PSME3

proteasome activator subunit 3, the group of Proteasome

Basic information

Region (hg38): 17:42824385-42843760

Links

ENSG00000131467 ∙ NCBI:10197 ∙ OMIM:605129 ∙ HGNC:9570 ∙ Uniprot:P61289 ∙ 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 PSME3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSME3 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	0	1

Variants in PSME3

This is a list of pathogenic ClinVar variants found in the PSME3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42833631-C-T			Benign (Nov 01, 2022)
17-42833635-G-T		not specified	Uncertain significance (Sep 08, 2024)
17-42834791-A-G		not specified	Uncertain significance (Dec 23, 2024)
17-42834854-A-G		not specified	Uncertain significance (Aug 30, 2021)
17-42838117-A-G		not specified	Uncertain significance (Oct 05, 2023)
17-42838714-T-C		not specified	Uncertain significance (Mar 01, 2025)
17-42838729-A-G			Uncertain significance (Dec 02, 2023)
17-42839162-A-C		not specified	Uncertain significance (Jun 04, 2024)
17-42839303-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-42839307-G-A		not specified	Uncertain significance (Nov 03, 2023)
17-42841549-C-T		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSME3	protein_coding	protein_coding	ENST00000293362	11	19373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00286	125735	0	2	125737	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	66	148	0.447	0.00000768	1768
Missense in Polyphen		12	48.296	0.24847		568
Synonymous	0.492	46	50.4	0.912	0.00000235	480
Loss of Function	3.84	0	17.2	0.00	8.07e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of the 11S REG-gamma (also called PA28-gamma) proteasome regulator, a doughnut-shaped homoheptamer which associates with the proteasome. 11S REG-gamma activates the trypsin-like catalytic subunit of the proteasome but inhibits the chymotrypsin-like and postglutamyl-preferring (PGPH) subunits. Facilitates the MDM2-p53/TP53 interaction which promotes ubiquitination- and MDM2-dependent proteasomal degradation of p53/TP53, limiting its accumulation and resulting in inhibited apoptosis after DNA damage. May also be involved in cell cycle regulation. Mediates CCAR2 and CHEK2-dependent SIRT1 inhibition (PubMed:25361978). {ECO:0000269|PubMed:10835274, ECO:0000269|PubMed:11185562, ECO:0000269|PubMed:11432824, ECO:0000269|PubMed:15111123, ECO:0000269|PubMed:18309296, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:9325261}.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.244

Intolerance Scores

• loftool: 0.438
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.976
• hipred: Y
• hipred_score: 0.794
• ghis: 0.683

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psme3
• Phenotype: immune system phenotype; hematopoietic system phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: apoptotic process;cell cycle;positive regulation of endopeptidase activity;protein deubiquitination;post-translational protein modification;regulation of proteasomal protein catabolic process;regulation of G1/S transition of mitotic cell cycle;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: proteasome complex;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome activator complex;membrane
• Molecular function: p53 binding;protein binding;identical protein binding;endopeptidase activator activity;MDM2/MDM4 family protein binding