Is KIT p.Val559Ile (c.1675G>A) pathogenic?

KIT p.Val559Ile (c.1675G>A) is classified Uncertain significance in KIT (ClinVar, Single submitter, 2 submitters; last evaluated 2022-12-31). AlphaMissense: likely benign (0.2773); Absent from gnomAD v4.1; Associated with gastrointestinal stromal tumor.

What condition is associated with KIT p.Val559Ile (c.1675G>A)?

KIT p.Val559Ile (c.1675G>A) is associated with gastrointestinal stromal tumor (ClinVar).

How common is KIT p.Val559Ile (c.1675G>A) in the general population?

KIT p.Val559Ile (c.1675G>A) 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.Val559Ile (c.1675G>A)?

AlphaMissense predicts likely benign (score 0.2773) — an in-silico prediction, not a clinical call.

KIT p.Val559Ile

c.1675G>A · rs121913520 · VCV376056

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2773 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

gastrointestinal stromal tumor

Computational evidence

Protein change
AlphaMissense	0.2773	likely benign
REVEL	0.408	indeterminate
SaProt	LLR -6.68	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 277 bp · p 0.96 · regional, not allelic
Overall
CADD	24.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Val559Ile
Coding: c.1675G>A
MANE Select: NM_000222
dbSNP: rs121913520
Type: single nucleotide variant
Location: chr4:54727443 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 559: a β-strand; a UniProt-annotated variant site (in gist; somatic mutation); a UniProt-annotated variant site (in gist)

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.Val559Ala Pathogenic/Likely pathogenic ★★ same residue
KIT p.Val559Phe Uncertain significance ★★ ⚠ same residue
KIT p.Val559= Likely benign ★ same residue
KIT p.Val559Asp Pathogenic same residue
KIT p.Val559_Thr574delinsAla Likely pathogenic ★ same residue
KIT p.Val559_Val560del Pathogenic same residue
KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same condition
KIT p.Asp820Tyr 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-val559ile (accessed [today's date]).

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