PIM3

Pim-3 proto-oncogene, serine/threonine kinase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:49960768-49964072

Links

ENSG00000198355 ∙ NCBI:415116 ∙ OMIM:610580 ∙ HGNC:19310 ∙ Uniprot:Q86V86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIM3 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	1
missense			22		3	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	4

Variants in PIM3

This is a list of pathogenic ClinVar variants found in the PIM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-49960975-G-T		not specified	Uncertain significance (Feb 12, 2025)
22-49960988-G-A		not specified	Uncertain significance (Oct 29, 2024)
22-49961024-T-C		not specified	Uncertain significance (May 15, 2024)
22-49961135-C-G			Benign (Nov 20, 2018)
22-49961208-G-A		not specified	Uncertain significance (Jun 06, 2022)
22-49961497-G-C		not specified	Uncertain significance (Nov 15, 2024)
22-49961505-C-T		not specified	Uncertain significance (Nov 14, 2023)
22-49961511-G-A		not specified	Uncertain significance (Dec 13, 2024)
22-49961518-G-A		not specified	Uncertain significance (Mar 23, 2023)
22-49961544-G-T		not specified	Uncertain significance (Dec 12, 2023)
22-49961622-G-A		not specified	Uncertain significance (Jan 20, 2023)
22-49961628-C-G		not specified	Uncertain significance (Apr 07, 2023)
22-49961681-C-G		not specified	Uncertain significance (Sep 26, 2023)
22-49961694-G-T		not specified	Uncertain significance (May 18, 2023)
22-49961704-A-G		not specified	Uncertain significance (Sep 26, 2022)
22-49961737-G-C		not specified	Uncertain significance (Dec 17, 2023)
22-49961805-T-C		not specified	Uncertain significance (Dec 14, 2021)
22-49962738-C-T			Benign (Nov 20, 2018)
22-49962817-G-A		not specified	Uncertain significance (Feb 07, 2023)
22-49962818-A-C		not specified	Uncertain significance (Jan 29, 2024)
22-49962836-G-T		not specified	Uncertain significance (Jan 21, 2025)
22-49962848-G-A		not specified	Uncertain significance (Dec 09, 2024)
22-49962960-T-G		not specified	Uncertain significance (Nov 08, 2021)
22-49963045-T-C			Benign (Jul 13, 2018)
22-49963051-A-C		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIM3	protein_coding	protein_coding	ENST00000360612	6	3568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0181	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	151	186	0.810	0.0000110	2036
Missense in Polyphen		20	58.441	0.34223		679
Synonymous	-4.54	139	85.5	1.62	0.00000528	680
Loss of Function	3.24	0	12.2	0.00	6.30e-7	133

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: dbNSFP

• Function: FUNCTION: Proto-oncogene with serine/threonine kinase activity that can prevent apoptosis, promote cell survival and protein translation. May contribute to tumorigenesis through: the delivery of survival signaling through phosphorylation of BAD which induces release of the anti-apoptotic protein Bcl-X(L), the regulation of cell cycle progression, protein synthesis and by regulation of MYC transcriptional activity. Additionally to this role on tumorigenesis, can also negatively regulate insulin secretion by inhibiting the activation of MAPK1/3 (ERK1/2), through SOCS6. Involved also in the control of energy metabolism and regulation of AMPK activity in modulating MYC and PPARGC1A protein levels and cell growth. {ECO:0000269|PubMed:15540201, ECO:0000269|PubMed:16818649, ECO:0000269|PubMed:17270021, ECO:0000269|PubMed:17876606, ECO:0000269|PubMed:18593906}.

Recessive Scores

• pRec: 0.154

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.673
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pim3
• Phenotype: growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype; normal phenotype

Gene ontology

• Biological process: protein phosphorylation;apoptotic process;cell cycle;regulation of mitotic cell cycle;negative regulation of apoptotic process;protein autophosphorylation;negative regulation of insulin secretion involved in cellular response to glucose stimulus
• Cellular component: cytoplasm;cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding