -3.7, phastCons 0.18 |
| Overall | ||
| CADD | 5.146 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
South Asian · 105/91,002 alleles
Filtering AF
0.0975%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0907%
Overall
0.0166%
268/1,611,970 alleles · rare
exomes 241/1,459,868 · genomes 27/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.115% | 867 |
| Finnishnot grpmax-eligible | 0.0875% | 1,143 |
| Middle Eastern | 0.0221% | 4,528 |
| European (non-Finnish) | 0.00805% | 12,420 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,462 |
| African / African-American | 0.00535% | 18,706 |
| Admixed American | 0.00333% | 29,998 |
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
- KRT17
- Protein
- p.Ala124=
- Coding
- c.372C>T
- MANE Select
- NM_000422
- dbSNP
- rs200866964
- Type
- single nucleotide variant
- Location
- chr17:41624138 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.28
- Residue 124
- the if rod domain; the 'linker 1' region
Similar variants
- KRT17 p.Ala124Asp Uncertain significance ★ same residue
- KRT17 p.Arg94Cys Pathogenic ★★ same type
- KRT17 p.Arg94His Pathogenic/Likely pathogenic ★★ same type
- KRT17 p.Arg94Leu Likely pathogenic ★★ same type
- KRT17 p.Asn92Asp Pathogenic ★★ same type
- KRT17 p.Asn92Ser Pathogenic ★★ same type
- KRT17 p.Leu99Pro Pathogenic/Likely pathogenic ★★ same type
- KRT17 p.Arg406Cys Uncertain significance ★★ ⚠ 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/krt17-p-ala124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown