KRT17 p.Ala202=
c.606C>T · rs141781644 · VCV727502
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0977%, sas)
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 -10 | GERP -3.7 |
| Overall | ||
| CADD | 3.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0977%
South Asian · 89/91,074 alleles
Filtering AF
0.0812%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0752%
Overall
0.0333%
538/1,614,092 alleles · ultra-rare
exomes 489/1,461,746 · genomes 49/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0977% | 1,023 |
| Middle Eastern | 0.0841% | 1,188 |
| Admixed American | 0.0816% | 1,225 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| European (non-Finnish) | 0.0307% | 3,260 |
| African / African-American | 0.0107% | 9,383 |
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.Ala202=
- Coding
- c.606C>T
- MANE Select
- NM_000422
- dbSNP
- rs141781644
- Type
- single nucleotide variant
- Location
- chr17:41622421 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.28
- Residue 202
- the if rod domain; the 'coil 1b' region
Similar variants
- 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
- KRT17 p.Pro125Arg 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-ala202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown