PSMA4

proteasome 20S subunit alpha 4, the group of Proteasome

Basic information

Region (hg38): 15:78540405-78552417

Links

ENSG00000041357

∙ NCBI:5685 ∙ OMIM:176846 ∙ HGNC:9533 ∙ Uniprot:P25789 ∙ 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 PSMA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMA4 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 clinvar	1
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in PSMA4

This is a list of pathogenic ClinVar variants found in the PSMA4 region.

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

Position	Phenotype	Significance	ClinVar
15-78544258-T-G	not specified	Uncertain significance (Jul 19, 2022)	2302401
15-78544920-G-A		Benign (Nov 03, 2018)	778997
15-78545760-G-A	not specified	Uncertain significance (Oct 26, 2022)	2320846
15-78546641-T-G	not specified	Uncertain significance (Feb 28, 2023)	2490495
15-78548856-T-C	not specified	Uncertain significance (Nov 18, 2023)	3220347
15-78548873-A-C	not specified	Uncertain significance (May 22, 2023)	2519757
15-78548882-G-A	not specified	Uncertain significance (Jun 27, 2022)	2297720

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMA4	protein_coding	protein_coding	ENST00000044462	8	8858

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.600	0.400	125717	0	5	125722	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	57	138	0.414	0.00000687	1704
Missense in Polyphen		13	58.353	0.22278		711
Synonymous	0.795	38	44.8	0.849	0.00000211	462
Loss of Function	2.99	3	15.9	0.189	7.31e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the 20S core proteasome complex involved in the proteolytic degradation of most intracellular proteins. This complex plays numerous essential roles within the cell by associating with different regulatory particles. Associated with two 19S regulatory particles, forms the 26S proteasome and thus participates in the ATP-dependent degradation of ubiquitinated proteins. The 26S proteasome plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins that could impair cellular functions, and by removing proteins whose functions are no longer required. Associated with the PA200 or PA28, the 20S proteasome mediates ubiquitin-independent protein degradation. This type of proteolysis is required in several pathways including spermatogenesis (20S-PA200 complex) or generation of a subset of MHC class I-presented antigenic peptides (20S-PA28 complex). {ECO:0000269|PubMed:15244466, ECO:0000269|PubMed:27176742, ECO:0000269|PubMed:8610016}.;
Pathway: Proteasome - Homo sapiens (human);Proteasome Degradation;Exercise-induced Circadian Regulation;TLR NFkB;proteasome complex;B cell receptor signaling;Post-translational protein modification;Metabolism of proteins;DroToll-like;Notch;Hedgehog;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;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

pRec: 0.388

Intolerance Scores

loftool: 0.388
rvis_EVS: -0.1
rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

pHI: 0.969
hipred: Y
hipred_score: 0.783
ghis: 0.702

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Psma4
Phenotype

Gene ontology

Biological process: proteasomal protein catabolic process;proteasomal ubiquitin-independent protein catabolic process;viral process;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
Cellular component: proteasome complex;P-body;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome core complex;proteasome core complex, alpha-subunit complex;intracellular membrane-bounded organelle;extracellular exosome
Molecular function: endopeptidase activity;threonine-type endopeptidase activity;protein binding