PSMD13

proteasome 26S subunit, non-ATPase 13, the group of Proteasome

Basic information

Region (hg38): 11:236966-252984

Links

ENSG00000185627NCBI:5719OMIM:603481HGNC:9558Uniprot:Q9UNM6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSMD13 gene.

  • not_specified (43 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002817.4. 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
2
clinvar
3
missense
37
clinvar
37
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 0 39 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PSMD13protein_codingprotein_codingENST00000431206 1116438
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9990.000987125475011254760.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6341882140.8780.00001172478
Missense in Polyphen3054.0590.55495673
Synonymous0.4727883.50.9340.00000475717
Loss of Function4.40124.50.04090.00000142254

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. {ECO:0000269|PubMed:1317798}.;
Pathway
Epstein-Barr virus infection - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;TLR NFkB;Neutrophil degranulation;B cell receptor signaling;Post-translational protein modification;Metabolism of proteins;DroToll-like;Notch;Hedgehog;Innate Immune System;Immune System;IL-1 NFkB;IL-1 p38;IL-1 JNK;TGF-beta super family signaling pathway canonical;TLR p38;UCH proteinases;Neddylation;Ub-specific processing proteases;JAK STAT pathway and regulation;Deubiquitination;TNFalpha;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Intolerance Scores

loftool
0.0938
rvis_EVS
1.11
rvis_percentile_EVS
92.04

Haploinsufficiency Scores

pHI
0.933
hipred
Y
hipred_score
0.748
ghis
0.540

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.848

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Psmd13
Phenotype

Zebrafish Information Network

Gene name
psmd13
Affected structure
thrombocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
ubiquitin-dependent protein catabolic process;meiosis I;protein deubiquitination;proteasome assembly;neutrophil degranulation;post-translational protein modification
Cellular component
proteasome complex;extracellular region;nucleus;nucleoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, lid subcomplex;membrane;proteasome accessory complex;secretory granule lumen;ficolin-1-rich granule lumen
Molecular function
structural molecule activity