Is KIT p.Asp579del (c.1735_1737del) pathogenic?

KIT p.Asp579del (c.17351737del) is classified Pathogenic in KIT (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-30). Absent from gnomAD; Associated with gastrointestinal stromal tumor.

What condition is associated with KIT p.Asp579del (c.1735_1737del)?

KIT p.Asp579del (c.1735_1737del) is associated with gastrointestinal stromal tumor, hereditary neoplastic syndrome (ClinVar).

How common is KIT p.Asp579del (c.1735_1737del) in the general population?

KIT p.Asp579del (c.1735_1737del) is absent from gnomAD (gnomAD).

How is Gastrointestinal stromal tumor inherited?

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

KIT p.Asp579del

c.1735_1737del · rs1060502543 · VCV409725

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

gastrointestinal stromal tumor

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 7.9	GERP 2.6, 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.

Cancer therapy — CIViC

Disease	Therapies	Level	Significance
Gastrointestinal Stromal Tumor	Imatinib	D	Sensitivity/Response
Gastrointestinal Stromal Tumor	Sunitinib	C	Resistance
Gastrointestinal Stromal Tumor	Sunitinib	C	Resistance
Sinonasal Undifferentiated Carcinoma	Imatinib Mesylate	C	Sensitivity/Response

Variant & gene context

Gene: KIT
Protein: p.Asp579del
Coding: c.1735_1737del
MANE Select: NM_000222
dbSNP: rs1060502543
Type: Deletion
Location: chr4:54727501 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB
Residue 579: 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

Also linked: hereditary neoplastic syndrome

For Gastrointestinal stromal tumor (Orphanet):

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

Similar variants

KIT p.Asp579Val Uncertain significance ★★ ⚠ same residue
KIT p.Asp579Glu Uncertain significance ★ ⚠ same residue
KIT p.Asn819fs Pathogenic ★★ same condition
KIT p.Asn945fs Uncertain significance ★★ same condition
KIT p.Asp458_Val459del Uncertain significance ★★ same condition
KIT c.1115+16del Benign/Likely benign ★★ same condition
KIT c.1116-16_1116-14del Likely benign ★★ same condition
KIT c.1540+2del 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-asp579del (accessed [today's date]).

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