PIM1 (P11309) variants and mutations
PIM1 (also known as P11309) is a human protein-coding gene encoding a serine/threonine-protein kinase pim-1 protein. It promotes cell survival, proliferation, and protein translation downstream of cytokine and oncogenic signaling. Overexpression or genomic activation is common in hematologic malignancies and some solid tumors, where it can cooperate with MYC and other oncogenes. This analysis covers 592 PIM1 variants and mutations. Of these, 76% have computational variant effect predictions. Disease context includes CODAS syndrome, neurodegenerative disease, and hereditary disease. Example PIM1 variants include L2F, L2H, and L2S.
Variant analysis overview
- Gene: PIM1
- Protein: P11309
- UniProt accession: P11309
- Organism: Homo sapiens
- Variants analyzed: 592
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 330 unspecified-consequence records; 11 frameshift variants; 132 synonymous variants; 4 stop-gained variants; 98 missense variants; 10 in-frame deletions; 4 splice-region variants; 1 in-frame insertions; 2 substitution
- Prediction scores: 450 variants have prediction scores (76% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: CODAS syndrome, neurodegenerative disease, hereditary disease, pyruvate dehydrogenase E1-alpha deficiency, neurodevelopmental disorder, poisoning, Developmental cataract, cancer, neoplasm, glioma, central nervous system cancer, posterior cortical atrophy.
Protein structure and variant hotspots
- Protein features: 1 domains; 4 binding sites; 4 post-translational modification sites.
- Structural context: 455 variants have structural context.
- PTM context: 6 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, MaveDB, LitVar.
Notable PIM1 variants
Examples include L2F, L2H, L2S, L2L, L3F, L3L, L3*, S4C. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- L2F (p.Leu2Phe), rs774518045, NCI-TCGA Cosmic COSV6516, ExAC rs774518045, REVEL 0.23, CADD 25.60, Variant assessed as somatic; moderate impact.
- L2H (p.Leu2His), TOPMed rs992290167
- L2S (p.Leu2Ser), gnomAD 6-37170578-GC-G, CADD 27.00
- L2L (p.Leu2Leu), rs576804627, gnomAD 6-37170581-C-G, CADD 13.90
- L3F (p.Leu3Phe), ExAC rs750842002, gnomAD rs750842002
- L3L (p.Leu3Leu), rs1231821627, gnomAD 6-37170582-T-C, CADD 13.30
- L3* (p.Leu3Ter), gnomAD 6-37170583-T-A, CADD 36.00
- S4C (p.Ser4Cys), gnomAD 6-37170586-C-G, REVEL 0.29, CADD 25.10
- K5R (p.Lys5Arg), Ensembl rs1762256395
- K5T (p.Lys5Thr), gnomAD 6-37170589-A-C, REVEL 0.23, CADD 24.50
- K5K (p.Lys5Lys), gnomAD 6-37170590-A-G, CADD 13.90
- I6F (p.Ile6Phe), gnomAD 6-37170591-A-T, REVEL 0.04, CADD 20.70
- I6L (p.Ile6Leu), gnomAD 6-37170591-A-C, REVEL 0.04, CADD 18.40
- I6T (p.Ile6Thr), gnomAD 6-37170592-T-C, REVEL 0.12, CADD 23.70
- I6I (p.Ile6Ile), gnomAD 6-37170593-C-A, CADD 14.70
- N7I (p.Asn7Ile), gnomAD rs1215548229, REVEL 0.20, CADD 25.30
- N7S (p.Asn7Ser), gnomAD rs1215548229, REVEL 0.10, CADD 20.90
- N7N (p.Asn7Asn), rs756412850, gnomAD 6-37170596-C-T, CADD 14.20
- S8S (p.Ser8Ser), rs545722595, gnomAD 6-37170599-G-T, CADD 13.30
- A10V (p.Ala10Val), NCI-TCGA Cosmic COSV6516, REVEL 0.14, CADD 23.90, Variant assessed as somatic; moderate impact.
- A10T (p.Ala10Thr), gnomAD 6-37170603-G-A, REVEL 0.12, CADD 26.90
- A10S (p.Ala10Ser), gnomAD 6-37170603-G-T, REVEL 0.11, CADD 22.60
- A10A (p.Ala10Ala), rs563911547, gnomAD 6-37170605-C-T, CADD 15.90
- H11N (p.His11Asn), TOPMed rs1762256870
- H11R (p.His11Arg), gnomAD rs1263817223, REVEL 0.07, CADD 23.10
- H11L (p.His11Leu), gnomAD 6-37170607-A-T, REVEL 0.09, CADD 23.50
- R13L (p.Arg13Leu), Ensembl rs2113769142
- R13S (p.Arg13Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- R13G (p.Arg13Gly), gnomAD 6-37170612-C-G, REVEL 0.12, CADD 22.60
- R13R (p.Arg13Arg), rs2113769143, gnomAD 6-37170614-C-T, CADD 14.80
- A14S (p.Ala14Ser), TOPMed rs1762256995, REVEL 0.06, CADD 14.30
- A14V (p.Ala14Val), NCI-TCGA Cosmic COSV1009, gnomAD rs1762257051, REVEL 0.11, CADD 22.60, Variant assessed as somatic; moderate impact.
- A14T (p.Ala14Thr), gnomAD 6-37170615-G-A, REVEL 0.06, CADD 17.60
- A14P (p.Ala14Pro), gnomAD 6-37170615-G-C, REVEL 0.12, CADD 19.10
- A14A (p.Ala14Ala), rs778415475, gnomAD 6-37170617-C-T, CADD 15.40
- A15E (p.Ala15Glu), gnomAD rs1205446918, REVEL 0.07, CADD 18.60
- A15S (p.Ala15Ser), NCI-TCGA Cosmic COSV6516, Variant assessed as somatic; moderate impact.
- A15T (p.Ala15Thr), gnomAD 6-37170617-CGCGCC, CADD 28.60
- A15V (p.Ala15Val), gnomAD 6-37170619-C-T, REVEL 0.13, CADD 20.60
- A15A (p.Ala15Ala), gnomAD 6-37170620-G-T, CADD 14.50
- P16S (p.Pro16Ser), gnomAD 6-37170621-C-T, REVEL 0.03, CADD 17.70
- P16H (p.Pro16His), gnomAD 6-37170622-C-A, REVEL 0.11, CADD 24.40
- C17F (p.Cys17Phe), 1000Genomes rs532972131, TOPMed rs532972131, gnomAD rs532972131, REVEL 0.06, CADD 21.90
- C17R (p.Cys17Arg), ExAC rs747616420, REVEL 0.14, CADD 21.00
- C17S (p.Cys17Ser), 1000Genomes rs532972131, TOPMed rs532972131, gnomAD rs532972131, REVEL 0.08, CADD 17.80
- C17Y (p.Cys17Tyr), gnomAD 6-37170625-G-A, REVEL 0.09, CADD 21.10
- C17C (p.Cys17Cys), rs1485392438, gnomAD 6-37170626-C-T, CADD 14.40
- N18D (p.Asn18Asp), TOPMed rs1186895104, gnomAD rs1186895104, REVEL 0.04, CADD 15.00
- N18H (p.Asn18His), TOPMed rs1186895104, gnomAD rs1186895104, REVEL 0.05, CADD 16.20
- N18S (p.Asn18Ser), gnomAD 6-37170628-A-G, REVEL 0.10, CADD 5.43
- N18K (p.Asn18Lys), gnomAD 6-37170629-C-G, REVEL 0.14, CADD 15.60
- D19G (p.Asp19Gly), TOPMed rs1762257677
- D19Y (p.Asp19Tyr), gnomAD rs1421480824, REVEL 0.21, CADD 21.90
- D19D (p.Asp19Asp), rs1583396565, gnomAD 6-37170632-C-T, CADD 13.90
- L20del (p.Leu20del), rs1431087077, gnomAD 6-37170632-CCTG-C, CADD 19.10
- L20L (p.Leu20Leu), rs758397716, gnomAD 6-37170633-C-T, CADD 13.90
- H21N (p.His21Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- H21Q (p.His21Gln), ExAC rs746875868, TOPMed rs746875868, gnomAD rs746875868, REVEL 0.07, CADD 20.30
- H21Y (p.His21Tyr), gnomAD 6-37170636-C-T, REVEL 0.03, CADD 20.90
- H21H (p.His21His), rs746875868, gnomAD 6-37170638-C-T, CADD 13.40
- A22P (p.Ala22Pro), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A22S (p.Ala22Ser), ExAC rs776506228, TOPMed rs776506228, gnomAD rs776506228, REVEL 0.03, CADD 15.40
- A22T (p.Ala22Thr), ExAC rs776506228, TOPMed rs776506228, gnomAD rs776506228, REVEL 0.07, CADD 18.20
- A22V (p.Ala22Val), NCI-TCGA Cosmic COSV1009, REVEL 0.06, CADD 20.60, Variant assessed as somatic; moderate impact.
- T23I (p.Thr23Ile), rs546301253, NCI-TCGA Cosmic COSV6516, 1000Genomes rs546301253, REVEL 0.04, CADD 17.30, Variant assessed as somatic; moderate impact.
- T23T (p.Thr23Thr), rs1762258363, gnomAD 6-37170644-C-T, CADD 14.40
- K24E (p.Lys24Glu), gnomAD rs1209123331, REVEL 0.13, CADD 19.80
- K24N (p.Lys24Asn), NCI-TCGA Cosmic COSV6516, REVEL 0.02, CADD 16.90, Variant assessed as somatic; moderate impact.
- K24* (p.Lys24Ter), gnomAD 6-37170645-A-T, CADD 36.00
- p.Lys24 Pro27delinsAsn, gnomAD 6-37170646-AGCTGG, CADD 21.70
- K24R (p.Lys24Arg), gnomAD 6-37170646-A-G, REVEL 0.06, CADD 20.90
- K24K (p.Lys24Lys), rs768952543, gnomAD 6-37170647-G-A, CADD 12.10
- L25R (p.Leu25Arg), TOPMed rs1310183432, gnomAD rs1310183432, REVEL 0.07, CADD 22.20
- L25V (p.Leu25Val), 1000Genomes rs774607869, ExAC rs774607869, TOPMed rs774607869, gnomAD rs774607869, REVEL 0.09, CADD 20.30
- L25L (p.Leu25Leu), rs774607869, gnomAD 6-37170648-C-T, CADD 13.80
- A26T (p.Ala26Thr), Ensembl rs1762258918, REVEL 0.09, CADD 22.50
- A26V (p.Ala26Val), gnomAD 6-37170652-C-T, REVEL 0.04, CADD 22.40
- A26G (p.Ala26Gly), gnomAD 6-37170652-C-G, REVEL 0.02, CADD 22.20
- A26A (p.Ala26Ala), gnomAD 6-37170653-G-T, CADD 15.10
- P27A (p.Pro27Ala), gnomAD 6-37170654-C-G, REVEL 0.11, CADD 21.30
- P27P (p.Pro27Pro), rs768121298, gnomAD 6-37170656-C-T, CADD 10.40
- G28D (p.Gly28Asp), rs377274719, NCI-TCGA Cosmic COSV6516, 1000Genomes rs377274719, ESP rs377274719, REVEL 0.08, CADD 24.40, Variant assessed as somatic; moderate impact.
- G28S (p.Gly28Ser), gnomAD rs1218840909, REVEL 0.07, CADD 25.30
- G28C (p.Gly28Cys), gnomAD 6-37170657-G-T, REVEL 0.10, CADD 28.60
- G28V (p.Gly28Val), gnomAD 6-37170773-G-T, REVEL 0.08, CADD 24.60
- G28G (p.Gly28Gly), rs759956612, gnomAD 6-37170774-C-T, CADD 19.00
- K29R (p.Lys29Arg), 1000Genomes rs568759949, ExAC rs568759949, gnomAD rs568759949, REVEL 0.10, CADD 23.90
- E30K (p.Glu30Lys), TOPMed rs1451151403, gnomAD rs1451151403, REVEL 0.20, CADD 23.80, Tier III - Unknown, Primary central nervous system lymphoma
- E30del (p.Glu30del), rs942893612, gnomAD 6-37170775-AAGG-A, CADD 22.70
- E30Q (p.Glu30Gln), gnomAD 6-37170778-G-C, REVEL 0.11, CADD 23.60
- E30E (p.Glu30Glu), rs537732412, gnomAD 6-37170780-G-A, CADD 12.60
- K31M (p.Lys31Met), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- K31N (p.Lys31Asn), Ensembl rs2113769414
- K31del (p.Lys31del), rs1762263833, gnomAD 6-37170778-GAGA-G, CADD 21.90
- K31R (p.Lys31Arg), gnomAD 6-37170782-A-G, REVEL 0.08, CADD 23.10
- K31K (p.Lys31Lys), gnomAD 6-37170783-G-A, CADD 14.50
- E32G (p.Glu32Gly), Ensembl rs2113769415, REVEL 0.26, CADD 27.10
- E32K (p.Glu32Lys), TOPMed rs1762263990, REVEL 0.26, CADD 25.20
- E32Q (p.Glu32Gln), NCI-TCGA Cosmic COSV6516, Variant assessed as somatic; moderate impact.
- E32D (p.Glu32Asp), gnomAD 6-37170786-G-C, REVEL 0.12, CADD 22.90
- E32E (p.Glu32Glu), gnomAD 6-37170786-G-A, CADD 13.50
- P33A (p.Pro33Ala), 1000Genomes rs775870535, ExAC rs775870535, TOPMed rs775870535, gnomAD rs775870535, REVEL 0.12, CADD 21.00
- P33H (p.Pro33His), gnomAD rs1437856130, REVEL 0.23, CADD 23.90
- P33S (p.Pro33Ser), rs775870535, NCI-TCGA Cosmic COSV6516, 1000Genomes rs775870535, REVEL 0.09, CADD 21.60, Tier III - Unknown, Primary central nervous system lymphoma
- P33T (p.Pro33Thr), NCI-TCGA Cosmic COSV6516, REVEL 0.27, CADD 22.30, Variant assessed as somatic; moderate impact.
- P33L (p.Pro33Leu), gnomAD 6-37170788-C-T, REVEL 0.28, CADD 24.30
- P33P (p.Pro33Pro), gnomAD 6-37170789-C-T, CADD 14.80
- L34Q (p.Leu34Gln), Ensembl rs1762264364
- L34L (p.Leu34Leu), gnomAD 6-37170792-G-A, CADD 14.90
- E35E (p.Glu35Glu), rs762539338, gnomAD 6-37170795-G-A, CADD 14.50
- S36A (p.Ser36Ala), ExAC rs763764313, gnomAD rs763764313, REVEL 0.06, CADD 21.90
- Q37H (p.Gln37His), rs751073896, NCI-TCGA Cosmic COSV6516, REVEL 0.06, CADD 18.90, Variant assessed as somatic; moderate impact.
- Q37K (p.Gln37Lys), 1000Genomes rs2113769440, REVEL 0.07, CADD 18.80
- Q37* (p.Gln37Ter), gnomAD 6-37170799-C-T, CADD 37.00
- Q37Q (p.Gln37Gln), rs751073896, gnomAD 6-37170801-G-A, CADD 13.10
- Y38* (p.Tyr38Ter), gnomAD rs1184805609, CADD 36.00
- Y38C (p.Tyr38Cys), 1000Genomes rs761386793, ExAC rs761386793, REVEL 0.40, CADD 29.90
- Y38N (p.Tyr38Asn), Ensembl rs1762264714
- Y38F (p.Tyr38Phe), gnomAD 6-37170803-A-T, REVEL 0.30, CADD 27.10
- Y38Y (p.Tyr38Tyr), rs1184805609, gnomAD 6-37170804-C-T, CADD 13.90
- Q39* (p.Gln39Ter), Ensembl rs2113769467
- Q39H (p.Gln39His), ExAC rs767621897, TOPMed rs767621897, gnomAD rs767621897, REVEL 0.09, CADD 22.80
- Q39L (p.Gln39Leu), TOPMed rs1387437361, gnomAD rs1387437361, REVEL 0.12, CADD 23.40
- Q39R (p.Gln39Arg), TOPMed rs1387437361, gnomAD rs1387437361, REVEL 0.08, CADD 21.40
- Q39Q (p.Gln39Gln), gnomAD 6-37170807-G-A, CADD 13.90
- V40G (p.Val40Gly), ExAC rs750381293, gnomAD rs750381293
- V40L (p.Val40Leu), gnomAD rs1167511555, REVEL 0.12, CADD 22.30
- V40V (p.Val40Val), rs1411666336, gnomAD 6-37170810-G-A, CADD 15.40
- G41G (p.Gly41Gly), rs756049239, gnomAD 6-37170813-C-T, CADD 15.40
- P42L (p.Pro42Leu), NCI-TCGA Cosmic COSV1009, ExAC rs766108688, gnomAD rs766108688, REVEL 0.08, CADD 24.20, Variant assessed as somatic; moderate impact.
- P42R (p.Pro42Arg), ExAC rs766108688, gnomAD rs766108688, REVEL 0.07, CADD 23.80
- P42S (p.Pro42Ser), gnomAD 6-37170814-C-T, REVEL 0.07, CADD 19.30
- P42P (p.Pro42Pro), rs753629252, gnomAD 6-37170816-G-A, CADD 14.90
- L43V (p.Leu43Val), Ensembl rs1762265603
- L43L (p.Leu43Leu), gnomAD 6-37170819-A-G, CADD 7.38
- L44W (p.Leu44Trp), gnomAD 6-37170819-AC-A, CADD 24.40
- L44L (p.Leu44Leu), gnomAD 6-37170820-C-T, CADD 13.30
- L44R (p.Leu44Arg), gnomAD 6-37170821-T-G, REVEL 0.47, CADD 29.90
- G45S (p.Gly45Ser), gnomAD rs1337351112
- G45D (p.Gly45Asp), gnomAD 6-37170824-G-A, REVEL 0.89, CADD 30.00
- G45G (p.Gly45Gly), rs1762265731, gnomAD 6-37170825-C-T, CADD 16.20
- S46R (p.Ser46Arg), gnomAD 6-37170828-C-A, REVEL 0.28, CADD 22.40
- S46S (p.Ser46Ser), rs1384673643, gnomAD 6-37170828-C-T, CADD 15.80
- G48D (p.Gly48Asp), rs758586647, NCI-TCGA Cosmic COSV6516, ExAC rs758586647, gnomAD rs758586647, REVEL 0.28, CADD 28.90, Variant assessed as somatic; moderate impact.
- G48S (p.Gly48Ser), gnomAD 6-37170832-G-A, REVEL 0.23, CADD 31.00
- G48G (p.Gly48Gly), rs1339662144, gnomAD 6-37170834-C-T, CADD 15.30
- p.Phe49 Gly50del, rs1224995800, gnomAD 6-37170830-GCGGCT, CADD 22.40
- F49L (p.Phe49Leu), gnomAD 6-37170835-T-C, REVEL 0.37, CADD 29.30
- G50A (p.Gly50Ala), ExAC rs778032371, gnomAD rs778032371, REVEL 0.79, CADD 28.00
- G50D (p.Gly50Asp), ExAC rs778032371, gnomAD rs778032371
- G50G (p.Gly50Gly), gnomAD 6-37170840-C-T, CADD 15.00
- S51L (p.Ser51Leu), 1000Genomes rs551680157, ExAC rs551680157, TOPMed rs551680157, gnomAD rs551680157, REVEL 0.19, CADD 24.30
- S51W (p.Ser51Trp), rs551680157, NCI-TCGA Cosmic COSV6516, 1000Genomes rs551680157, REVEL 0.41, CADD 28.40, Variant assessed as somatic; moderate impact.
- S51S (p.Ser51Ser), rs1460518397, gnomAD 6-37170843-G-T, CADD 5.62
- V52G (p.Val52Gly), Ensembl rs2113769533
- V52L (p.Val52Leu), Ensembl rs2113769531
- V52V (p.Val52Val), gnomAD 6-37170846-C-T, CADD 11.90
- Y53* (p.Tyr53Ter), NCI-TCGA Cosmic COSV1009, NCI-TCGA Cosmic COSV6516, Variant assessed as somatic; high impact., in a colorectal adenocarcinoma sample
- Y53H (p.Tyr53His), UniProt VAR 041004, Uncertain significance, in a colorectal adenocarcinoma sample
- Y53D (p.Tyr53Asp), gnomAD 6-37170847-T-G, REVEL 0.48, CADD 31.00
- Y53S (p.Tyr53Ser), gnomAD 6-37170848-A-C, REVEL 0.35, CADD 27.40
- Y53Y (p.Tyr53Tyr), rs2113769538, gnomAD 6-37170849-C-T, CADD 13.70
- S54T (p.Ser54Thr), ExAC rs781178342, TOPMed rs781178342, gnomAD rs781178342, REVEL 0.16, CADD 23.50
- S54S (p.Ser54Ser), rs201760858, gnomAD 6-37170852-A-G, CADD 8.21
- G55S (p.Gly55Ser), gnomAD 6-37170853-G-A, REVEL 0.67, CADD 32.00
- G55V (p.Gly55Val), gnomAD 6-37170854-G-T, REVEL 0.66, CADD 31.00
- G55G (p.Gly55Gly), rs770241032, gnomAD 6-37170855-C-A, CADD 14.70
- I56M (p.Ile56Met), Ensembl rs2113769562
- I56N (p.Ile56Asn), Ensembl rs2113769559
- I56V (p.Ile56Val), Ensembl rs1762266784, REVEL 0.05, CADD 14.30
- I56I (p.Ile56Ile), gnomAD 6-37170858-C-T, CADD 13.80
- R57C (p.Arg57Cys), rs1222607867, NCI-TCGA Cosmic COSV6516, TOPMed rs1222607867, REVEL 0.47, CADD 28.40, Variant assessed as somatic; moderate impact.
- R57H (p.Arg57His), TOPMed rs1323508876, REVEL 0.24, CADD 32.00
- R57P (p.Arg57Pro), TOPMed rs1323508876
- R57S (p.Arg57Ser), TOPMed rs1222607867
- R57R (p.Arg57Arg), gnomAD 6-37170861-C-A, CADD 9.46
- V58A (p.Val58Ala), Ensembl rs2113769577
- V58F (p.Val58Phe), TOPMed rs896496531, gnomAD rs896496531
- V58G (p.Val58Gly), Ensembl rs2113769577
- V58I (p.Val58Ile), TOPMed rs896496531, gnomAD rs896496531, REVEL 0.11, CADD 18.40
Public PIM1 analysis runs
- PIM1 analysis run — PIM1 (592 variants) — completed 2026-08-20