KRT14 p.Ser379=
c.1137C>T · rs563641073 · VCV2989918
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0523%, mid)
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 -4.9 | GERP -3.1 |
| Overall | ||
| CADD | 0.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0523%
Middle Eastern · 3/5,738 alleles
Filtering AF
0.0142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00758%
Overall
0.00118%
19/1,613,710 alleles · ultra-rare
exomes 17/1,461,470 · genomes 2/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0523% | 1,913 |
| African / African-American | 0.00267% | 37,510 |
| South Asian | 0.0022% | 45,522 |
| European (non-Finnish) | 0.00102% | 98,334 |
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.Ser379=
- Coding
- c.1137C>T
- MANE Select
- NM_000526
- dbSNP
- rs563641073
- Type
- single nucleotide variant
- Location
- chr17:41583372 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.00 · 6 PDB
- Residue 379
- the if rod domain; the 'coil 2' region; an α-helix
Similar variants
- 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
- KRT14 p.Arg388His 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-ser379 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown