PSMD5

proteasome 26S subunit, non-ATPase 5, the group of Proteasome|Armadillo like helical domain containing

Basic information

Region (hg38): 9:120815496-120842951

Links

ENSG00000095261 ∙ NCBI:5711 ∙ OMIM:604452 ∙ HGNC:9563 ∙ Uniprot:Q16401 ∙ 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 PSMD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD5 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						0
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in PSMD5

This is a list of pathogenic ClinVar variants found in the PSMD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-120817982-C-T		not specified	Uncertain significance (Dec 14, 2021)
9-120818046-G-T		not specified	Uncertain significance (Jun 01, 2023)
9-120818054-T-C		not specified	Uncertain significance (May 14, 2024)
9-120818099-A-G		not specified	Uncertain significance (Jun 17, 2024)
9-120820864-T-A		not specified	Uncertain significance (Nov 30, 2021)
9-120821369-G-T		not specified	Uncertain significance (Jan 22, 2024)
9-120821371-G-A		not specified	Uncertain significance (Aug 12, 2021)
9-120821411-G-A		not specified	Likely benign (Mar 29, 2022)
9-120821439-C-T		not specified	Uncertain significance (Dec 13, 2021)
9-120821450-G-A		not specified	Uncertain significance (Mar 06, 2023)
9-120824625-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-120826801-C-A		not specified	Uncertain significance (Dec 12, 2023)
9-120826809-A-G		not specified	Uncertain significance (Jul 09, 2021)
9-120826821-A-C		not specified	Uncertain significance (Mar 16, 2024)
9-120829103-C-T		not specified	Uncertain significance (Mar 25, 2024)
9-120829187-C-T		not specified	Uncertain significance (Jan 26, 2022)
9-120829201-A-C		not specified	Uncertain significance (Jul 06, 2021)
9-120831339-C-A		not specified	Uncertain significance (Nov 18, 2022)
9-120831459-C-G		not specified	Uncertain significance (Jun 14, 2024)
9-120831851-T-G		not specified	Uncertain significance (Mar 27, 2023)
9-120833375-C-G		not specified	Uncertain significance (Dec 07, 2023)
9-120833385-C-A		not specified	Uncertain significance (May 30, 2024)
9-120833386-G-A		not specified	Uncertain significance (Dec 17, 2023)
9-120842789-C-T		not specified	Uncertain significance (Sep 22, 2023)
9-120842818-G-C		not specified	Uncertain significance (Mar 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD5	protein_coding	protein_coding	ENST00000210313	10	27489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.24e-8	0.774	125680	0	66	125746	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.287	255	268	0.951	0.0000135	3235
Missense in Polyphen		138	141.32	0.97651		1791
Synonymous	0.559	93	100	0.929	0.00000475	1020
Loss of Function	1.43	15	22.3	0.674	0.00000108	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000406	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000241	0.000237
Middle Eastern	0.000406	0.000381
South Asian	0.0000681	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a chaperone during the assembly of the 26S proteasome, specifically of the base subcomplex of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD5:PSMC2:PSMC1:PSMD2 module which probably assembles with a PSMD10:PSMC4:PSMC5:PAAF1 module followed by dissociation of PSMD5. {ECO:0000269|PubMed:19412159, ECO:0000269|PubMed:19490896}.
• Pathway: Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;TLR NFkB;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: 0.132

Intolerance Scores

• loftool: 0.721
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.694
• hipred: N
• hipred_score: 0.498
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd5

Gene ontology

• Biological process: protein deubiquitination;post-translational protein modification;proteasome regulatory particle assembly
• Cellular component: proteasome complex;nucleoplasm;cytosol;proteasome regulatory particle, base subcomplex;proteasome accessory complex
• Molecular function: protein binding