GeneBe

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.

  • not_specified (22 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000006263.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
19
clinvar
 19
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 19 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PSME1protein_codingprotein_codingENST00000382708 102810
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1320.8641257360121257480.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5201181350.8740.000007621647
Missense in Polyphen2742.3590.6374560
Synonymous0.6004449.40.8910.00000240453
Loss of Function2.50414.20.2826.18e-7189

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.0001630.000109
Finnish0.000.00
European (Non-Finnish)0.00006150.0000615
Middle Eastern0.0001630.000109
South Asian0.000.00
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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