PSMD1

proteasome 26S subunit, non-ATPase 1, the group of Proteasome|Armadillo like helical domain containing

Basic information

Region (hg38): 2:231056845-231173116

Links

ENSG00000173692 ∙ NCBI:5707 ∙ OMIM:617842 ∙ HGNC:9554 ∙ Uniprot:Q99460 ∙ 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 PSMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD1 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	2
missense			19			19
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			22	2	7	31
Total	0	0	42	3	8

Variants in PSMD1

This is a list of pathogenic ClinVar variants found in the PSMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-231062311-G-A		not specified	Uncertain significance (Aug 21, 2023)
2-231062637-A-G		not specified	Uncertain significance (Jun 22, 2024)
2-231062673-T-C		not specified	Uncertain significance (Feb 28, 2024)
2-231067019-C-T		not specified	Uncertain significance (Apr 16, 2021)
2-231067086-T-C		not specified	Uncertain significance (Apr 23, 2024)
2-231070068-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-231070095-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-231070101-A-T		not specified	Uncertain significance (Jan 31, 2024)
2-231070166-C-G		not specified	Uncertain significance (Jun 13, 2024)
2-231072269-A-G			Likely benign (Apr 01, 2023)
2-231072309-C-A		not specified	Uncertain significance (Sep 13, 2023)
2-231077092-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-231077134-C-T		not specified	Uncertain significance (Apr 28, 2023)
2-231078656-C-T			Benign (Aug 20, 2018)
2-231080303-G-A		not specified	Uncertain significance (Jun 22, 2021)
2-231083735-C-T		not specified	Uncertain significance (Mar 28, 2022)
2-231108553-T-G		not specified	Uncertain significance (Jun 02, 2023)
2-231108575-G-T		not specified	Uncertain significance (Jul 06, 2021)
2-231108649-G-A			Benign (Jun 18, 2018)
2-231108702-T-C			Benign (Jul 15, 2018)
2-231108710-C-T		not specified	Likely benign (Dec 07, 2023)
2-231108720-T-A		not specified	Uncertain significance (Oct 06, 2023)
2-231108732-G-A		not specified	Likely benign (Jun 29, 2023)
2-231108978-C-A		not specified	Uncertain significance (Oct 17, 2023)
2-231109008-C-T		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD1	protein_coding	protein_coding	ENST00000308696	24	115964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.12e-7	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.70	271	505	0.537	0.0000254	6279
Missense in Polyphen		43	143.1	0.30049		1705
Synonymous	0.594	170	180	0.944	0.00000960	1788
Loss of Function	6.50	2	53.2	0.0376	0.00000290	652

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000923	0.0000923
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000552	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.0787
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.948
• hipred: Y
• hipred_score: 0.839
• ghis: 0.620

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• 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: Psmd1

Gene ontology

• Biological process: protein deubiquitination;regulation of protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;neutrophil degranulation;post-translational protein modification;regulation of catalytic activity
• Cellular component: proteasome complex;extracellular region;nucleus;nucleoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, base subcomplex;membrane;proteasome accessory complex;proteasome storage granule;azurophil granule lumen
• Molecular function: endopeptidase activity;protein binding;enzyme regulator activity;ubiquitin protein ligase binding