KRT14 p.Ser321=
c.963C>T · VCV3616983
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0116%, nfe)
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 -0.16 | GERP -2.8, phastCons 0.044 |
| Overall | ||
| CADD | 13.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0116%
European (non-Finnish) · 137/1,180,030 alleles
Filtering AF
0.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00939%
Overall
0.00874%
141/1,614,062 alleles · ultra-rare
exomes 139/1,461,888 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0116% | 8,613 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| East Asian | 0.00223% | 44,896 |
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
- KRT14
- Protein
- p.Ser321=
- Coding
- c.963C>T
- MANE Select
- NM_000526
- Type
- single nucleotide variant
- Location
- chr17:41583641 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.00 · 6 PDB
- Residue 321
- the if rod domain; the 'coil 2' region
Similar variants
- KRT14 p.Ser321fs Pathogenic ★ same residue
- KRT14 c.526-2A>C Likely pathogenic ★★ same type
- KRT14 c.927+1G>A Pathogenic ★★ same type
- KRT14 p.Arg125Cys Pathogenic ★★ same type
- KRT14 p.Arg125His Pathogenic ★★ same type
- KRT14 p.Arg125Leu Pathogenic ★★ same type
- KRT14 p.Arg288Leu Pathogenic/Likely pathogenic ★★ same type
- KRT14 p.Arg388Cys Pathogenic/Likely pathogenic ★★ 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/krt14-p-ser321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown