Is KIT c.*2017T>C pathogenic?

KIT c.2017T>C is classified Benign/Likely benign in KIT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.844%, nfe); Associated with gastrointestinal stromal tumor.

What condition is associated with KIT c.*2017T>C?

KIT c.*2017T>C is associated with gastrointestinal stromal tumor, mastocytosis, piebaldism (ClinVar).

How common is KIT c.*2017T>C in the general population?

KIT c.*2017T>C is rare (popmax 0.844%, nfe) (gnomAD).

How is Gastrointestinal stromal tumor inherited?

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

KIT c.*2017T>C

rs115028437 · VCV902287

Benign/Likely benign Single submitter

Classification

Benign/Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.844%, nfe)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.3, phastCons 1
Non-coding constraint	Z 1.37	1 kb window · o/e 0.90 · regional · uncalibrated
Overall
CADD	17.31	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.844% European (non-Finnish) · 994/117,726 alleles

Filtering AF 0.801% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.783%

Overall 0.559% 1,303/233,124 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.844%	118
Finnishnot grpmax-eligible	0.711%	141
Remaining individualsnot grpmax-eligible	0.645%	155
Admixed American	0.393%	254
South Asian	0.29%	345
Ashkenazi Jewishnot grpmax-eligible	0.21%	476
African / African-American	0.147%	678
Middle Eastern	0.129%	778
East Asian	0.00608%	16,440

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: KIT
Coding: c.*2017T>C
MANE Select: NM_000222
dbSNP: rs115028437
Type: single nucleotide variant
Location: chr4:54740574 (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

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

Also linked: mastocytosis piebaldism

For Gastrointestinal stromal tumor (Orphanet):

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

Similar variants

KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same condition
KIT p.Asp820Tyr Pathogenic ★★ same condition
KIT p.Gln190Ter Pathogenic ★★ same condition
KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same condition
KIT p.Lys642Glu Pathogenic ★★ same condition
KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same condition
KIT p.Val559Ala Pathogenic/Likely pathogenic ★★ same condition
KIT c.1232-3T>C Uncertain significance ★★ 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-star-2017t-c (accessed [today's date]).

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