PSME1

proteasome activator subunit 1, the group of Proteasome

Basic information

Region (hg38): 14:24136163-24138967

Links

ENSG00000092010 ∙ NCBI:5720 ∙ OMIM:600654 ∙ HGNC:9568 ∙ Uniprot:Q06323 ∙ 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 PSME1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSME1 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			15			15
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	16	1	0

Variants in PSME1

This is a list of pathogenic ClinVar variants found in the PSME1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24137191-G-A		not specified	Uncertain significance (Jan 02, 2024)
14-24137192-A-G		not specified	Uncertain significance (Jan 22, 2025)
14-24137324-C-G		not specified	Uncertain significance (Oct 09, 2024)
14-24137376-C-T		not specified	Uncertain significance (Jul 14, 2021)
14-24137414-C-T		not specified	Uncertain significance (Dec 01, 2022)
14-24137415-G-A		not specified	Uncertain significance (May 02, 2024)
14-24137421-A-C		not specified	Uncertain significance (Nov 17, 2022)
14-24137740-G-T			Likely benign (Feb 01, 2023)
14-24138109-G-A		not specified	Uncertain significance (Mar 31, 2023)
14-24138242-G-C		not specified	Uncertain significance (Oct 04, 2022)
14-24138251-C-T		not specified	Uncertain significance (Nov 07, 2023)
14-24138259-T-G		not specified	Uncertain significance (May 08, 2024)
14-24138358-C-T		not specified	Uncertain significance (Nov 26, 2024)
14-24138484-G-A		not specified	Uncertain significance (Jun 06, 2022)
14-24138484-G-C		not specified	Uncertain significance (Aug 12, 2021)
14-24138528-C-T		not specified	Uncertain significance (Dec 21, 2023)
14-24138549-C-T		not specified	Uncertain significance (Dec 21, 2023)
14-24138640-G-C		not specified	Uncertain significance (Mar 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSME1	protein_coding	protein_coding	ENST00000382708	10	2810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.132	0.864	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.520	118	135	0.874	0.00000762	1647
Missense in Polyphen		27	42.359	0.6374		560
Synonymous	0.600	44	49.4	0.891	0.00000240	453
Loss of Function	2.50	4	14.2	0.282	6.18e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000615	0.0000615
Middle Eastern	0.000163	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

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;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.885
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.391
• hipred: Y
• hipred_score: 0.503
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psme1
• Phenotype: neoplasm

Gene ontology

• Biological process: positive regulation of endopeptidase activity;protein deubiquitination;antigen processing and presentation of exogenous antigen;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;extracellular exosome
• Molecular function: protein binding;endopeptidase activator activity