KIT

Chr 4ADIsolated cases

KIT proto-oncogene, receptor tyrosine kinase

Also known as: C-Kit, CD117, MASTC, PBT, SCFR

This gene encodes a receptor tyrosine kinase. This gene was initially identified as a homolog of the feline sarcoma viral oncogene v-kit and is often referred to as proto-oncogene c-Kit. The canonical form of this glycosylated transmembrane protein has an N-terminal extracellular region with five immunoglobulin-like domains, a transmembrane region, and an intracellular tyrosine kinase domain at the C-terminus. Upon activation by its cytokine ligand, stem cell factor (SCF), this protein phosphorylates multiple intracellular proteins that play a role in in the proliferation, differentiation, migration and apoptosis of many cell types and thereby plays an important role in hematopoiesis, stem cell maintenance, gametogenesis, melanogenesis, and in mast cell development, migration and function. This protein can be a membrane-bound or soluble protein. Mutations in this gene are associated with gastrointestinal stromal tumors, mast cell disease, acute myelogenous leukemia, and piebaldism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]

OMIMResearchGenerating clinical summary…
LOFmechanismAD/Isolated casesLOEUF 0.306 OMIM phenotypes
Clinical SummaryKIT
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Gene-Disease Validity (ClinGen)
gastrointestinal stromal tumor · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.30LOEUF
pLI 0.981
Z-score 5.30
OE 0.17 (0.100.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.58Z-score
OE missense 0.69 (0.630.75)
375 obs / 544.4 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.17 (0.100.30)
00.351.4
Missense OE?0.69 (0.630.75)
00.61.4
Synonymous OE?1.09
01.21.6
LoF obs/exp: 8 / 47.4Missense obs/exp: 375 / 544.4Syn Z: -1.00
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveKIT-related piebaldismLOFAD
definitiveKIT-related familial gastro-intestinal stromal tumoursOTHERAD

This gene — mechanism propensity

DN
0.5673th %ile
GOF
0.6833th %ile
LOF
0.51top 25%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function, gain-of-function and dominant-negative). The Badonyi & Marsh model scores gain-of-function highest among its predictions, but genomic evidence (constraint, ClinVar variant spectrum, and literature) most strongly supports loss-of-function (haploinsufficiency). Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFLOEUF 0.30 · ClinGen HI: Sufficient evidence for dosage pathogenicity
GOFprediction above median · 1 literature citation
DN1 literature citation

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNThis is consistent with a possible """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""dominant negative"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" effect of missense c-kit polypeptides on the function of the dimeric receptor.1
GOFGain-of-function mutations of c-kit in human gastrointestinal stromal tumors2

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

KIT · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

Pancreas CancerPancreas CystPancreatic Ductal Adenocarcinoma

Pancreatic Cancer Early Detection Consortium

RECRUITING
NCT04970056Arbor Research Collaborative for HealthStarted 2020-09-18
NSCLC

Analysis of Deoxyribonucleic Acid and Ribonucleic Acid Next-Generation Sequencing in Non-Small Cell Lung Cancer Patients Without Pathological Complete Response Following Neoadjuvant Immunotherapy

NOT YET RECRUITING
NCT07179445Tianjin Medical University Cancer Institute and HospitalStarted 2025-09-20
Not applicable- observational study
Cardiometabolic SyndromePhysical InactivityHypertension

Black Impact: The Mechanisms Underlying Psychosocial Stress Reduction in a Cardiovascular Health Intervention

RECRUITING
NCT06055036Phase NAOhio State UniversityStarted 2023-08-24
Black Impact Intervention
Huntington Disease

Study of BDNF Pathway Biomarkers in the Cerebrospinal Fluid in Patients With Huntington's Disease

RECRUITING
NCT04012411Phase NAUniversity Hospital, MontpellierStarted 2020-03-03
Brain MRILumbar PunctionBlood sample
Kidney DiseaseKidney Disease, ChronicKidney Disease, End-Stage

Rutgers University Study of the Genetics of Kidney Disease

RECRUITING
NCT07217535Rutgers, The State University of New JerseyStarted 2026-04-23
Saliva sampleHealth surveys
Graves DiseaseGraves' Disease in RemissionEpstein-Barr Virus

Graves' Disease Induced by Epstein-Barr Virus Lytic Reactivation

NOT YET RECRUITING
NCT06426758Xiao-Ming MaoStarted 2024-05-30
Extrapulmonary Tuberculosis

A Multicentric Cohort and Biomarker Study for Improved Care of Patients with Extrapulmonary Tuberculosis

RECRUITING
NCT06875336University of CologneStarted 2023-03-06
biomarker analysis
Gut Microbiota Dysbiosis in Lupus Nepheritis

Gut Microbiota Dysbiosis in Lupus Nephritis

NOT YET RECRUITING
NCT06231303Hager ZanatyStarted 2025-01
DNA extraction and PCR amplification
Gene Expression ProfilingOrthodentic Appliances

Genes Associated With Bone Metabolism in the Saliva During Orthodontic Treatment

ACTIVE NOT RECRUITING
NCT07303647Kurdistan Higher Council of Medical SpecialtiesStarted 2025-10-12
PCR
Metastatic Colorectal Cancer (mCRC)

DHF-20-1839-2: Clinical Performance Study Protocol for Therascreen® KRAS RGQ PCR Kit

RECRUITING
NCT06645236Phase NAQIAGEN Gaithersburg, IncStarted 2023-12-22
therascreen® KRAS RGQ PCR Kit
Schizophrenia

Tryptophan-Kynurenine Pathway Metabolism in the Pathophysiology of Cognitive Impairment in Schizophrenia.

ENROLLING BY INVITATION
NCT07162467Tianjin Anding HospitalStarted 2024-02-19
Inflammatory Bowel DiseasesCrohn Disease

Predicting IBD Treatment Outcomes With Gut Microbiome Analysis

RECRUITING
NCT06453720University of British ColumbiaStarted 2024-08-01
Colonoscopy