PSMD3

proteasome 26S subunit, non-ATPase 3, the group of Proteasome

Basic information

Region (hg38): 17:39980807-39997959

Previous symbols: [ "TSTA2" ]

Links

ENSG00000108344 ∙ NCBI:5709 ∙ OMIM:617676 ∙ HGNC:9560 ∙ Uniprot:O43242 ∙ 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 PSMD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD3 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	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	1

Variants in PSMD3

This is a list of pathogenic ClinVar variants found in the PSMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39980987-C-T		not specified	Uncertain significance (Apr 08, 2022)
17-39981000-C-T			Likely benign (Mar 01, 2022)
17-39981053-C-T		not specified	Likely benign (Sep 15, 2021)
17-39984298-C-G		not specified	Uncertain significance (Dec 26, 2023)
17-39984352-C-G		not specified	Uncertain significance (Oct 18, 2021)
17-39984392-C-T		not specified	Uncertain significance (Jun 02, 2023)
17-39984393-G-A		not specified	Uncertain significance (Apr 18, 2023)
17-39984429-G-T		not specified	Uncertain significance (Jun 07, 2024)
17-39986627-C-T		not specified	Uncertain significance (May 31, 2022)
17-39986630-C-T		not specified	Uncertain significance (Mar 07, 2023)
17-39986638-C-T		not specified	Uncertain significance (Oct 27, 2022)
17-39986702-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-39986702-G-T		not specified	Uncertain significance (Jul 11, 2023)
17-39988696-C-G		not specified	Uncertain significance (Jun 27, 2022)
17-39988768-A-C		not specified	Uncertain significance (Aug 21, 2023)
17-39988776-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-39988814-G-C			Benign (Dec 31, 2019)
17-39989768-C-T		not specified	Uncertain significance (Nov 18, 2022)
17-39989831-A-G		not specified	Uncertain significance (Nov 23, 2022)
17-39989842-T-C		not specified	Uncertain significance (Oct 05, 2021)
17-39989898-CAAT-C			Likely benign (Mar 01, 2022)
17-39995250-A-G		not specified	Uncertain significance (Apr 12, 2022)
17-39996211-G-C		not specified	Uncertain significance (Jan 02, 2024)
17-39996240-T-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD3	protein_coding	protein_coding	ENST00000264639	12	17164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000330	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	216	333	0.648	0.0000213	3456
Missense in Polyphen		54	110.94	0.48677		1045
Synonymous	0.738	122	133	0.919	0.00000780	1067
Loss of Function	5.00	0	29.1	0.00	0.00000164	318

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)	0.00	0.00
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. {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;proteasome complex;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: 0.299

Intolerance Scores

• loftool: 0.0519
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.947
• hipred: Y
• hipred_score: 0.737
• ghis: 0.570

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd3

Zebrafish Information Network

• Gene name: psmd3
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;regulation of 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, lid subcomplex;membrane;proteasome accessory complex;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: protein binding;enzyme regulator activity