KIT p.Leu14=
c.40C>T · rs1297912833 · VCV1737834
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
2
hereditary neoplastic syndrome
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 2.6 | GERP 2, phastCons 0.99 |
| Overall | ||
| CADD | 13.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,900 alleles
Overall
0.000657%
1/152,104 alleles · very rare
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
- KIT
- Protein
- p.Leu14=
- Coding
- c.40C>T
- MANE Select
- NM_000222
- dbSNP
- rs1297912833
- Type
- single nucleotide variant
- Location
- chr4:54658054 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
Similar variants
- KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same condition
- KIT p.Asp820Tyr Pathogenic ★★ same condition
- KIT p.Gln190Ter Pathogenic ★★ same condition
- KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same condition
- KIT p.Lys642Glu Pathogenic ★★ same condition
- KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same condition
- KIT p.Val559Ala Pathogenic/Likely pathogenic ★★ same condition
- KIT c.1232-3T>C Uncertain significance ★★ same condition
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/kit-p-leu14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown