PSMA1

proteasome 20S subunit alpha 1, the group of Proteasome

Basic information

Region (hg38): 11:14504211-14643635

Links

ENSG00000129084 ∙ NCBI:5682 ∙ OMIM:602854 ∙ HGNC:9530 ∙ Uniprot:P25786 ∙ 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 PSMA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMA1 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	6	1	1

Variants in PSMA1

This is a list of pathogenic ClinVar variants found in the PSMA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-14507704-C-T			Benign (Feb 19, 2018)
11-14507720-T-C		not specified	Uncertain significance (Feb 16, 2023)
11-14513616-T-A		not specified	Uncertain significance (Mar 21, 2023)
11-14513633-T-C		not specified	Uncertain significance (Jun 12, 2023)
11-14514448-C-T		not specified	Uncertain significance (Apr 17, 2023)
11-14514480-C-A		not specified	Uncertain significance (Aug 21, 2023)
11-14517676-T-C		not specified	Uncertain significance (May 08, 2024)
11-14517688-T-C		not specified	Uncertain significance (Aug 16, 2021)
11-14519038-G-A			Uncertain significance (Nov 13, 2020)
11-14519042-CTAAAAG-C			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMA1	protein_coding	protein_coding	ENST00000418988	10	149853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0175	120825	2	213	121040	0.000889

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	79	142	0.555	0.00000724	1747
Missense in Polyphen		9	41.399	0.2174		548
Synonymous	-0.535	52	47.3	1.10	0.00000235	514
Loss of Function	3.56	1	16.7	0.0598	8.57e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00955	0.00943
Ashkenazi Jewish	0.00491	0.00480
East Asian	0.0000567	0.0000562
Finnish	0.00	0.00
European (Non-Finnish)	0.0000927	0.0000899
Middle Eastern	0.0000567	0.0000562
South Asian	0.00	0.00
Other	0.000174	0.000170

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;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: 0.506

Intolerance Scores

• loftool: 0.282
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.943
• hipred: N
• hipred_score: 0.374
• ghis: 0.634

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psma1

Gene ontology

• Biological process: immune system process;proteasomal protein catabolic process;proteasomal ubiquitin-independent protein catabolic process;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: proteasome complex;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;proteasome core complex;polysome;proteasome core complex, alpha-subunit complex;extracellular exosome
• Molecular function: RNA binding;endopeptidase activity;threonine-type endopeptidase activity;protein binding