Is KIT p.Val643fs (c.1926dup) pathogenic?

KIT p.Val643fs (c.1926dup) is classified Pathogenic in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-12). Associated with gastrointestinal stromal tumor.

What condition is associated with KIT p.Val643fs (c.1926dup)?

KIT p.Val643fs (c.1926dup) is associated with gastrointestinal stromal tumor (ClinVar).

How is Gastrointestinal stromal tumor inherited?

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

KIT p.Val643fs

c.1926dup · VCV4725322

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

gastrointestinal stromal tumor

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 13 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.19	GERP -0.23, phastCons 0.48

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: KIT
Protein: p.Val643fs
Coding: c.1926dup
MANE Select: NM_000222
Type: Duplication
Location: chr4:54728054 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 643: the protein kinase domain; an α-helix

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.Val643Ala Uncertain significance ★★ ⚠ same residue
KIT p.Val643= Likely benign ★ same residue
KIT p.Leu707_Ser713dup Uncertain significance ★★ same condition
KIT p.Val422dup Uncertain significance ★★ same condition
KIT c.338-6dup Likely benign ★★ same condition
KIT c.67+5_67+18dup Likely benign ★★ same condition
KIT p.Ala597fs Pathogenic ★ same condition
KIT p.Arg588_Leu589insProGlnLeuProTyrAspHisLysTrpGluPheProArgAsnArg 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-val643fs (accessed [today's date]).

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