KIT p.Ile315=
c.945C>A · rs2475478307 · VCV1767018
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00112%, sas)
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 | all four deltas below 0.2 · C>T here scores Δ0.30 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 11.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00112%
South Asian · 1/89,382 alleles
Overall
0.000144%
2/1,390,718 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00112% | 89,382 |
| European (non-Finnish) | 8.96e-05% | 1,115,780 |
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.Ile315=
- Coding
- c.945C>A
- MANE Select
- NM_000222
- dbSNP
- rs2475478307
- Type
- single nucleotide variant
- Location
- chr4:54707117 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
- Residue 315
- a β-strand
Similar variants
- KIT p.Ile315Asn Uncertain significance ★★ ⚠ same residue
- KIT p.Ile315Thr Uncertain significance ★★ ⚠ same residue
- KIT p.Ile315Val Uncertain significance ★★ ⚠ same residue
- KIT p.Ile315Met 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
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-ile315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown