KRT9 p.Ile451=
c.1353C>T · rs369840064 · VCV1901840
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00935%, 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 0.33 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 6.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00935%
African / African-American · 7/74,862 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00161%
26/1,613,862 alleles · very rare
exomes 22/1,461,776 · genomes 4/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00935% | 10,695 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| European (non-Finnish) | 0.00136% | 73,751 |
| South Asian | 0.0011% | 91,060 |
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
- KRT9
- Protein
- p.Ile451=
- Coding
- c.1353C>T
- MANE Select
- NM_000226
- dbSNP
- rs369840064
- Type
- single nucleotide variant
- Location
- chr17:41568203 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.43
- Residue 451
- the if rod domain; the 'coil 2' region
Similar variants
- KRT9 p.Arg163Gln Pathogenic/Likely pathogenic ★★ same type
- KRT9 p.Arg163Leu Pathogenic/Likely pathogenic ★★ same type
- KRT9 p.Arg163Trp Pathogenic/Likely pathogenic ★★ same type
- KRT9 p.Asn161Lys Pathogenic/Likely pathogenic ★★ same type
- KRT9 p.Asn161Ser Pathogenic ★★ same type
- KRT9 p.Leu160Pro Likely pathogenic ★★ same type
- KRT9 p.Met157Val Pathogenic ★★ same type
- KRT9 p.Arg13His 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/krt9-p-ile451 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown