KRT14 p.Thr2=
c.6C>T · rs11551759 · VCV256364
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 95.8%, eas) — too common for a highly-penetrant pathogenic allele
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 3 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 11.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
95.8%
East Asian · 41,514/43,340 alleles
Filtering AF
95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 94.7%
Overall
58.3%
924,141/1,583,934 alleles · common
exomes 836,734/1,431,882 · genomes 87,407/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 95.8% | 1 |
| Amishnot grpmax-eligible | 78% | 1 |
| Admixed American | 73.6% | 1 |
| South Asian | 71.5% | 1 |
| Finnishnot grpmax-eligible | 66.3% | 2 |
| Remaining individualsnot grpmax-eligible | 58.4% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 55.9% | 2 |
| European (non-Finnish) | 55.6% | 2 |
| Middle Eastern | 51.2% | 2 |
| African / African-American | 47.2% | 2 |
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.Thr2=
- Coding
- c.6C>T
- MANE Select
- NM_000526
- dbSNP
- rs11551759
- Type
- single nucleotide variant
- Location
- chr17:41586829 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.00 · 6 PDB
- Residue 2
- the 'head' region
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-thr2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown