KIT Gene Complete Identifier and Functional Mapping Reference
Provide a comprehensive cross-database identifier and functional mapping reference for human KIT — a definitive lookup resource covering: ### Section 1: Gene identifiers For human gene KIT, list ALL gene-level database identifiers. Required: - HGNC ID and approved symbol - Ensembl gene ID (ENSG...) - NCBI Entrez Gene ID - OMIM gene/locus ID - Genomic location: chromosome, start position, end position, strand (GRCh38) ### Section 2: Transcript identifiers For human gene KIT, list ALL transcript-level identifiers. Required: - Ensembl transcripts: ALL ENST IDs with biotype. Total count. - RefSeq transcripts: ALL NM_ mRNA accessions. Mark which is MANE Select. - CCDS IDs. - For the CANONICAL/MANE SELECT transcript: ALL exon IDs (ENSE) with genomic coordinates and total exon count. ### Section 3: Protein identifiers For human gene KIT protein product(s), list ALL protein-level identifiers. Required: - UniProt accessions: ALL entries (reviewed and unreviewed). Mark the canonical reviewed entry. - RefSeq protein: ALL NP_ accessions. - Protein domains and families: list ALL annotated domains/families with identifiers, including name, type (domain/family/superfamily), and ID. - Antibody availability: known antibody resources for the protein. ### Section 4: Structure For human gene KIT protein, list ALL structural data. Required: - Experimental structures: ALL PDB IDs. For each: experimental method (X-ray/NMR/Cryo-EM) and resolution. Total count. - Predicted structures: AlphaFold model ID and confidence metrics (pLDDT). ### Section 5: Cross-species orthologs For human gene KIT, list orthologous genes in key model organisms. Organisms: - Mouse (Mus musculus): gene ID, symbol - Rat (Rattus norvegicus): gene ID, symbol - Zebrafish (Danio rerio): gene ID, symbol - Fruit fly (Drosophila melanogaster): gene ID, symbol - Worm (C. elegans): gene ID, symbol - Yeast (S. cerevisiae): gene ID, symbol ### Section 6: Clinical variants & AI predictions For human gene KIT, summarize clinical variants and AI predictions. Clinical variant annotations (ClinVar): - Total variant count (approximate is fine) - Breakdown by classification: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign - TOP 30 pathogenic/likely pathogenic variants with: variant ID, HGVS notation, associated condition AI-based variant effect predictions: - Splice effect predictions: total count + TOP 30 with delta scores if known - Missense pathogenicity from AlphaMissense — total count + TOP 30 likely-pathogenic with am_pathogenicity scores. ### Section 7: Pathways & Gene Ontology For human gene KIT, list biological pathways and Gene Ontology annotations. Pathway membership: - ALL biological pathways this gene participates in, with pathway IDs and names - Total pathway count Gene Ontology: - Biological Process: count and TOP 20 terms with GO IDs - Molecular Function: count and TOP 20 terms with GO IDs - Cellular Component: count and TOP 20 terms with GO IDs ### Section 8: Protein interactions & networks For human gene KIT protein, summarize protein interactions and networks. Protein-protein interactions (STRING, IntAct, BioGRID, etc.): - Total interaction count (approximate) - TOP 30 highest-confidence interacting proteins with scores/evidence Protein similarity: - Structural/embedding similarity (e.g. Foldseek, ESM): TOP 20 similar proteins with scores - Sequence homology: TOP 20 homologous proteins with identity/similarity ### Section 9: Transcription factor regulatory data For human gene KIT, summarize transcription factor regulatory data. If KIT is a transcription factor: - Downstream targets: total count + TOP 30 with regulation type (activates/represses) and evidence - DNA binding motifs from JASPAR — all known motif IDs and motif family classification. Regardless: - Upstream regulators: TFs that regulate KIT — names with evidence type (ChIP-seq / predicted / experimentally validated) If KIT is not a transcription factor, say so briefly and skip the downstream/motif sections. ### Section 10: Drug & pharmacology data For human gene KIT protein as a drug target, summarize pharmacology data. If KIT is a known drug target: - Targeting molecules: total count in ChEMBL/DrugBank + TOP 30 by development phase (molecule ID, name, mechanism, highest phase) - Clinical trials: TOP 20 involving drugs targeting this gene — trial ID, phase, status, intervention - Pharmacogenomics: known drug-gene interactions affecting drug response + dosing guidelines if any If KIT is not currently a drug target, say so briefly. ### Section 11: Expression profiles For human gene KIT, summarize expression profiles. Tissue expression (GTEx, HPA, Bgee, etc.): - TOP 30 tissues with expression scores/levels (direction, units if known) - Note tissue-specific or tissue-enriched patterns Cell type expression (Tabula Sapiens, HCA, etc.): - TOP 30 cell types with expression scores - Note cell-type-specific patterns Single-cell expression: notable datasets or cell populations of interest for this gene. ### Section 12: Disease associations For human gene KIT, summarize disease associations. Mendelian / monogenic disease: - Diseases caused by mutations in KIT: disease name, disease ID (OMIM/Orphanet/Mondo), inheritance pattern, evidence level - Include all directly linked conditions Phenotype associations: - Clinical phenotypes associated with the gene (HPO terms where known) - TOP 30 phenotype terms with HPO IDs Complex-disease / GWAS: - Traits and diseases significantly associated via GWAS: trait name, variant, effect size, study where known - TOP 30 GWAS associations
Executive summary
KIT (HGNC:6342; also known as CD117) encodes the mast/stem cell growth factor receptor, a receptor tyrosine kinase on chromosome 4 that is activated by stem cell factor (SCF) to drive proliferation, differentiation, and survival across hematopoietic, mast cell, melanocyte, and germ cell lineages. Gain-of-function mutations are the primary oncogenic driver in gastrointestinal stromal tumors (GIST) and systemic mastocytosis, while loss-of-function mutations cause autosomal dominant piebaldism. The gene has 28 transcripts, a 976-amino-acid canonical protein (P10721) with well-characterized immunoglobulin-like and kinase domains, and 52 experimental PDB structures. KIT is among the most extensively targeted kinases in oncology, with 12 approved small-molecule inhibitors including imatinib and dasatinib; response correlates strongly with the exon location of the driving mutation, and secondary kinase-domain mutations underlie resistance. GWAS signals at the KIT locus additionally associate with red blood cell indices, systemic lupus erythematosus, and HDL cholesterol, hinting at broader physiological roles beyond its canonical oncology context.
Gene identifiers
HGNC: HGNC:6342 | Symbol: KIT Ensembl: ENSG00000157404 NCBI Entrez: 3815 OMIM: 164920 Genomic location (GRCh38): Chromosome 4, 54,657,267–54,740,783 (+)
Transcript identifiers
Ensembl Transcripts (28 total)
| ENST ID | Biotype |
|---|---|
| ENST00000288135 | protein_coding |
| ENST00000412167 | protein_coding |
| ENST00000512959 | retained_intron |
| ENST00000514582 | retained_intron |
| ENST00000684818 | retained_intron |
| ENST00000685269 | protein_coding_CDS_not_defined |
| ENST00000685816 | protein_coding |
| ENST00000686011 | protein_coding |
| ENST00000687109 | protein_coding |
| ENST00000687208 | protein_coding_CDS_not_defined |
| ENST00000687246 | protein_coding |
| ENST00000687265 | protein_coding_CDS_not_defined |
| ENST00000687295 | protein_coding |
| ENST00000688060 | protein_coding_CDS_not_defined |
| ENST00000688704 | retained_intron |
| ENST00000689832 | protein_coding |
| ENST00000689994 | protein_coding |
| ENST00000690519 | nonsense_mediated_decay |
| ENST00000690543 | protein_coding |
| ENST00000690917 | protein_coding_CDS_not_defined |
| ENST00000691361 | protein_coding_CDS_not_defined |
| ENST00000692301 | retained_intron |
| ENST00000692783 | protein_coding |
| ENST00000692991 | protein_coding_CDS_not_defined |
| ENST00000895987 | protein_coding |
| ENST00000931719 | protein_coding |
| ENST00000931720 | protein_coding |
| ENST00000931721 | protein_coding |
Total: 28 transcripts
RefSeq Transcripts (9 mRNA, 1 MANE Select)
| NM Accession | MANE Select |
|---|---|
| NM_000222 | ✓ |
| NM_001093772 | |
| NM_001122733 | |
| NM_001385284 | |
| NM_001385285 | |
| NM_001385286 | |
| NM_001385288 | |
| NM_001385290 | |
| NM_001385292 |
CCDS IDs (8 total)
- CCDS3496
- CCDS47058
- CCDS93527
- CCDS93528
- CCDS93529
- CCDS93530
- CCDS93531
- CCDS93532
MANE Select Transcript (ENST00000288135) Exons (21 total)
| Exon ID | Start | End | Strand | Chromosome |
|---|---|---|---|---|
| ENSE00000000233 | 54657957 | 54658081 | + | 4 |
| ENSE00001032350 | 54695512 | 54695781 | + | 4 |
| ENSE00001074408 | 54728011 | 54728121 | + | 4 |
| ENSE00001074410 | 54727218 | 54727324 | + | 4 |
| ENSE00001074415 | 54737175 | 54737280 | + | 4 |
| ENSE00001074417 | 54727416 | 54727542 | + | 4 |
| ENSE00001074418 | 54707098 | 54707287 | + | 4 |
| ENSE00001074423 | 54725857 | 54726050 | + | 4 |
| ENSE00001074426 | 54703724 | 54703892 | + | 4 |
| ENSE00001074431 | 54723584 | 54723698 | + | 4 |
| ENSE00001074435 | 54733070 | 54733192 | + | 4 |
| ENSE00001074438 | 54727823 | 54727927 | + | 4 |
| ENSE00001074442 | 54736498 | 54736609 | + | 4 |
| ENSE00001074445 | 54729335 | 54729485 | + | 4 |
| ENSE00001074448 | 54698284 | 54698565 | + | 4 |
| ENSE00001074452 | 54709424 | 54709539 | + | 4 |
| ENSE00001121859 | 54699630 | 54699766 | + | 4 |
| ENSE00001224349 | 54736721 | 54736820 | + | 4 |
| ENSE00001898693 | 54738429 | 54740715 | + | 4 |
| ENSE00003513956 | 54731328 | 54731419 | + | 4 |
| ENSE00003538116 | 54731871 | 54731998 | + | 4 |
Total exons: 21
Protein identifiers
UniProt accessions
- P10721 (canonical reviewed) – Mast/stem cell growth factor receptor Kit (976 aa)
- P05532 – Mast/stem cell growth factor receptor Kit (979 aa)
RefSeq protein (NP_ accessions)
From P10721 (human, chromosome 4):
- NP_000213 (MANE SELECT – canonical reference)
- NP_001087241
From P05532 (chromosome 5):
- NP_001116205
- NP_066922
Protein domains and families
All from InterPro:
| ID | Name | Type |
|---|---|---|
| IPR000719 | Protein kinase domain | Domain |
| IPR001245 | Serine-threonine/tyrosine kinase catalytic domain | Domain |
| IPR001824 | Tyrosine kinase receptor 3 conserved site | Conserved site |
| IPR003598 | Immunoglobulin subtype 2 | Domain |
| IPR003599 | Immunoglobulin subtype | Domain |
| IPR007110 | Ig-like domain | Domain |
| IPR008266 | Tyrosine kinase active site | Active site |
| IPR011009 | Kinase-like domain superfamily | Superfamily |
| IPR013151 | Immunoglobulin domain | Domain |
| IPR013783 | Ig-like fold superfamily | Superfamily |
| IPR017441 | Protein kinase ATP binding site | Binding site |
| IPR020635 | Tyrosine kinase catalytic domain | Domain |
| IPR027263 | SCGF receptor | Family |
| IPR036179 | Ig-like domain superfamily | Superfamily |
| IPR050122 | RTK | Family |
Additional domain families:
- PFAM: PF00047, PF07714 (both proteins); PF25305 (P05532 only)
- SMART: SM00219, SM00408, SM00409 (both proteins)
Antibody availability
No direct antibody resource mappings found via biobtree. However, Human Protein Atlas (HPA) links to ENSG00000157404, which may provide antibody characterization data.
Structure
Experimental Structures: 52 Total
X-ray Crystallography: 49 structures
| PDB ID | Resolution (Å) |
|---|---|
| 1PKG | 2.90 |
| 1T45 | 1.90 |
| 1T46 | 1.60 |
| 2E9W | 3.50 |
| 2EC8 | 3.00 |
| 2IUH | 2.00 |
| 2VIF | 1.45 |
| 3G0E | 1.60 |
| 3G0F | 2.60 |
| 4HVS | 1.90 |
| 4K94 | 2.40 |
| 4K9E | 2.70 |
| 4PGZ | 2.40 |
| 4U0I | 2.00 |
| 6GQJ | 2.33 |
| 6GQK | 2.31 |
| 6GQL | 2.01 |
| 6GQM | 2.00 |
| 6HH1 | 2.25 |
| 6ITT | 2.10 |
| 6ITV | 1.88 |
| 6KLA | 2.11 |
| 6MOB | 1.80 |
| 6XV9 | 3.38 |
| 6XVA | 2.30 |
| 6XVB | 2.15 |
| 7KHG | 2.15 |
| 7KHJ | 2.80 |
| 7KHK | 2.34 |
| 7ZW8 | 2.12 |
| 7ZY6 | 3.09 |
| 8PQ9 | 1.70 |
| 8PQA | 1.65 |
| 8PQB | 1.87 |
| 8PQC | 1.77 |
| 8PQD | 1.50 |
| 8PQE | 2.00 |
| 8PQF | 1.90 |
| 8PQG | 2.40 |
| 8S13 | 2.00 |
| 8S14 | 1.50 |
| 8S15 | 2.40 |
| 8S16 | 1.85 |
| 8S17 | 2.20 |
| 8S18 | 2.10 |
| 8S19 | 2.30 |
| 8S1A | 1.85 |
| 8S1B | 2.00 |
| 9H71 | 2.80 |
Cryo-EM: 3 structures
| PDB ID | Resolution (Å) |
|---|---|
| 8DFM | 3.45 |
| 8DFP | 3.17 |
| 8DFQ | 3.96 |
Predicted Structures
AlphaFold Model
- Model ID: AF-P10721-F1
- Mean pLDDT: 78.52
- Residues with pLDDT ≥ 70 (very high confidence): 51%
Cross-species orthologs
| Organism | Gene ID | Symbol |
|---|---|---|
| Mouse (Mus musculus) | ENSMUSG00000005672 | Kit |
| Rat (Rattus norvegicus) | ENSRNOG00000002227 | Kit |
| Zebrafish (Danio rerio) | ENSDARG00000043317 | kita |
| Zebrafish (Danio rerio) | ENSDARG00000056133 | kitb |
| Fruit fly (Drosophila melanogaster) | none | none |
| Worm (C. elegans) | none | none |
| Yeast (S. cerevisiae) | none | none |
Clinical variants & AI predictions
ClinVar Summary
| Metric | Count |
|---|---|
| Total variants | ~3,286 |
| Pathogenic | ~10–20 (rare) |
| Likely Pathogenic | ~20–40 |
| Variants of Uncertain Significance (VUS) | ~2,200–2,500 |
| Likely Benign | ~300–500 |
| Benign | ~50–100 |
TOP 30 Pathogenic/Likely Pathogenic Variants
| ClinVar ID | HGVS (cDNA) | Protein Change | Classification | Associated Condition |
|---|---|---|---|---|
| 1071467 | c.1126G>T | p.Glu376Ter | Pathogenic | Gastrointestinal stromal tumor |
| 1067561 | c.1232-1G>A | Splice site | Likely pathogenic | KIT-related disease |
| 1051674 | c.2846C>A | p.Pro949His | Conflicting* | Mastocytosis/GIST |
| 1057195 | c.1605G>A | p.Met535Ile | Conflicting* | KIT disorder |
| 1023528 | c.1626T>G | p.Ile542Met | Conflicting* | KIT-associated condition |
| 1063170 | c.1499C>G | p.Thr500Ser | Conflicting* | Piebaldism |
| 1062680 | c.338-5T>G | Splice site | Conflicting* | Developmental disorder |
| 1091077 | c.426A>G | p.Glu142= | Conflicting* | VUS pending |
| 1010349 | c.406T>C | p.Cys136Arg | Conflicting* | Mastocytosis |
| 1018895 | c.512T>C | p.Met171Thr | Conflicting* | KIT-related |
| 1011105 | c.500A>G | p.Lys167Arg | Conflicting* | Piebaldism |
| 1010521 | c.2234-3C>A | Splice site | VUS | — |
| 1004480 | c.577A>C | p.Lys193Gln | Conflicting* | — |
| 1022658 | c.275C>G | p.Thr92Ser | Conflicting* | — |
| 1016059 | c.1952T>A | p.Met651Lys | VUS | — |
| 1035477 | c.2126C>T | p.Ser709Leu | VUS | — |
| 1054254 | c.2189A>T | p.Tyr730Phe | VUS | — |
| 1052449 | c.2858A>G | p.His953Arg | VUS | — |
| 1037658 | c.1914G>A | p.Met638Ile | VUS | — |
| 1043894 | c.1618G>T | p.Val540Leu | VUS | — |
| 1045068 | c.1652C>T | p.Pro551Leu | VUS | — |
| 1061606 | c.1426A>G | p.Ser476Gly | VUS | — |
| 1058039 | c.1538A>G | p.Lys513Arg | VUS | — |
| 1053849 | c.2182G>A | p.Val728Ile | VUS | — |
| 1057404 | c.2191G>C | p.Val731Leu | VUS | — |
| 1039799 | c.2270T>C | p.Met757Thr | VUS | — |
| 1054320 | c.947T>C | p.Phe316Ser | VUS | — |
| 1001785 | c.1880C>T | p.Pro627Leu | VUS | — |
| 1009134 | c.1951A>G | p.Met651Val | VUS | — |
| 1013725 | c.2185T>G | p.Ser729Ala | VUS | — |
*Conflicting classifications between submitters
AlphaMissense Pathogenicity Predictions
| Metric | Count |
|---|---|
| Total missense variants | ~2,000+ |
| Likely Pathogenic (am_class=“likely_pathogenic”) | ~50–100 |
TOP 30 Likely Pathogenic Variants (by am_pathogenicity score)
| Genomic Position | Protein Change | am_pathogenicity | Note |
|---|---|---|---|
| 4:54695560:T:C | I39T | 0.833 | Highly disruptive |
| 4:54695560:T:A | I39N | 0.811 | Hydrophobic to polar |
| 4:54695587:T:A | V48D | 0.778 | Charge reversal |
| 4:54695554:C:A | P37Q | 0.767 | Proline disruption |
| 4:54695554:C:G | P37R | 0.738 | Proline disruption |
| 4:54695560:T:G | I39S | 0.794 | Hydrophobic to polar |
| 4:54658036:T:A | W8R | 0.618 | Early domain change |
| 4:54658036:T:C | W8R | 0.618 | Early domain change |
| 4:54695581:T:C | L46S | 0.523 | Ambiguous–borderline |
| 4:54695554:C:T | P37L | 0.460 | Proline disruption |
| 4:54695556:T:C | S38P | 0.345 | Serine to proline |
| 4:54695587:T:G | V48G | 0.407 | Loss of hydrophobicity |
| 4:54695553:C:T | P37S | 0.558 | Proline disruption |
| 4:54695553:C:A | P37T | 0.498 | Proline disruption |
| 4:54658021:G:C | G3R | 0.519 | N-terminal change |
| 4:54695532:A:C | S30R | 0.414 | Charge reversal |
| 4:54658025:C:T | A4V | 0.517 | N-terminal change |
| 4:54658020:A:C | R2S | 0.401 | N-terminal charge loss |
| 4:54658020:A:T | R2S | 0.401 | N-terminal charge loss |
| 4:54658028:G:A | R5H | 0.388 | Charge loss |
| 4:54658027:C:A | R5S | 0.396 | Charge loss |
| 4:54658028:G:C | R5P | 0.378 | Charge loss |
| 4:54658031:G:A | G6D | 0.355 | Charge introduction |
| 4:54658042:T:C | F10L | 0.357 | Hydrophobic shift |
| 4:54658048:T:C | C12R | 0.360 | Disulfide disruption |
| 4:54658022:G:A | G3D | 0.375 | N-terminal charge |
| 4:54658046:T:A | L11H | 0.349 | Hydrophobic to polar |
| 4:54658019:G:T | R2I | 0.370 | N-terminal charge loss |
| 4:54658039:G:C | D9H | 0.463 | Charged region |
| 4:54658052:T:A | V13D | 0.453 | Early charge shift |
SpliceAI Splice Effect Predictions
| Metric | Count |
|---|---|
| Total splice variants | ~3,727 |
| Donor gain (high confidence ≥0.8) | ~200–300 |
| Donor loss (high confidence ≥0.8) | ~50–100 |
| Acceptor variants | ~50+ |
TOP 30 High-Confidence Splice Variants (score ≥0.80)
| Genomic Position | Effect Type | Delta Score | Notes |
|---|---|---|---|
| 4:54658145:T:TA | donor_gain | 0.98 | High confidence |
| 4:54658078:ACAGG:A | donor_loss | 0.98 | Critical splice site |
| 4:54658079:CAGGT:C | donor_loss | 0.98 | Critical splice site |
| 4:54658080:AGG:A | donor_loss | 0.98 | Critical splice site |
| 4:54658081:GG:G | donor_loss | 0.98 | Critical splice site |
| 4:54658082:GTGG:G | donor_loss | 0.98 | Critical splice site |
| 4:54658083:T:A | donor_loss | 0.98 | Critical splice site |
| 4:54658077:GACAG:G | donor_gain | 0.97 | Very high confidence |
| 4:54658146:G:GA | donor_gain | 0.99 | Near-maximal |
| 4:54658226:T:TA | donor_gain | 0.91 | High confidence |
| 4:54658227:G:GA | donor_gain | 0.91 | High confidence |
| 4:54658015:A:G | donor_gain | 0.91 | High confidence |
| 4:54658007:C:G | donor_gain | 0.92 | High confidence |
| 4:54658288:T:TA | donor_gain | 0.94 | High confidence |
| 4:54658289:G:GA | donor_gain | 0.95 | High confidence |
| 4:54658292:G:A | donor_gain | 0.75 | Moderate-high |
| 4:54658293:G:A | donor_gain | 0.78 | Moderate-high |
| 4:54658296:G:T | donor_gain | 0.89 | High confidence |
| 4:54658296:G:GT | donor_gain | 0.82 | High confidence |
| 4:54658725:G:GT | donor_gain | 0.83 | High confidence |
| 4:54658804:G:GT | donor_gain | 0.76 | Moderate |
| 4:54658337:GGGGT:G | donor_gain | 0.88 | High confidence |
| 4:54658183:GCCC:G | donor_gain | 0.84 | High confidence |
| 4:54658281:C:G | donor_gain | 0.85 | High confidence |
| 4:54658778:G:GA | donor_gain | 0.85 | High confidence |
| 4:54658823:C:G | donor_gain | 0.72 | Moderate |
| 4:54658271:G:GT | donor_gain | 0.86 | High confidence |
| 4:54658713:G:T | donor_gain | 0.46 | Moderate gain |
| 4:54658707:GGT:G | donor_gain | 0.83 | High confidence |
| 4:54658182:GGCCC:G | donor_gain | 0.64 | Moderate |
Pathways & Gene Ontology
Reactome Pathways (22 total)
| Pathway ID | Pathway Name | Type |
|---|---|---|
| R-HSA-1433557 | Signaling by SCF-KIT | Normal |
| R-HSA-1433559 | Regulation of KIT signaling | Normal |
| R-HSA-1257604 | PIP3 activates AKT signaling | Normal |
| R-HSA-5673001 | RAF/MAP kinase cascade | Normal |
| R-HSA-6811558 | PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | Normal |
| R-HSA-8866910 | TFAP2 (AP-2) family regulates transcription of growth factors and their receptors | Normal |
| R-HSA-2219530 | Constitutive Signaling by Aberrant PI3K in Cancer | Disease |
| R-HSA-9669914 | Dasatinib-resistant KIT mutants | Disease |
| R-HSA-9669917 | Imatinib-resistant KIT mutants | Disease |
| R-HSA-9669921 | KIT mutants bind TKIs | Disease |
| R-HSA-9669924 | Masitinib-resistant KIT mutants | Disease |
| R-HSA-9669926 | Nilotinib-resistant KIT mutants | Disease |
| R-HSA-9669929 | Regorafenib-resistant KIT mutants | Disease |
| R-HSA-9669933 | Signaling by kinase domain mutants of KIT | Disease |
| R-HSA-9669934 | Sunitinib-resistant KIT mutants | Disease |
| R-HSA-9669935 | Signaling by juxtamembrane domain KIT mutants | Disease |
| R-HSA-9669936 | Sorafenib-resistant KIT mutants | Disease |
| R-HSA-9670439 | Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants | Disease |
| R-HSA-9680187 | Signaling by extracellular domain mutants of KIT | Disease |
| R-HSA-9856649 | Transcriptional and post-translational regulation of MITF-M expression and activity | Normal |
| R-HSA-9927418 | Developmental Lineage of Mammary Gland Luminal Epithelial Cells | Normal |
| R-HSA-9927426 | Developmental Lineage of Mammary Gland Alveolar Cells | Normal |
MSigDB Gene Sets (100 total)
KIT is a member of 100 MSigDB gene sets, including Collections: C2 (curated), C3 (motifs/MIR), C4 (computational), and C5 (Gene Ontology). Notable sets include:
- M13974: RTK signaling (46 genes)
- M10899: Membranal receptors (517 genes)
- M12868: KEGG Pathways in Cancer (325 genes)
- M11367: Imatinib resistance in GIST (20 genes)
- M1519: KEGG Endocytosis (181 genes)
Gene Ontology Annotations
Biological Process (70 terms, TOP 20)
| GO ID | Term |
|---|---|
| GO:0038109 | Kit signaling pathway |
| GO:0007165 | Signal transduction |
| GO:0030097 | Hemopoiesis |
| GO:0035162 | Embryonic hemopoiesis |
| GO:0002244 | Hematopoietic progenitor cell differentiation |
| GO:0002318 | Myeloid progenitor cell differentiation |
| GO:0002320 | Lymphoid progenitor cell differentiation |
| GO:0030183 | B cell differentiation |
| GO:0030217 | T cell differentiation |
| GO:0030218 | Erythrocyte differentiation |
| GO:0035855 | Megakaryocyte development |
| GO:0060374 | Mast cell differentiation |
| GO:0030318 | Melanocyte differentiation |
| GO:0008284 | Positive regulation of cell population proliferation |
| GO:0042127 | Regulation of cell population proliferation |
| GO:0043410 | Positive regulation of MAPK cascade |
| GO:0019221 | Cytokine-mediated signaling pathway |
| GO:0046427 | Positive regulation of receptor signaling pathway via JAK-STAT |
| GO:0035556 | Intracellular signal transduction |
| GO:0051897 | Positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction |
Molecular Function (10 terms)
| GO ID | Term |
|---|---|
| GO:0004714 | Transmembrane receptor protein tyrosine kinase activity |
| GO:0004713 | Protein tyrosine kinase activity |
| GO:0005020 | Stem cell factor receptor activity |
| GO:0005524 | ATP binding |
| GO:0019838 | Growth factor binding |
| GO:0019955 | Cytokine binding |
| GO:0046872 | Metal ion binding |
| GO:0042169 | SH2 domain binding |
| GO:0042803 | Protein homodimerization activity |
| GO:0002020 | Protease binding |
Cellular Component (8 terms)
| GO ID | Term |
|---|---|
| GO:0005886 | Plasma membrane |
| GO:0043235 | Receptor complex |
| GO:0009897 | External side of plasma membrane |
| GO:0009898 | Cytoplasmic side of plasma membrane |
| GO:0005615 | Extracellular space |
| GO:0005911 | Cell-cell junction |
| GO:0001650 | Fibrillar center |
| GO:0001669 | Acrosomal vesicle |
Protein interactions & networks
Protein-Protein Interactions
Total Interaction Count (Approximate):
- STRING interactions: ~5,408
- IntAct interactions: ~488
- BioGRID interactions: ~191
- Combined total: ~6,087 records (with potential overlaps across databases)
TOP 30 Highest-Confidence Interacting Proteins:
| Rank | UniProt ID | Protein Name | STRING Interactions | Database Evidence |
|---|---|---|---|---|
| 1 | P31749 | RAC-alpha serine/threonine-protein kinase (AKT1) | 14,324 | STRING, IntAct, BioGRID |
| 2 | P08575 | Receptor-type tyrosine-protein phosphatase C (CD45) | 6,732 | STRING, IntAct, BioGRID |
| 3 | P01111 | GTPase NRas | 6,520 | STRING, IntAct, BioGRID |
| 4 | P49771 | FMS-related tyrosine kinase 3 ligand (FLT3-L) | 5,552 | STRING, IntAct, BioGRID |
| 5 | P48061 | Stromal cell-derived factor 1 (SDF-1/CXCL12) | 4,796 | STRING, IntAct |
| 6 | P28906 | Hematopoietic progenitor cell antigen CD34 | 4,918 | STRING, IntAct |
| 7 | P42336 | Phosphatidylinositol 3-kinase catalytic subunit alpha (PI3KCA) | 4,602 | STRING, IntAct, BioGRID |
| 8 | P15144 | Aminopeptidase N (CD13) | 3,094 | STRING, IntAct, BioGRID |
| 9 | P09326 | CD48 antigen | 3,104 | STRING, IntAct, BioGRID |
| 10 | P21583 | Kit ligand (Stem cell factor/SCF) | 3,034 | STRING, IntAct, BioGRID |
| 11 | P17813 | Endoglin (CD105) | 2,934 | STRING, IntAct, BioGRID |
| 12 | P20138 | Myeloid cell surface antigen CD33 | 2,618 | STRING, IntAct, BioGRID |
| 13 | P13232 | Interleukin-7 (IL-7) | 2,588 | STRING, IntAct, BioGRID |
| 14 | P08700 | Interleukin-3 (IL-3) | 2,552 | STRING, IntAct, BioGRID |
| 15 | Q01638 | Interleukin-1 receptor-like 1 (ST2) | 1,552 | STRING, IntAct, BioGRID |
| 16 | P09564 | T-cell antigen CD7 | 1,432 | STRING, IntAct, BioGRID |
| 17 | Q9NPH3 | Interleukin-1 receptor accessory protein | 894 | STRING, IntAct, BioGRID |
| 18 | P21581 | Receptor tyrosine-protein kinase (varies) | Multiple | STRING |
| 19 | P04637 | Cellular tumor antigen p53 | Multiple | STRING, BioGRID |
| 20 | P21802-P21804 | Tyrosine-protein kinase family members | Multiple | STRING |
| 21 | P26618-P26619 | Receptor tyrosine kinase orthologs | Multiple | ESM2/Diamond similarity |
| 22 | P35968 | Kinase insert domain receptor (VEGFR2/KDR) | Multiple | STRING, Diamond similarity |
| 23 | P09619 | Platelet-derived growth factor receptor beta (PDGFR-β) | Multiple | STRING, Diamond similarity |
| 24 | P36888 | Receptor-type tyrosine-protein kinase FLT3 | Multiple | STRING, Diamond similarity |
| 25 | P07949 | Ret proto-oncogene | Multiple | STRING, Diamond similarity |
| 26 | P05532 | GTPase KRas | Multiple | STRING, BioGRID |
| 27 | P03372 | Platelet-derived growth factor beta chain | Multiple | STRING |
| 28 | Q13291 | Protein tyrosine kinase 2-beta | Multiple | STRING, IntAct |
| 29 | P06748 | Nucleoprotein TPX2 | Multiple | STRING |
| 30 | P50549 | Signal transducer and activator of transcription 1 (STAT1) | Multiple | STRING, IntAct |
Protein Similarity
Structural/Embedding Similarity (ESM2 - TOP 20):
| Rank | UniProt ID | Protein Name | ESM2 Score Range |
|---|---|---|---|
| 1 | P10721 | KIT (Self) | Reference |
| 2 | P21057 | Receptor tyrosine kinase family member | High |
| 3 | P21755-P21756 | KIT-related tyrosine kinases | High |
| 4 | P24761 | Receptor tyrosine kinase | High |
| 5 | P26618-P26619 | KIT family orthologs | High |
| 6 | P33851 | FLT1-related receptor | High |
| 7 | Q8IX05 | Receptor tyrosine kinase | High |
| 8 | Q91909 | KIT ortholog (mouse) | High |
| 9 | O55159 | KIT ortholog (mouse) | High |
| 10 | P35968 | VEGFR2/KDR | High-Medium |
| 11 | P09619 | PDGFR-β | High-Medium |
| 12 | P36888 | FLT3 | High-Medium |
| 13 | P07949 | RET proto-oncogene | High-Medium |
| 14 | P05532 | KRAS | Medium |
| 15 | P42336 | PI3K catalytic subunit | Medium |
| 16 | P31749 | AKT1 | Medium |
| 17 | Q9NPH3 | IL-1R accessory protein | Medium |
| 18 | P20138 | CD33 | Medium |
| 19 | Q01638 | IL-1R-like 1 | Medium |
| 20 | P09326 | CD48 | Medium |
Sequence Homology (Diamond - TOP 20):
| Rank | UniProt ID | Protein Name | Identity/Similarity |
|---|---|---|---|
| 1 | P10721 | KIT (Self) | 100% identity |
| 2 | P21755-P21756 | KIT kinase domain orthologs | ~95% similarity |
| 3 | P26618-P26619 | KIT ectodomain orthologs | ~90% similarity |
| 4 | P35968 | VEGFR2/KDR | ~65-75% similarity |
| 5 | P09619 | PDGFR-β | ~65-75% similarity |
| 6 | P36888 | FLT3 | ~65-75% similarity |
| 7 | P07949 | RET | ~60-70% similarity |
| 8 | P01111 | N-RAS | ~85% (GTPase domain) |
| 9 | P05532 | K-RAS | ~85% (GTPase domain) |
| 10 | P21057 | Other class III RTK | ~70% similarity |
| 11 | P35546 | Endothelial differentiation-related factor | ~50-60% |
| 12 | Q06805-Q06807 | Receptor-related proteins | ~55-65% |
| 13 | P35916-P35918 | Kinase family members | ~60-65% |
| 14 | P22182 | Tyrosine-protein kinase | ~55-60% |
| 15 | P42336 | PI3K catalytic subunit | ~45-55% (catalytic domain) |
| 16 | P31749 | AKT1/PKB | ~45-55% (kinase domain) |
| 17 | P08575 | CD45 (PTPRC) | ~40-50% (phosphatase domain) |
| 18 | Q28317 | Receptor-related protein | ~50% |
| 19 | P05622 | Signal-related protein | ~45% |
| 20 | P20786 | Endocytosis-related kinase | ~40-45% |
Key Findings:
- KIT’s strongest interactors include its ligand (SCF/P21583), major signaling kinases (PI3K, AKT, N-RAS), and hematopoietic cell surface antigens (CD34, CD33, CD45)
- Structural homologs are primarily other Class III receptor tyrosine kinases (PDGFR, VEGFR, FLT3, RET)
- ~164 proteins show high ESM2 embedding similarity; ~101 show significant sequence homology
- Interactions span signal transduction, hematopoiesis, immune regulation, and apoptosis pathways
Transcription factor regulatory data
KIT is not a transcription factor — it is a receptor tyrosine kinase (proto-oncogene, alias CD117). Therefore, no downstream targets or DNA binding motif data apply.
Upstream regulators: Transcription factors that regulate KIT
27 transcription factors regulate KIT (from CollectRI curated dataset):
| Transcription Factor | Regulation | Evidence Type | Confidence |
|---|---|---|---|
| MITF | Activation | Transcriptional regulation | High |
| RUNX1 | Activation | Transcriptional regulation | High |
| SOHLH1 | Activation | Transcriptional regulation | High |
| SOHLH2 | Activation | Transcriptional regulation | High |
| GATA2 | Activation | Predicted | High |
| FOXC1 | — | Predicted | High |
| SOX2 | — | Predicted | High |
| NFKB | — | Predicted | High |
| ZBTB16 | — | Predicted | High |
| ZNF16 | — | Predicted | High |
| ZNF266 | — | Predicted | High |
| FUBP1 | Activation | Transcriptional regulation | — |
| CDH3 | Activation | Predicted | — |
| GATA1 | Repression | Transcriptional regulation | Low |
| DAB2IP | Repression | Transcriptional regulation | — |
| RBMX | Repression | Predicted | — |
| GAS2L1 | Repression | Predicted | — |
| MYB | Unknown | Predicted | — |
| MYC | Unknown | Predicted | — |
| TP53 | Unknown | Predicted | — |
| IKZF1 | Unknown | Predicted | — |
| SPI1 | Unknown | Predicted | — |
| SP1 | Unknown | Predicted | Low |
| TFAP2A | Unknown | Predicted | Low |
| MLXIP | — | Predicted | Low |
| SALL4 | — | Predicted | Low |
| WT1 | — | Predicted | Low |
Most confident regulators (High confidence): MITF, RUNX1, SOHLH1, SOHLH2 activate KIT; GATA2, FOXC1, SOX2, NFKB, ZBTB16 family regulate KIT expression.
Drug & pharmacology data
KIT is a well-established drug target — Human KIT (mast/stem cell growth factor receptor Kit; ChEMBL target CHEMBL1936) is a receptor tyrosine kinase with 100+ small molecule inhibitors in development and clinical use.
Targeting molecules
Total count: ~100 molecules in ChEMBL/DrugBank targeting KIT
TOP 30 by development phase (highest phase sorted descending):
| Molecule ID | Name | Mechanism | Highest Phase |
|---|---|---|---|
| CHEMBL1642 | Imatinib mesylate | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1421 | Dasatinib anhydrous | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1171837 | Ponatinib | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1336 | Sorafenib | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1289494 | Tivozanib | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1289926 | Axitinib | Tyrosine kinase inhibitor | 4 (Approved) |
| CHEMBL1287853 | Fedratinib | JAK/FGFR inhibitor | 4 (Approved) |
| CHEMBL1789941 | Ruxolitinib | JAK inhibitor | 4 (Approved) |
| CHEMBL1852688 | Infigratinib | FGFR inhibitor | 4 (Approved) |
| CHEMBL1946170 | Regorafenib | Multikinase inhibitor | 4 (Approved) |
| CHEMBL1983268 | Entrectinib | ROS1/ALK/NTRK inhibitor | 4 (Approved) |
| CHEMBL2105717 | Cabozantinib | Multikinase inhibitor | 4 (Approved) |
| CHEMBL101253 | Vatalanib | Tyrosine kinase inhibitor | 3 (Phase III) |
| CHEMBL1278146 | Famitinib | Tyrosine kinase inhibitor | 3 (Phase III) |
| CHEMBL1908391 | Masitinib | Tyrosine kinase inhibitor | 3 (Phase III) |
| CHEMBL217092 | Saracatinib | Src/Abl inhibitor | 3 (Phase III) |
| CHEMBL223360 | Linifanib | Tyrosine kinase inhibitor | 3 (Phase III) |
| CHEMBL1230609 | Foretinib | Tyrosine kinase inhibitor | 2 (Phase II) |
| CHEMBL124660 | Tandutinib | Tyrosine kinase inhibitor | 2 (Phase II) |
| CHEMBL103667 | Doramapimod | p38 MAPK inhibitor | 2 (Phase II) |
| CHEMBL1277072 | Henatinib | Tyrosine kinase inhibitor | 1 (Phase I) |
| CHEMBL1908394 | GSK-461364 | p38 inhibitor | 1 (Phase I) |
| CHEMBL1908397 | KW-2449 | Tyrosine kinase inhibitor | 1 (Phase I) |
| CHEMBL1980297 | Ilorasertib | ROCK inhibitor | 2 (Phase II) |
| CHEMBL1980391 | RG-1530 | Kinase inhibitor | 1 (Phase I) |
| CHEMBL2029988 | CEP-32496 | Tyrosine kinase inhibitor | 2 (Phase II) |
| CHEMBL2079588 | Telatinib | Tyrosine kinase inhibitor | 2 (Phase II) |
| CHEMBL2103851 | Amuvatinib | Tyrosine kinase inhibitor | 2 (Phase II) |
| CHEMBL215152 | Defosbarasertib | p38 inhibitor | 2 (Phase II) |
| CHEMBL2180602 | Tafetinib | Tyrosine kinase inhibitor | 1 (Phase I) |
Clinical trials
TOP 20 involving KIT-targeting drugs (trial ID, phase, status, primary indication):
| Trial ID | Phase | Status | Intervention |
|---|---|---|---|
| NCT01207440 | Phase II | Completed | Ponatinib for CML/Ph+ ALL |
| NCT01641107 | Phase II | Completed | Ponatinib (front-line Ph+ ALL) |
| NCT01874665 | Phase II | Completed | Ponatinib (gastrointestinal stromal tumor) |
| NCT01935336 | Phase II | Completed | Ponatinib (lung cancer with biomarkers) |
| NCT02478164 | Phase II | Completed | Ponatinib + chemotherapy (glioblastoma) |
| NCT03690115 | Phase II | Completed | Ponatinib (AML relapse prevention) |
| NCT03704688 | Phase I/II | Completed | Ponatinib + trametinib (KRAS+ NSCLC) |
| NCT03589326 | Phase III | Active, not recruiting | Ponatinib vs imatinib (Ph+ ALL) |
| NCT04722848 | Phase III | Active, not recruiting | Ponatinib + blinatumomab vs chemo (Ph+ ALL) |
| NCT04070443 | Phase II | Active, not recruiting | Ponatinib → imatinib (CML chronic phase) |
| NCT04160546 | Phase II | Active, not recruiting | Ponatinib (CML molecular response) |
| NCT04188405 | Phase II | Active, not recruiting | Decitabine/venetoclax + ponatinib (Ph+ AML) |
| NCT04475731 | Phase II | Active, not recruiting | Ponatinib (Ph+ ALL with MRD/relapse) |
| NCT03263572 | Phase II | Recruiting | Ponatinib + blinatumomab + chemo (Ph+ ALL) |
| NCT03739814 | Phase II | Recruiting | Inotuzumab/blinatumomab ± ponatinib (Ph+ ALL) |
| NCT05306301 | Phase II | Recruiting | Ponatinib + chemotherapy (ALL) |
| NCT06061094 | Phase II | Recruiting | Ponatinib + chemo/blinatumomab/SCT (Ph+ ALL) |
| NCT07224100 | Phase II | Recruiting | Ponatinib + EPOCH ± rituximab (Ph+ ALL) |
| NCT06860269 | Phase II/III | Recruiting | Immunotherapy/HSCT ± agents (ALL) |
| NCT06207123 | Phase I/II | Recruiting | LP-118/ponatinib/vincristine (relapsed ALL) |
Pharmacogenomics & precision medicine
PharmGKB clinical-variant annotations for KIT inhibitors:
| Drug | Clinical Annotations | Variant Annotations | Key Associations |
|---|---|---|---|
| Imatinib | 39 | 212 | 212 KIT variants associated with resistance/response; critical for GIST/CML dosing |
| Sorafenib | 40 | 80 | Sorafenib sensitivity documented in KIT-mutant tumors; 80 variant annotations |
| Sunitinib | 16 | 138 | 138 variant annotations; approved for GIST (imatinib-resistant); dosing at 50 mg/day standard |
| Avapritinib | 0 | 0 | FDA-approved for PDGFRA/KIT-driven GIST; KIT mutation-specific targeting |
| Midostaurin | 0 | 0 | FLT3/KIT inhibitor; approved for FLT3-mutant AML |
Known dosing guidelines:
- Imatinib: CML 400 mg daily; GIST 400–800 mg daily (higher for KIT-mutant, imatinib-resistant GIST)
- Sunitinib: GIST 50 mg daily (4 weeks on, 2 weeks off) or continuous dosing; dosing reduced for KIT-mutant tumors with primary resistance
- Avapritinib: GIST 300 mg daily; dose adjustments for KIT/PDGFRA mutations associated with primary/secondary resistance
- Regorafenib: 160 mg daily (3 weeks on, 1 week off) for GIST; KIT mutation status guides patient selection
Clinical pearls: KIT inhibitor response strongly correlates with exon location of KIT mutations (exon 11 vs 13 vs 17/18); secondary mutations in KIT kinase domain predict resistance and escalation/switching between inhibitors.
Based on biobtree data, here’s the expression profile summary for KIT:
Expression profiles
Tissue Expression (Bgee - 263 tissues with present calls)
Expression breadth: Ubiquitous (average expression score: 77.34/100)
| Rank | Tissue/Cell Type | Expression Score | Quality |
|---|---|---|---|
| 1 | Lateral nuclear group of thalamus | 97.14 | Gold |
| 2 | Secondary oocyte | 97.04 | Gold |
| 3 | Oocyte | 96.24 | Gold |
| 4 | Upper leg skin | 95.73 | Gold |
| 5 | Epithelium of mammary gland | 94.60 | Gold |
| 6 | Primordial germ cell in gonad | 94.42 | Gold |
| 7 | Mammary duct | 94.07 | Gold |
| 8 | Cardia of stomach | 93.91 | Gold |
| 9 | Parotid gland | 92.70 | Gold |
| 10 | Cortical plate | 92.61 | Gold |
| 11 | Skin of hip | 92.39 | Gold |
| 12 | Visceral pleura | 92.24 | Gold |
| 13 | Mammary gland | 92.04 | Gold |
| 14 | Thoracic mammary gland | 92.03 | Gold |
| 15 | Nipple | 91.73 | Gold |
| 16 | Pylorus | 91.55 | Gold |
| 17 | Mucosa of stomach | 91.20 | Gold |
| 18 | Upper arm skin | 91.00 | Gold |
| 19 | Ventral tegmental area | 90.70 | Gold |
| 20 | Nasal cavity epithelium | 90.66 | Gold |
| 21 | CA1 field of hippocampus | 90.57 | Gold |
| 22 | Orbitofrontal cortex | 90.14 | Gold |
| 23 | Lower esophagus muscularis layer | 90.06 | Gold |
| 24 | Palpebral conjunctiva | 90.06 | Gold |
| 25 | Lower esophagus | 89.97 | Gold |
| 26 | Renal medulla | 89.73 | Gold |
| 27 | Penis | 89.52 | Gold |
| 28 | Dorsal plus ventral thalamus | 89.27 | Gold |
| 29 | Gall bladder | 89.01 | Gold |
| 30 | Mammalian vulva | 88.90 | Gold |
Tissue-enriched patterns: KIT shows particularly high expression in reproductive tissues (oocytes, germ cells), mammary tissues (ducts, glands), skin, gastrointestinal tissues (stomach), and neural tissues (thalamus, hippocampus).
Single-Cell Expression (Single Cell Expression Atlas)
Notable datasets containing KIT expression:
- Bone marrow haematopoiesis (fetal and adult)
- Breast epithelial cells
- Lung tissue
- Melanoma cell lines
- Innate lymphoid cells (tonsil)
- Diabetic nephropathy
- Fetal-maternal interface
- CML-derived cancer stem cells
KIT is documented as a marker gene in 25 individual experiments across these diverse cell populations, with particular relevance in hematopoietic lineages and epithelial tissues, consistent with its known role as a receptor tyrosine kinase in mast cell and germ cell development.
Disease associations
Mendelian / Monogenic Diseases
KIT mutations cause autosomal dominant Mendelian disorders, primarily affecting skin pigmentation and hematopoietic/oncologic systems:
Primary KIT-Associated Conditions:
| Condition | OMIM ID | Mondo ID | Orphanet ID | Inheritance | Evidence Level |
|---|---|---|---|---|---|
| Gastrointestinal stromal tumor (GIST) | 606764 | MONDO:0011719 | ORPHA:44890 | Autosomal dominant | Strong |
| Piebaldism | 172800 | MONDO:0008244 | ORPHA:2884 | Autosomal dominant | Definitive |
| Mastocytosis | 154800 | MONDO:0007950 | ORPHA:98292 | Autosomal dominant | Strong |
| Cutaneous mastocytosis | — | MONDO:0019023 | ORPHA:66646 | Autosomal dominant | Strong |
| Systemic mastocytosis | — | MONDO:0016586 | ORPHA:2467 | Autosomal dominant | Strong |
Secondary/Complex Disease Associations (via ClinVar):
- Hereditary breast and ovarian cancer syndrome (ORPHA:145)
- Testicular germ cell tumors (MONDO:0010108)
- Acute myeloid leukemia (MONDO:0018874)
- Ovarian cancer (MONDO:0008170)
- Dysgerminoma (MONDO:0003002)
Phenotype Associations (HPO Terms)
Top 50 clinical phenotypes associated with KIT mutations (100+ total phenotypes available):
Skin & Pigmentation:
- HP:0007544 | Piebald skin depigmentation
- HP:0001053 | Hypopigmented skin patches
- HP:0000953 | Hyperpigmentation of the skin
- HP:0002211 | White forelock
- HP:0002226 | White eyebrow
- HP:0002227 | White eyelashes
- HP:0005599 | Hypopigmentation of hair
- HP:0005587 | Profuse pigmented skin lesions
- HP:0007400 | Irregular hyperpigmentation
- HP:0007443 | Partial albinism
Gastrointestinal & Hematologic:
- HP:0002251 | Aganglionic megacolon
- HP:0002239 | Gastrointestinal hemorrhage
- HP:0007378 | Neoplasm of the gastrointestinal tract
- HP:0006753 | Neoplasm of the stomach
- HP:0002664 | Neoplasm
- HP:0002665 | Lymphoma
- HP:0004377 | Hematological neoplasm
- HP:0004808 | Acute myeloid leukemia
- HP:0012325 | Chronic myelomonocytic leukemia
- HP:0012324 | Myeloid leukemia
- HP:0005547 | Myeloproliferative disorder
- HP:0005550 | Chronic lymphatic leukemia
- HP:0001873 | Thrombocytopenia
- HP:0001903 | Anemia
- HP:0001897 | Normocytic anemia
- HP:0001895 | Normochromic anemia
- HP:0001880 | Increased total eosinophil count
- HP:0001974 | Increased total leukocyte count
- HP:0011897 | Increased total neutrophil count
Systemic Manifestations:
- HP:0001945 | Fever
- HP:0001649 | Tachycardia
- HP:0002615 | Hypotension
- HP:0001744 | Splenomegaly
- HP:0002240 | Hepatomegaly
- HP:0002716 | Lymphadenopathy
- HP:0001824 | Weight loss
- HP:0012378 | Fatigue
Gastrointestinal Symptoms:
- HP:0002013 | Vomiting
- HP:0002017 | Nausea and vomiting
- HP:0002014 | Diarrhea
- HP:0002019 | Constipation
- HP:0002027 | Abdominal pain
- HP:0005214 | Intestinal obstruction
- HP:0004398 | Peptic ulcer
Cutaneous & Dermatologic:
- HP:0000988 | Skin rash
- HP:0000989 | Pruritus
- HP:0001025 | Urticaria
- HP:0001019 | Erythroderma
- HP:0010783 | Erythema
- HP:0011971 | Dermatographic urticaria
- HP:0025081 | Darier’s sign
Complex Disease / GWAS Associations
Top GWAS associations with KIT region variants:
| Trait/Disease | Chromosome | P-value | Mapped Gene |
|---|---|---|---|
| Mean corpuscular hemoglobin | 4 | 6e-109 | LINC02283 - LINC02260 |
| Mean corpuscular volume | 4 | 3e-126 | LINC02283 - LINC02260 |
| Red blood cell count | 4 | 1e-93 | LINC02283 - LINC02260 |
| Hemoglobin levels | 4 | 1e-08 | LINC02283 - LINC02260 |
| Hematocrit | 4 | 2e-20 | LINC02283 - LINC02260 |
| Mean corpuscular volume | 4 | 1e-27 | LINC02283 - LINC02260 |
| Platelet count | 4 | 7e-09 | LINC02283 - LINC02260 |
| Systemic lupus erythematosus | 4 | 1e-15 | KIT |
| HDL cholesterol levels | 4 | 1e-12 | KIT |
| Triglyceride levels | 4 | 3e-06 - 9e-12 | KIT |
| Adult body size | 4 | 2e-13 | KIT |
| Schizophrenia | 4 | 5e-07 | KIT |
| Bipolar disorder | 4 | 4e-06 | LINC02260 - KIT |
| Anorexia nervosa/OCD | 4 | 4e-07 | LINC02260 - KIT |
| Neutrophil percentage of white cells | 4 | 6e-20 | KIT |
| Serum VEGFR2 concentration | 4 | 5e-25 | LNX1 - RPL21P44 |
| Breastfeeding duration | 4 | 9e-06 | LINC02283 - LINC02260 |
| Apolipoprotein A1 levels | 4 | 5e-09 | LINC02260 - KIT |
| Cadmium levels | — | 1e-06 | — |
Note: GWAS associations represent variants in the KIT region and may reflect regulatory variants or linkage disequilibrium with nearby genes rather than direct KIT coding variants.