Is KIT c.925+5del pathogenic?

KIT c.925+5del is classified Uncertain significance in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-22). Associated with hereditary neoplastic syndrome.

What condition is associated with KIT c.925+5del?

KIT c.925+5del is associated with hereditary neoplastic syndrome (ClinVar).

KIT c.925+5del

VCV4858933

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +5	donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 2.4, phastCons 1
Non-coding constraint	Z 1.69	1 kb window · o/e 0.87 · regional · uncalibrated

Variant & gene context

Gene: KIT
Coding: c.925+5del
MANE Select: NM_000222
Type: Deletion
Location: chr4:54703895 (GRCh38)
Gene constraint: LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 65 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KIT p.Asp579del Pathogenic ★★ same condition
KIT p.Asn945fs Uncertain significance ★★ same condition
KIT p.Asp458_Val459del Uncertain significance ★★ same condition
KIT p.Ser688fs Pathogenic ★ same condition
KIT c.1990+1del Conflicting classifications of pathogenicity ★ ⚠ same condition
KIT p.Arg740del Uncertain significance ★ same condition
KIT p.Asp975fs Uncertain significance ★ same condition
KIT p.Ile748fs Conflicting classifications of pathogenicity ★ ⚠ 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-c-925-plus-5del (accessed [today's date]).

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