KIT (P10721) variants and mutations
KIT (also known as P10721) is a human protein-coding gene encoding a mast/stem cell growth factor receptor protein. Stem-cell-factor signaling through this pathway supports hematopoietic progenitors, mast cells, melanocytes, and germ cells. Activating variants drive gastrointestinal stromal tumors, systemic mastocytosis, and other malignancies, whereas loss-of-function variants can cause piebaldism. This analysis covers 3,520 KIT variants and mutations. Of these, 45% have computational variant effect predictions. Disease context includes gastrointestinal stromal tumor, piebaldism, and cutaneous mastocytosis. Example KIT variants include R2*, R2G, and R2I.
Variant analysis overview
- Gene: KIT
- Protein: P10721
- UniProt accession: P10721
- Organism: Homo sapiens
- Variants analyzed: 3520
- Variant scope: all variants
- Completed: 2026-08-10
Variant and mutation evidence
- Variant composition: 3,362 unspecified-consequence records; 118 synonymous variants; 25 missense variants; 3 splice-region variants; 5 frameshift variants; 6 substitution
- Prediction scores: 1,568 variants have prediction scores (45% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: gastrointestinal stromal tumor, piebaldism, cutaneous mastocytosis, acute myeloid leukemia, chronic myelogenous leukemia, BCR-ABL1 positive, hepatocellular carcinoma, mastocytosis, cancer, systemic mastocytosis, neoplasm, acute lymphoblastic leukemia, renal cell carcinoma.
Protein structure and variant hotspots
- Protein features: 1 transmembrane segments; 6 domains; 7 binding sites; 25 post-translational modification sites.
- Structural context: 2,896 variants have structural context.
- PTM context: 96 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable KIT variants
Examples include R2*, R2G, R2I, R2K, R2S, G3C, G3D, G3R. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- R2* (p.Arg2Ter), Ensembl rs2109520633
- R2G (p.Arg2Gly), Ensembl rs2109520633
- R2I (p.Arg2Ile), Ensembl rs2109520651
- R2K (p.Arg2Lys), Ensembl rs2109520651
- R2S (p.Arg2Ser), Ensembl rs2109520669
- G3C (p.Gly3Cys), Ensembl rs1577898451, Uncertain significance
- G3D (p.Gly3Asp), rs1560366535, ClinGen CA356897838, ClinVar RCV000700352, Ensembl rs1560366535, AlphaMissense 0.41, MetaLR 0.21, Uncertain significance, Gastrointestinal stromal tumor
- G3R (p.Gly3Arg), rs1577898451, ClinGen CA356897834, ClinVar RCV000812772, ClinVar RCV001027043, REVEL 0.21, MetaLR 0.22, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- G3S (p.Gly3Ser), Ensembl rs1577898451, Uncertain significance, Gastrointestinal stromal tumor
- G3G (p.Gly3Gly), rs755780019, gnomAD 4-54658023-C-T, CADD 17.70
- A4F (p.Ala4Phe), rs1553881759, ClinGen CA658796437, ClinVar RCV000633790, ClinVar RCV005348163, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- A4P (p.Ala4Pro), rs1192807264, ClinGen CA356897846, ClinVar RCV000633721, TOPMed rs1192807264, AlphaMissense 0.37, MetaLR 0.37, Uncertain significance, Gastrointestinal stromal tumor
- A4S (p.Ala4Ser), rs1192807264, ClinGen CA356897847, ClinVar RCV002431012, ClinVar RCV003101889, REVEL 0.17, AlphaMissense 0.37, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- A4T (p.Ala4Thr), rs1192807264, ClinGen CA356897845, ClinVar RCV003039532, ClinVar RCV005648251, REVEL 0.40, AlphaMissense 0.37, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- A4V (p.Ala4Val), rs1423062466, ClinGen CA356897853, ClinVar RCV001209803, ClinVar RCV002348685, REVEL 0.41, MetaLR 0.25, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Gastrointestinal stromal
- A4G (p.Ala4Gly), gnomAD 4-54658025-C-G, REVEL 0.29, CADD 24.10
- R5C (p.Arg5Cys), rs1716939221, ClinGen CA356897858, ClinVar RCV003469889, Ensembl rs1716939221, AlphaMissense 0.68, MetaLR 0.23, Uncertain significance, Gastrointestinal stromal tumor
- R5G (p.Arg5Gly), rs1716939221, ClinGen CA356897856, ClinVar RCV001305274, ClinVar RCV005367820, AlphaMissense 0.68, MetaLR 0.23, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- R5H (p.Arg5His), Ensembl rs1716939382, REVEL 0.33, MetaLR 0.40, Uncertain significance
- R5L (p.Arg5Leu), Ensembl rs1716939382, Uncertain significance
- R5P (p.Arg5Pro), rs1716939382, ClinGen CA356897861, ClinVar RCV001223517, Ensembl rs1716939382, REVEL 0.43, MetaLR 0.41, Uncertain significance, Gastrointestinal stromal tumor
- R5S (p.Arg5Ser), Ensembl rs1716939221, Uncertain significance
- R5R (p.Arg5Arg), rs1357038342, gnomAD 4-54658029-C-G, CADD 14.80
- G6A (p.Gly6Ala), Ensembl rs1716939970, Uncertain significance
- G6C (p.Gly6Cys), TOPMed rs1716939806, Uncertain significance
- G6D (p.Gly6Asp), rs1716939970, ClinGen CA356897871, ClinVar RCV001067043, NCI-TCGA TCGA novel, AlphaMissense 0.16, MetaLR 0.19, Uncertain significance, Gastrointestinal stromal tumor
- G6R (p.Gly6Arg), TOPMed rs1716939806, Uncertain significance
- G6S (p.Gly6Ser), rs1716939806, ClinGen CA356897866, ClinVar RCV003638309, TOPMed rs1716939806, AlphaMissense 0.37, MetaLR 0.32, Uncertain significance, Gastrointestinal stromal tumor
- G6V (p.Gly6Val), gnomAD 4-54658031-G-T, REVEL 0.38, CADD 23.10
- A7G (p.Ala7Gly), rs2109520869, ClinGen CA356897882, ClinVar RCV002424189, AlphaMissense 0.44, MetaLR 0.25, Uncertain significance, Hereditary cancer-predisposing syndrome
- A7S (p.Ala7Ser), rs1285711357, ClinGen CA356897877, ClinVar RCV002045431, ClinVar RCV005350857, REVEL 0.08, MetaLR 0.22, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- A7T (p.Ala7Thr), rs1285711357, ClinGen CA356897875, ClinVar RCV000693196, ClinVar RCV002422507, REVEL 0.24, MetaLR 0.23, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome; not pro
- A7V (p.Ala7Val), rs2109520869, ClinGen CA356897884, ClinVar RCV001872300, ClinVar RCV003228008, AlphaMissense 0.44, MetaLR 0.25, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor; not pro
- W8* (p.Trp8Ter), Ensembl rs2109520922
- W8C (p.Trp8Cys), Ensembl rs2109520935, Uncertain significance, Gastrointestinal stromal tumor
- W8G (p.Trp8Gly), rs1577898533, ClinGen CA356897889, ClinVar RCV002446317, REVEL 0.31, MetaLR 0.19, Uncertain significance, Hereditary cancer-predisposing syndrome
- W8R (p.Trp8Arg), rs1577898533, ClinGen CA356897886, ClinVar RCV001218175, Ensembl rs1577898533, REVEL 0.46, MetaLR 0.23, Uncertain significance, Gastrointestinal stromal tumor
- D9E (p.Asp9Glu), NCI-TCGA TCGA novel, Ensembl rs2109520970, Variant assessed as somatic; moderate impact.
