KRT5 p.Ser242=
c.726A>G · VCV4916986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.115 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -20 | |
| Overall | ||
| CADD | 0.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.000681%
11/1,614,100 alleles · ultra-rare
exomes 8/1,461,890 · genomes 3/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00667% | 14,984 |
| South Asian | 0.0011% | 91,094 |
| European (non-Finnish) | 0.000339% | 295,010 |
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
- KRT5
- Protein
- p.Ser242=
- Coding
- c.726A>G
- MANE Select
- NM_000424
- Type
- single nucleotide variant
- Location
- chr12:52518990 (GRCh38)
- Gene constraint
- LOEUF 0.538 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 68.86 · 2 PDB
- Residue 242
- the if rod domain; a UniProt-annotated variant site (in ddd1); the 'coil 1b' region
Similar variants
- KRT5 c.555+1G>A Pathogenic ★★ same type
- KRT5 p.Ala428Thr Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Ala428Val Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Arg165Ser Pathogenic ★★ same type
- KRT5 p.Arg331Cys Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Arg331His Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Asn176Ser Pathogenic/Likely pathogenic ★★ same type
- KRT5 p.Asn177Ser 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/krt5-p-ser242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown