KIT p.Val459=
c.1377G>A · rs2109768296 · VCV1895702
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
2
hereditary neoplastic syndrome
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 1.1 | GERP -4.9, phastCons 1 |
| Overall | ||
| CADD | 3.766 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,992 alleles
Overall
6.2e-05%
1/1,614,062 alleles · very rare
exomes 1/1,461,820 · genomes 0/152,242 · joint denominator
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.Val459=
- Coding
- c.1377G>A
- MANE Select
- NM_000222
- dbSNP
- rs2109768296
- Type
- single nucleotide variant
- Location
- chr4:54725887 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
- Residue 459
- a β-strand; the ig-like c2-type 5 domain
Similar variants
- KIT p.Val459Ala Uncertain significance ★★ ⚠ same residue
- KIT p.Val459Gly Uncertain significance ★★ ⚠ same residue
- KIT p.Val459Met Uncertain significance ★★ ⚠ same residue
- 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
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-val459 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown