Is KIT p.Asp309Val (c.926A>T) pathogenic?

KIT p.Asp309Val (c.926A>T) is classified Uncertain significance in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-29). AlphaMissense: ambiguous (0.3972); Absent from gnomAD v4.1; Associated with gastrointestinal stromal tumor.

What condition is associated with KIT p.Asp309Val (c.926A>T)?

KIT p.Asp309Val (c.926A>T) is associated with gastrointestinal stromal tumor (ClinVar).

How common is KIT p.Asp309Val (c.926A>T) in the general population?

KIT p.Asp309Val (c.926A>T) is absent from gnomAD v4.1 (gnomAD).

How is Gastrointestinal stromal tumor inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about KIT p.Asp309Val (c.926A>T)?

AlphaMissense predicts ambiguous (score 0.3972) — an in-silico prediction, not a clinical call.

KIT p.Asp309Val

c.926A>T · VCV4807870

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3972 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

gastrointestinal stromal tumor

Computational evidence

Protein change
AlphaMissense	0.3972	ambiguous
REVEL	0.463	indeterminate
SaProt	LLR -6.42	tolerated
Splicing
SpliceAI	Δ0.36	acceptor gain · deltas
Pangolin	Δ0.29	gain · loss 0.17 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 5.4	GERP 1.3, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 32 kb · p 3.4e-16 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Asp309Val
Coding: c.926A>T
MANE Select: NM_000222
Type: single nucleotide variant
Location: chr4:54707098 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 309: a β-strand

Full KIT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

gastrointestinal stromal tumor — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Gastrointestinal stromal tumor (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

KIT p.Asp309Glu Uncertain significance ★ ⚠ same residue
KIT p.Asp309= Likely benign ★ 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
KIT p.Trp557Arg 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-asp309val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown