PIM2
Pim-2 proto-oncogene, serine/threonine kinase
Basic information
Region (hg38): X:48913182-48919024
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIM2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in PIM2
This is a list of pathogenic ClinVar variants found in the PIM2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-48914204-G-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| X-48914246-C-T | not specified | Uncertain significance (Feb 07, 2025) | ||
| X-48914286-C-T | not specified | Uncertain significance (Jan 16, 2025) | ||
| X-48914523-T-C | not specified | Uncertain significance (Jul 12, 2022) | ||
| X-48914558-G-A | Likely benign (Apr 01, 2023) | |||
| X-48915029-C-A | not specified | Uncertain significance (Nov 17, 2023) | ||
| X-48915044-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
| X-48915202-C-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| X-48915202-C-T | not specified | Uncertain significance (Aug 04, 2024) | ||
| X-48915251-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| X-48917788-G-C | not specified | Uncertain significance (Mar 04, 2025) | ||
| X-48918601-G-A | not specified | Uncertain significance (Nov 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PIM2 | protein_coding | protein_coding | ENST00000376509 | 6 | 5843 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.948 | 0.0518 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 83 | 125 | 0.664 | 0.0000100 | 1973 |
| Missense in Polyphen | 19 | 45.24 | 0.41998 | 761 | ||
| Synonymous | -0.631 | 54 | 48.4 | 1.12 | 0.00000351 | 676 |
| Loss of Function | 2.83 | 0 | 9.32 | 0.00 | 7.12e-7 | 143 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Proto-oncogene with serine/threonine kinase activity involved in cell survival and cell proliferation. Exerts its oncogenic activity through: the regulation of MYC transcriptional activity, the regulation of cell cycle progression, the regulation of cap-dependent protein translation and through survival signaling by phosphorylation of a pro-apoptotic protein, BAD. Phosphorylation of MYC leads to an increase of MYC protein stability and thereby an increase transcriptional activity. The stabilization of MYC exerted by PIM2 might explain partly the strong synergism between these 2 oncogenes in tumorigenesis. Regulates cap-dependent protein translation in a mammalian target of rapamycin complex 1 (mTORC1)-independent manner and in parallel to the PI3K-Akt pathway. Mediates survival signaling through phosphorylation of BAD, which induces release of the anti- apoptotic protein Bcl-X(L)/BCL2L1. Promotes cell survival in response to a variety of proliferative signals via positive regulation of the I-kappa-B kinase/NF-kappa-B cascade; this process requires phosphorylation of MAP3K8/COT. Promotes growth factor-independent proliferation by phosphorylation of cell cycle factors such as CDKN1A and CDKN1B. Involved in the positive regulation of chondrocyte survival and autophagy in the epiphyseal growth plate. {ECO:0000269|PubMed:18593906, ECO:0000269|PubMed:18675992, ECO:0000269|PubMed:20307683}.;
- Pathway
- Acute myeloid leukemia - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Imatinib and Chronic Myeloid Leukemia
(Consensus)
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.777
- hipred
- Y
- hipred_score
- 0.572
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pim2
- Phenotype
- growth/size/body region phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;protein phosphorylation;male meiotic nuclear division;cell population proliferation;negative regulation of cell population proliferation;apoptotic mitochondrial changes;response to virus;positive regulation of autophagy;positive regulation of macroautophagy;negative regulation of protein binding;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of transcription, DNA-templated;protein autophosphorylation;protein stabilization
- Cellular component
- cytoplasm
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding