KIT p.Asn268=
c.804T>C · rs1720604075 · VCV1761812
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
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 -0.17 | GERP -4.5, phastCons 0.001 |
| Overall | ||
| CADD | 4.759 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,808 alleles
Overall
6.2e-05%
1/1,613,806 alleles · very rare
exomes 0/1,461,624 · genomes 1/152,182 · 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.Asn268=
- Coding
- c.804T>C
- MANE Select
- NM_000222
- dbSNP
- rs1720604075
- Type
- single nucleotide variant
- Location
- chr4:54703771 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
- Residue 268
- the ig-like c2-type 3 domain
Similar variants
- KIT p.Asn268Asp Uncertain significance ★ ⚠ same residue
- KIT p.Asn268His Uncertain significance ★ ⚠ same residue
- KIT p.Asn268Lys Uncertain significance ★ ⚠ same residue
- KIT p.Asn268Ser Uncertain significance ★ ⚠ same residue
- KIT p.Asp820Tyr Pathogenic ★★ same condition
- KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same condition
- KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same condition
- KIT p.Val559Ala 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-asn268 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown