KIT p.Gln549=
c.1647G>A · VCV4967209
Uncertain significance
Single submitter
Classification
Uncertain significance
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/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.42 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.83 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 21.4 | 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
- KIT
- Protein
- p.Gln549=
- Coding
- c.1647G>A
- MANE Select
- NM_000222
- Type
- single nucleotide variant
- Location
- chr4:54727324 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
- Residue 549
- an α-helix
Similar variants
- KIT p.Gln549His Likely pathogenic ★ ⚠ same residue
- KIT p.Gln549Arg Uncertain significance ★ ⚠ same residue
- KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same type
- KIT p.Asp816His Pathogenic ★★ same type
- KIT p.Asp820Tyr Pathogenic ★★ same type
- KIT p.Gln190Ter Pathogenic ★★ same type
- KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same type
- KIT p.Lys642Glu 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/kit-p-gln549 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown