PSME2

proteasome activator subunit 2, the group of Proteasome|MicroRNA protein coding host genes

Basic information

Region (hg38): 14:24143362-24147570

Links

ENSG00000100911 ∙ NCBI:5721 ∙ OMIM:602161 ∙ HGNC:9569 ∙ Uniprot:Q9UL46 ∙ 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 PSME2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSME2 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					2	2
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	2

Variants in PSME2

This is a list of pathogenic ClinVar variants found in the PSME2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24143423-G-A		not specified	Uncertain significance (Dec 13, 2022)
14-24143489-C-T		not specified	Uncertain significance (Mar 31, 2023)
14-24143586-T-C		not specified	Uncertain significance (May 09, 2023)
14-24143593-C-A		not specified	Uncertain significance (Aug 08, 2023)
14-24143599-G-C		not specified	Uncertain significance (Dec 13, 2022)
14-24143652-A-G		not specified	Uncertain significance (Nov 18, 2022)
14-24143661-C-T		not specified	Uncertain significance (Aug 22, 2023)
14-24144015-C-T		not specified	Uncertain significance (Oct 30, 2023)
14-24144230-G-C			Benign (Jun 11, 2018)
14-24145409-G-A			Benign (Mar 02, 2018)
14-24145422-G-T		not specified	Uncertain significance (Jun 21, 2023)
14-24145425-G-T		not specified	Uncertain significance (Oct 22, 2021)
14-24146219-G-T		not specified	Uncertain significance (Dec 13, 2022)
14-24146233-A-G		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSME2	protein_coding	protein_coding	ENST00000216802	11	4206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0158	0.979	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	88	127	0.695	0.00000621	1566
Missense in Polyphen		13	34.654	0.37514		517
Synonymous	1.89	30	46.3	0.647	0.00000213	434
Loss of Function	2.47	6	17.0	0.353	8.07e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.657
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.830
• hipred: Y
• hipred_score: 0.648
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psme2
• Phenotype: hematopoietic system phenotype; neoplasm; immune system phenotype

Gene ontology

• Biological process: positive regulation of endopeptidase activity;protein deubiquitination;interleukin-12-mediated signaling pathway;post-translational protein modification;regulation of proteasomal protein catabolic process;regulation of G1/S transition of mitotic cell cycle
• Cellular component: proteasome complex;nucleoplasm;cytoplasm;cytosol;proteasome activator complex;membrane;extracellular exosome
• Molecular function: protein binding;identical protein binding;endopeptidase activator activity