PSMD2

proteasome 26S subunit ubiquitin receptor, non-ATPase 2, the group of Proteasome|Armadillo like helical domain containing

Basic information

Region (hg38): 3:184299197-184309050

Links

ENSG00000175166 ∙ NCBI:5708 ∙ OMIM:606223 ∙ HGNC:9559 ∙ Uniprot:Q13200 ∙ 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 PSMD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD2 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in PSMD2

This is a list of pathogenic ClinVar variants found in the PSMD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184299345-A-G		not specified	Uncertain significance (Apr 14, 2022)
3-184299353-C-A		not specified	Uncertain significance (Mar 29, 2022)
3-184299376-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-184299384-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-184299906-G-A		not specified	Uncertain significance (Jan 19, 2022)
3-184300334-C-T		not specified	Uncertain significance (Jun 11, 2024)
3-184300412-A-G		not specified	Uncertain significance (May 24, 2023)
3-184300418-G-A		not specified	Uncertain significance (May 02, 2023)
3-184301537-C-T		not specified	Uncertain significance (Dec 12, 2023)
3-184301538-G-A		not specified	Uncertain significance (Dec 28, 2022)
3-184301576-A-G		not specified	Uncertain significance (Jan 04, 2022)
3-184301983-G-T		not specified	Uncertain significance (Jan 16, 2024)
3-184302002-A-G		not specified	Uncertain significance (Jan 17, 2024)
3-184302035-A-T		not specified	Uncertain significance (Aug 04, 2023)
3-184302046-G-A		not specified	Uncertain significance (Apr 13, 2023)
3-184302407-C-G		not specified	Uncertain significance (Jul 08, 2022)
3-184302470-G-A		not specified	Uncertain significance (Jun 05, 2023)
3-184302489-T-C		not specified	Uncertain significance (Jun 02, 2023)
3-184302714-G-A		not specified	Uncertain significance (Dec 20, 2023)
3-184303050-C-G		not specified	Uncertain significance (Mar 31, 2023)
3-184303055-G-C		not specified	Uncertain significance (Apr 07, 2022)
3-184303422-T-A		not specified	Uncertain significance (Feb 13, 2024)
3-184303660-G-T		not specified	Uncertain significance (Oct 26, 2021)
3-184303740-C-G		not specified	Uncertain significance (Feb 14, 2023)
3-184303989-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD2	protein_coding	protein_coding	ENST00000310118	21	10346

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.80e-7	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	308	503	0.613	0.0000278	5901
Missense in Polyphen		86	171.94	0.50016		1921
Synonymous	-0.173	193	190	1.02	0.00000967	1823
Loss of Function	6.17	1	46.3	0.0216	0.00000257	540

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	0.000163	0.000163

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;TNF alpha Signaling Pathway;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: 0.750

Intolerance Scores

• loftool: 0.0309
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.91

Haploinsufficiency Scores

• pHI: 0.949
• hipred: Y
• hipred_score: 0.802
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd2

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;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: endopeptidase activity;protein binding;enzyme regulator activity