- D9G (p.Asp9Gly), rs2109520961, ClinGen CA356897908, ClinVar RCV001963763, Ensembl rs2109520961, REVEL 0.28, MetaLR 0.30, Uncertain significance, Gastrointestinal stromal tumor
- D9H (p.Asp9His), gnomAD rs1476871700, Uncertain significance, Hereditary cancer-predisposing syndrome
- D9N (p.Asp9Asn), rs1476871700, ClinGen CA356897904, ClinVar RCV000633743, ClinVar RCV005582362, REVEL 0.29, MetaLR 0.38, Conflicting interpretations, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- D9Y (p.Asp9Tyr), gnomAD rs1476871700, Uncertain significance
- F10L (p.Phe10Leu), gnomAD rs1406974984
- F10S (p.Phe10Ser), rs1716941044, ClinGen CA356897921, ClinVar RCV001239060, ClinVar RCV005582630, AlphaMissense 0.35, MetaLR 0.25, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- F10F (p.Phe10Phe), rs1406974984, gnomAD 4-54658044-T-C, CADD 13.30
- L11F (p.Leu11Phe), rs934366239, ClinGen CA96859694, ClinVar RCV001221034, ClinVar RCV002322071, REVEL 0.32, MetaLR 0.35, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome; not pro
- L11H (p.Leu11His), Ensembl rs2109521016
- L11L (p.Leu11Leu), rs894439242, gnomAD 4-54658047-C-T, CADD 14.90
- C12* (p.Cys12Ter), Ensembl rs1716942038, Likely benign
- C12F (p.Cys12Phe), Ensembl rs1716941861, Uncertain significance
- C12R (p.Cys12Arg), rs2109521041, ClinGen CA356897936, ClinVar RCV002999912, REVEL 0.34, MetaLR 0.17, Uncertain significance, Gastrointestinal stromal tumor
- C12S (p.Cys12Ser), rs1716941861, ClinGen CA356897943, ClinVar RCV001044765, Ensembl rs1716941861, AlphaMissense 0.08, MetaLR 0.14, Uncertain significance, Gastrointestinal stromal tumor
- C12W (p.Cys12Trp), Ensembl rs1716942038, Likely benign
- C12C (p.Cys12Cys), rs1716942038, gnomAD 4-54658050-C-T, CADD 15.10
- V13D (p.Val13Asp), Ensembl rs2109521095
- V13G (p.Val13Gly), Ensembl rs2109521095
- V13I (p.Val13Ile), rs753316557, ClinGen CA2923114, ClinVar RCV001960070, ClinVar RCV005648188, REVEL 0.06, AlphaMissense 0.14, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- V13L (p.Val13Leu), rs753316557, ClinGen CA356897953, ClinVar RCV002355174, ExAC rs753316557, AlphaMissense 0.14, MetaLR 0.19, Likely benign, Hereditary cancer-predisposing syndrome
- V13V (p.Val13Val), gnomAD 4-54658053-T-G, CADD 13.90
- L14P (p.Leu14Pro), Ensembl rs2109521115
- L14Q (p.Leu14Gln), Ensembl rs2109521115
- L14V (p.Leu14Val), TOPMed rs1297912833, gnomAD rs1297912833, REVEL 0.12, MetaLR 0.23, Likely benign
- L14L (p.Leu14Leu), rs1297912833, gnomAD 4-54658054-C-T, CADD 14.70
- L15F (p.Leu15Phe), rs2109521134, ClinGen CA356897971, ClinVar RCV002299692, ClinVar RCV004948688, REVEL 0.17, MetaLR 0.21, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- L15I (p.Leu15Ile), Ensembl rs2109521134, Uncertain significance
- L15P (p.Leu15Pro), rs1230808481, ClinGen CA356897974, ClinVar RCV001907335, ClinVar RCV004039758, REVEL 0.58, MetaLR 0.23, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- L15L (p.Leu15Leu), rs755527973, gnomAD 4-54658059-C-G, CADD 8.34
- L16I (p.Leu16Ile), ExAC rs779421107, TOPMed rs779421107, gnomAD rs779421107, Likely benign
- L16P (p.Leu16Pro), rs2475323484, ClinGen CA356897983, ClinVar RCV002337873, Uncertain significance, Hereditary cancer-predisposing syndrome
- L16V (p.Leu16Val), ExAC rs779421107, TOPMed rs779421107, gnomAD rs779421107, Likely benign
- L16L (p.Leu16Leu), rs779421107, gnomAD 4-54658060-C-T, CADD 11.60
- L17P (p.Leu17Pro), rs748615975, ClinGen CA356897989, ClinVar RCV000543355, ClinVar RCV001374487, REVEL 0.54, MetaLR 0.29, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor; Heredit
- L17Q (p.Leu17Gln), ExAC rs748615975, gnomAD rs748615975, REVEL 0.37, MetaLR 0.29, Uncertain significance
- L17V (p.Leu17Val), rs2109521210, ClinGen CA356897987, ClinVar RCV001941479, Ensembl rs2109521210, AlphaMissense 0.09, MetaLR 0.25, Uncertain significance, Gastrointestinal stromal tumor
- L18F (p.Leu18Phe), rs370787811, ClinGen CA2923118, ClinVar RCV000470178, ClinVar RCV001023887, REVEL 0.12, MetaLR 0.27, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided; Gastrointestinal stromal
- L18P (p.Leu18Pro), Ensembl rs2109521273, REVEL 0.59, AlphaMissense 0.21
- L18R (p.Leu18Arg), rs2109521273, ClinGen CA356897996, ClinVar RCV003527386, AlphaMissense 0.21, MetaLR 0.38, Uncertain significance, Gastrointestinal stromal tumor
- L18V (p.Leu18Val), rs370787811, ClinGen CA2923119, ClinVar RCV000544864, ESP rs370787811, REVEL 0.08, MetaLR 0.24, Uncertain significance, Gastrointestinal stromal tumor
- L18I (p.Leu18Ile), gnomAD 4-54658066-C-A, REVEL 0.09, CADD 17.00
- R19C (p.Arg19Cys), rs1490714621, NCI-TCGA Cosmic COSV5538, NCI-TCGA Cosmic COSV5539, gnomAD rs1490714621, REVEL 0.22, AlphaMissense 0.20, Uncertain significance, Hereditary cancer-predisposing syndrome
- R19G (p.Arg19Gly), gnomAD rs1490714621, Uncertain significance
- R19H (p.Arg19His), rs747253141, ClinGen CA2923121, ClinVar RCV001024428, ClinVar RCV001862287, REVEL 0.23, MetaLR 0.25, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- R19L (p.Arg19Leu), rs1577898667, ClinGen CA915943132, ClinVar RCV000811659, ClinVar RCV002345844, REVEL 0.21, MetaLR 0.24, Uncertain significance, Hereditary cancer-predisposing syndrome
- R19P (p.Arg19Pro), ExAC rs747253141, gnomAD rs747253141, Uncertain significance
- R19Q (p.Arg19Gln), rs1577898667, ClinGen CA2697546705, ClinVar RCV003527203, Uncertain significance, Gastrointestinal stromal tumor
- R19S (p.Arg19Ser), rs1490714621, ClinGen CA356897998, ClinVar RCV002008895, ClinVar RCV006396826, AlphaMissense 0.20, MetaLR 0.32, Conflicting interpretations, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- R19R (p.Arg19Arg), rs776887125, gnomAD 4-54658071-C-T, CADD 15.40
- V20F (p.Val20Phe), rs1553881787, ClinGen CA356898011, ClinVar RCV000633811, ClinVar RCV004025432, AlphaMissense 0.08, MetaLR 0.20, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- V20G (p.Val20Gly), rs1393581394, ClinGen CA356898012, ClinVar RCV001024778, ClinVar RCV001799720, REVEL 0.18, MetaLR 0.21, Uncertain significance, not provided; Gastrointestinal stromal tumor; Hereditary cancer-predisposing syn
- V20I (p.Val20Ile), rs1553881787, ClinGen CA356898007, ClinVar RCV001326658, Ensembl rs1553881787, AlphaMissense 0.08, MetaLR 0.20, Uncertain significance, Gastrointestinal stromal tumor
- V20L (p.Val20Leu), Ensembl rs1553881787, Uncertain significance, Gastrointestinal stromal tumor
- V20V (p.Val20Val), rs759662674, gnomAD 4-54658074-C-T, CADD 14.90
- Q21* (p.Gln21Ter), Ensembl rs2109521392, Uncertain significance
- Q21H (p.Gln21His), gnomAD rs1197233271, Likely benign
- Q21K (p.Gln21Lys), rs2109521392, ClinGen CA356898017, ClinVar RCV002366444, ClinVar RCV003638848, AlphaMissense 0.18, MetaLR 0.22, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- Q21L (p.Gln21Leu), TOPMed rs931395990, Uncertain significance
- Q21R (p.Gln21Arg), rs931395990, ClinGen CA96859735, ClinVar RCV000551257, ClinVar RCV001025103, REVEL 0.22, MetaLR 0.19, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor; not pro
- Q21Q (p.Gln21Gln), rs1197233271, gnomAD 4-54658077-G-A, CADD 13.60
- T22I (p.Thr22Ile), rs769943127, ClinGen CA2923124, ClinVar RCV000814947, ClinVar RCV003318644, REVEL 0.22, MetaLR 0.24, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome; Gastrointestinal stromal
- T22K (p.Thr22Lys), ExAC rs769943127, TOPMed rs769943127, gnomAD rs769943127, REVEL 0.24, MetaLR 0.24, Uncertain significance, Hereditary cancer-predisposing syndrome
- T22S (p.Thr22Ser), Ensembl rs2109521456
- G23A (p.Gly23Ala), Ensembl rs2109660271, Uncertain significance
- G23C (p.Gly23Cys), Ensembl rs2109521514
- G23D (p.Gly23Asp), rs2109660271, ClinGen CA356896781, ClinVar RCV003081880, Ensembl rs2109660271, REVEL 0.36, MetaLR 0.37, Uncertain significance, Gastrointestinal stromal tumor
- G23R (p.Gly23Arg), Ensembl rs2109521514, Uncertain significance, Gastrointestinal stromal tumor
- G23G (p.Gly23Gly), gnomAD 4-54695513-C-G, CADD 13.70
- S24C (p.Ser24Cys), rs1577952322, ClinGen CA356896788, ClinVar RCV000822651, ClinVar RCV002372355, REVEL 0.23, MetaLR 0.27, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- S24F (p.Ser24Phe), gnomAD rs1577952322, Uncertain significance
- S24P (p.Ser24Pro), rs1719995693, ClinGen CA356896785, ClinVar RCV001320416, Ensembl rs1719995693, REVEL 0.25, MetaLR 0.24, Uncertain significance, Gastrointestinal stromal tumor
- S25A (p.Ser25Ala), rs2475439963, ClinGen CA356896790, ClinVar RCV003640227, Uncertain significance, Gastrointestinal stromal tumor
- S25F (p.Ser25Phe), Ensembl rs2109660325
- S25P (p.Ser25Pro), gnomAD 4-54695517-T-C, REVEL 0.33, CADD 23.40
- Q26* (p.Gln26Ter), ExAC rs759129060, TOPMed rs759129060, gnomAD rs759129060, CADD 36.00, Uncertain significance
- Q26E (p.Gln26Glu), rs759129060, ClinGen CA2923151, ClinVar RCV001036232, ClinVar RCV002298851, REVEL 0.18, MetaLR 0.39, Uncertain significance, not provided; Gastrointestinal stromal tumor
- Q26H (p.Gln26His), rs764782713, ClinGen CA2923152, ClinVar RCV001063511, ClinVar RCV001147077, REVEL 0.25, MetaLR 0.39, Conflicting interpretations, Piebaldism; Mastocytosis; Hereditary cancer-predisposing syndrome
- Q26R (p.Gln26Arg), rs1560393066, ClinGen CA356896799, ClinVar RCV000703052, ClinVar RCV004026615, AlphaMissense 0.10, MetaLR 0.42, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- P27L (p.Pro27Leu), rs1307431391, ClinGen CA356896804, ClinVar RCV000792200, ClinVar RCV004027411, AlphaMissense 0.13, MetaLR 0.53, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- P27S (p.Pro27Ser), rs1553887242, ClinGen CA356896803, ClinVar RCV000558903, Ensembl rs1553887242, REVEL 0.46, MetaLR 0.47, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- P27P (p.Pro27Pro), gnomAD 4-54695525-A-G, CADD 12.20
- S28A (p.Ser28Ala), rs1330171716, ClinGen CA356896808, ClinVar RCV003071116, ClinVar RCV004070352, REVEL 0.16, MetaLR 0.27, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- S28P (p.Ser28Pro), rs1330171716, ClinGen CA356896809, ClinVar RCV001057161, gnomAD rs1330171716, REVEL 0.33, MetaLR 0.37, Uncertain significance, Gastrointestinal stromal tumor
- S28S (p.Ser28Ser), rs758868843, gnomAD 4-54695528-T-C, CADD 12.80
- V29A (p.Val29Ala), rs864622699, ClinGen CA356896815, ClinVar RCV001942420, TOPMed rs864622699, AlphaMissense 0.08, MetaLR 0.19, Uncertain significance, Gastrointestinal stromal tumor
- V29E (p.Val29Glu), rs864622699, ClinGen CA348866, ClinVar RCV000204661, ClinVar RCV002444831, REVEL 0.29, AlphaMissense 0.08, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor; not pro
- V29L (p.Val29Leu), rs764636807, ClinGen CA2923155, ClinVar RCV003639830, ExAC rs764636807, REVEL 0.23, MetaLR 0.34, Uncertain significance, Gastrointestinal stromal tumor
- V29V (p.Val29Val), rs2109660422, gnomAD 4-54695531-G-A, CADD 9.44
- S30C (p.Ser30Cys), Ensembl rs2109660428
- S30G (p.Ser30Gly), Ensembl rs2109660428
- S30I (p.Ser30Ile), rs926559231, ClinGen CA96845542, ClinVar RCV000697580, ClinVar RCV002369899, REVEL 0.26, MetaLR 0.48, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- S30N (p.Ser30Asn), TOPMed rs926559231, Uncertain significance
- S30R (p.Ser30Arg), rs2109660456, ClinGen CA356896822, ClinVar RCV001955217, ClinVar RCV004042891, REVEL 0.35, MetaLR 0.43, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- S30S (p.Ser30Ser), gnomAD 4-54695534-T-C, CADD 11.40
- P31A (p.Pro31Ala), rs1431394530, ClinGen CA356896825, ClinVar RCV000796723, ClinVar RCV002370087, AlphaMissense 0.07, MetaLR 0.46, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- P31R (p.Pro31Arg), Ensembl rs1560393121
- P31T (p.Pro31Thr), rs1431394530, ClinGen CA356896824, ClinVar RCV000556799, ClinVar RCV005348146, REVEL 0.36, AlphaMissense 0.07, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- P31L (p.Pro31Leu), gnomAD 4-54695536-C-T, REVEL 0.32, CADD 25.20
- P31P (p.Pro31Pro), gnomAD 4-54695537-A-G, CADD 9.39
- G32A (p.Gly32Ala), gnomAD rs1719999027, Uncertain significance
- G32E (p.Gly32Glu), rs1719999027, ClinGen CA356896834, ClinVar RCV001326361, ClinVar RCV003169530, REVEL 0.06, MetaLR 0.20, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- E33K (p.Glu33Lys), rs1553887257, ClinGen CA356896836, ClinVar RCV000633760, Ensembl rs1553887257, AlphaMissense 0.08, MetaLR 0.30, Uncertain significance, Gastrointestinal stromal tumor
- E33E (p.Glu33Glu), gnomAD 4-54695543-A-G, CADD 3.84
- P34L (p.Pro34Leu), rs55755457, ClinGen CA2923156, ClinVar RCV000459377, ClinVar RCV001009720, REVEL 0.16, MetaLR 0.14, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not specified; not provided
- P34Q (p.Pro34Gln), rs55755457, ClinGen CA160365, ClinVar RCV000121319, ClinVar RCV001303956, REVEL 0.20, MetaLR 0.16, Uncertain significance, Gastrointestinal stromal tumor
- P34S (p.Pro34Ser), Ensembl rs2109660544
- P34P (p.Pro34Pro), rs757725466, gnomAD 4-54695546-G-A, CADD 6.17
- S35C (p.Ser35Cys), Ensembl rs2109660591
- S35Y (p.Ser35Tyr), Ensembl rs2109660591
- S35P (p.Ser35Pro), gnomAD 4-54695547-T-C, REVEL 0.17, CADD 23.60
- S35S (p.Ser35Ser), gnomAD 4-54695549-T-A, CADD 7.91
- P36A (p.Pro36Ala), rs781633384, ClinGen CA356896854, ClinVar RCV003526264, ClinVar RCV005648300, AlphaMissense 0.09, MetaLR 0.08, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- P36L (p.Pro36Leu), rs2109660621, ClinGen CA356896857, ClinVar RCV003638400, Ensembl rs2109660621, AlphaMissense 0.07, MetaLR 0.10, Uncertain significance, Gastrointestinal stromal tumor
- P36S (p.Pro36Ser), rs781633384, ClinGen CA2923158, ClinVar RCV000633807, ClinVar RCV003225103, REVEL 0.03, AlphaMissense 0.09, Conflicting interpretations, Hereditary cancer-predisposing syndrome; KIT-related disorder; not provided
- P36T (p.Pro36Thr), rs781633384, ClinGen CA2923159, NCI-TCGA Cosmic COSV5538, ClinVar RCV001301325, REVEL 0.03, AlphaMissense 0.09, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- P37L (p.Pro37Leu), Ensembl rs2109660670
- P37S (p.Pro37Ser), Ensembl rs2109660646
- P37P (p.Pro37Pro), gnomAD 4-54695555-A-G, CADD 6.94
- S38F (p.Ser38Phe), rs2475440410, ClinGen CA356896869, ClinVar RCV002988645, Uncertain significance, Gastrointestinal stromal tumor
- S38T (p.Ser38Thr), rs1720002282, ClinGen CA356896864, ClinVar RCV002045037, ClinVar RCV004947025, REVEL 0.03, MetaLR 0.07, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- S38P (p.Ser38Pro), rs2109660694, gnomAD 4-54695555-AT-A, CADD 23.10
- S38S (p.Ser38Ser), rs756403734, gnomAD 4-54695558-C-T, CADD 6.58
- I39L (p.Ile39Leu), rs1298190443, ClinGen CA356896870, ClinVar RCV003525698, AlphaMissense 0.18, MetaLR 0.23, Uncertain significance, Gastrointestinal stromal tumor
- I39V (p.Ile39Val), rs1298190443, ClinGen CA356896871, ClinVar RCV001318034, gnomAD rs1298190443, REVEL 0.21, AlphaMissense 0.18, Uncertain significance, Gastrointestinal stromal tumor
- H40R (p.His40Arg), rs373374682, ClinGen CA2923162, ClinVar RCV001238035, ClinVar RCV003373078, REVEL 0.04, MetaLR 0.06, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- H40Y (p.His40Tyr), ExAC rs780042351, gnomAD rs780042351
- H40Q (p.His40Gln), gnomAD 4-54695552-ACCAT-, CADD 24.60
- P41A (p.Pro41Ala), rs768569749, ClinGen CA356896883, ClinVar RCV002815181, ClinVar RCV004642045, REVEL 0.24, MetaLR 0.31, Uncertain significance, Gastrointestinal stromal tumor; Hereditary cancer-predisposing syndrome
- P41L (p.Pro41Leu), rs2109660787, ClinGen CA356896885, ClinVar RCV001893255, Ensembl rs2109660787, AlphaMissense 0.34, MetaLR 0.31, Uncertain significance, Gastrointestinal stromal tumor
- P41Q (p.Pro41Gln), Ensembl rs2109660787, Uncertain significance
- P41S (p.Pro41Ser), ExAC rs768569749, gnomAD rs768569749
- P41T (p.Pro41Thr), ExAC rs768569749, gnomAD rs768569749
- P41P (p.Pro41Pro), rs72549300, gnomAD 4-54695567-A-T, CADD 5.69
- G42A (p.Gly42Ala), ExAC rs746856550, gnomAD rs746856550, Uncertain significance
- G42E (p.Gly42Glu), rs746856550, ClinGen CA356896891, ClinVar RCV000633768, ClinVar RCV004025431, REVEL 0.11, MetaLR 0.07, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- G42R (p.Gly42Arg), rs2475440518, ClinGen CA356896888, ClinVar RCV003444442, Uncertain significance, Gastrointestinal stromal tumor
- G42V (p.Gly42Val), ExAC rs746856550, gnomAD rs746856550, Uncertain significance
- G42S (p.Gly42Ser), rs1161473997, gnomAD 4-54695552-A-ACCA, CADD 24.80
- K43E (p.Lys43Glu), rs770727656, ClinGen CA2923165, ClinVar RCV000814006, ClinVar RCV002381818, REVEL 0.04, MetaLR 0.05, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- K43I (p.Lys43Ile), rs2475440555, ClinGen CA356896897, ClinVar RCV003095325, ClinVar RCV006381836, REVEL 0.05, MetaLR 0.09, Uncertain significance, Hereditary cancer-predisposing syndrome; Gastrointestinal stromal tumor
- K43N (p.Lys43Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- S44P (p.Ser44Pro), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
Public KIT analysis runs
- KIT analysis run — KIT (3,520 variants) — completed 2026-08-10