PSMD4

proteasome 26S subunit ubiquitin receptor, non-ATPase 4, the group of Proteasome

Basic information

Region (hg38): 1:151254709-151267479

Links

ENSG00000159352 ∙ NCBI:5710 ∙ OMIM:601648 ∙ HGNC:9561 ∙ Uniprot:P55036 ∙ 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 PSMD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD4 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						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	1

Variants in PSMD4

This is a list of pathogenic ClinVar variants found in the PSMD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151262176-G-T		not specified	Uncertain significance (Dec 17, 2023)
1-151262258-C-G		not specified	Uncertain significance (Jul 30, 2024)
1-151262258-C-T		not specified	Uncertain significance (Sep 26, 2024)
1-151262261-A-G		not specified	Uncertain significance (May 20, 2024)
1-151262297-G-T		not specified	Uncertain significance (Feb 12, 2025)
1-151264022-G-C			Benign/Likely benign (May 01, 2023)
1-151264872-G-A		not specified	Uncertain significance (May 09, 2022)
1-151265202-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-151265431-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-151265462-T-G		not specified	Uncertain significance (Mar 11, 2024)
1-151265478-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-151265538-G-A		not specified	Uncertain significance (Feb 07, 2025)
1-151266037-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-151266059-G-A		not specified	Uncertain significance (Jan 10, 2025)
1-151266098-C-T		not specified	Uncertain significance (Dec 09, 2024)
1-151266099-G-A			Benign (Dec 31, 2019)
1-151266319-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-151266320-C-A		not specified	Uncertain significance (Jul 06, 2021)
1-151266337-A-G		not specified	Uncertain significance (Apr 13, 2022)
1-151266358-C-T		not specified	Uncertain significance (Feb 18, 2025)
1-151266361-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-151266526-G-A		not specified	Uncertain significance (Dec 04, 2024)
1-151266564-A-G		not specified	Uncertain significance (Jan 18, 2025)
1-151267337-G-C		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD4	protein_coding	protein_coding	ENST00000368884	10	12777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00274	125742	0	2	125744	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	113	218	0.518	0.0000124	2476
Missense in Polyphen		28	73.024	0.38343		884
Synonymous	0.597	73	79.8	0.915	0.00000444	735
Loss of Function	3.86	0	17.3	0.00	8.89e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
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 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. PSMD4 acts as an ubiquitin receptor subunit through ubiquitin-interacting motifs and selects ubiquitin-conjugates for destruction. Displays a preferred selectivity for longer polyubiquitin chains. {ECO:0000269|PubMed:1317798, ECO:0000269|PubMed:15826667}.
• Pathway: Epstein-Barr virus infection - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;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;ID;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Intolerance Scores

• loftool: 0.0498
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.965
• hipred: Y
• hipred_score: 0.726
• ghis: 0.636

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

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

Mouse Genome Informatics

• Gene name: Psmd4
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; embryo phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;proteasome assembly;post-translational protein modification
• Cellular component: proteasome complex;nucleus;nucleoplasm;cytosol;proteasome regulatory particle, base subcomplex;proteasome accessory complex
• Molecular function: RNA binding;protein binding;polyubiquitin modification-dependent protein binding;identical protein binding