PSMC5

proteasome 26S subunit, ATPase 5, the group of Proteasome|AAA ATPases

Basic information

Region (hg38): 17:63827151-63832026

Links

ENSG00000087191 ∙ NCBI:5705 ∙ OMIM:601681 ∙ HGNC:9552 ∙ Uniprot:P62195 ∙ 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 PSMC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMC5 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					2	2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	6	0	3

Variants in PSMC5

This is a list of pathogenic ClinVar variants found in the PSMC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63828156-A-C		not specified	Uncertain significance (Feb 16, 2023)
17-63829486-T-C			Benign (Jul 13, 2021)
17-63829511-G-T		not specified	Uncertain significance (Nov 03, 2022)
17-63829958-A-G			Benign (Apr 26, 2019)
17-63830474-C-G		not specified	Uncertain significance (Apr 25, 2022)
17-63830911-C-T			Benign (Jun 14, 2018)
17-63831071-C-T		not specified	Uncertain significance (Nov 14, 2023)
17-63831196-C-T			Benign (Jan 07, 2019)
17-63831418-A-G		not specified	Uncertain significance (Apr 12, 2023)
17-63831926-A-G		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMC5	protein_coding	protein_coding	ENST00000310144	12	4868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.933	0.0669	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.16	59	240	0.245	0.0000139	2639
Missense in Polyphen		12	89.968	0.13338		1040
Synonymous	-0.371	95	90.5	1.05	0.00000493	797
Loss of Function	3.73	3	21.8	0.137	0.00000109	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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. PSMC5 belongs to the heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitinated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. {ECO:0000269|PubMed:1317798}.
• Pathway: Epstein-Barr virus infection - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;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: 0.207

Intolerance Scores

• loftool: 0.141
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.571
• hipred: Y
• hipred_score: 0.831
• ghis: 0.622

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmc5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;protein deubiquitination;negative regulation of programmed cell death;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of RNA polymerase II transcriptional preinitiation complex assembly;modulation of chemical synaptic transmission;positive regulation of inclusion body assembly;positive regulation of proteasomal protein catabolic process
• Cellular component: proteasome complex;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome regulatory particle, base subcomplex;membrane;inclusion body;proteasome accessory complex;cytoplasmic vesicle;nuclear proteasome complex;cytosolic proteasome complex;extracellular exosome;blood microparticle;postsynapse
• Molecular function: protein binding;ATP binding;transcription factor binding;ATPase activity;TBP-class protein binding;thyrotropin-releasing hormone receptor binding;proteasome-activating ATPase activity