KRT4 p.Leu52=
c.156C>G · rs1592312379 · VCV743163
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 2.6 | GERP -0.22, phastCons 1 |
| Overall | ||
| CADD | 5.285 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KRT4
- Protein
- p.Leu52=
- Coding
- c.156C>G
- MANE Select
- NM_002272
- dbSNP
- rs1592312379
- Type
- single nucleotide variant
- Location
- chr12:52813903 (GRCh38)
- Gene constraint
- LOEUF 1.089 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.77
- Residue 52
- the 'head' region
Similar variants
- KRT4 p.Leu52fs Likely benign same residue
- KRT4 p.Ala106Gly Uncertain significance ★★ ⚠ same type
- KRT4 p.Asp153Asn Uncertain significance ★★ ⚠ same type
- KRT4 p.Asp247Glu Uncertain significance ★★ same type
- KRT4 c.1126-32G>A Benign ★★ same type
- KRT4 c.1346+15A>G Benign ★★ same type
- KRT4 c.1346+15A>T Likely benign ★★ same type
- KRT4 c.1381+15C>T Benign ★★ 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/krt4-p-leu52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown