Is KIT p.Val560del (c.1676TTG[1]) pathogenic?

KIT p.Val560del (c.1676TTG[1]) is classified Pathogenic in KIT (ClinVar, No assertion criteria, 2 submitters; last evaluated 2003-05-27). No gnomAD frequency available for this variant; Associated with Gastrointestinal stromal tumor, familial.

What condition is associated with KIT p.Val560del (c.1676TTG[1])?

KIT p.Val560del (c.1676TTG[1]) is associated with Gastrointestinal stromal tumor, familial (ClinVar).

How common is KIT p.Val560del (c.1676TTG[1]) in the general population?

KIT p.Val560del (c.1676TTG[1]) is no gnomAD frequency available for this variant (gnomAD).

KIT p.Val560del

c.1676TTG[1] · rs121913685 · VCV375913

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Gastrointestinal stromal tumor, familial

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5	GERP -0.42, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: KIT
Protein: p.Val560del
Coding: c.1676TTG[1]
MANE Select: NM_000222
dbSNP: rs121913685
Type: Microsatellite
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 560: a β-strand; a UniProt-annotated variant site (in gist; somatic mutation)

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

Disease context

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

Similar variants

KIT p.Val560Ala Uncertain significance ★★ ⚠ same residue
KIT p.Val560Asp Likely pathogenic ★ same residue
KIT p.Val560_Leu576del Uncertain significance ★ same residue
KIT p.Val560Ile Uncertain significance ★ ⚠ same residue
KIT p.Val560Phe Uncertain significance ★ ⚠ same residue
KIT p.Glu562del Uncertain significance ★★ same type
KIT c.2597-7_2597-6del Likely benign ★★ same type
KIT c.756+22_756+24del Likely benign ★★ 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-val560del (accessed [today's date]).

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