PSMD8

proteasome 26S subunit, non-ATPase 8, the group of Proteasome

Basic information

Region (hg38): 19:38374562-38383850

Links

ENSG00000099341 ∙ NCBI:5714 ∙ OMIM:617844 ∙ HGNC:9566 ∙ Uniprot:P48556 ∙ 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 PSMD8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD8 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			7	1	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	3

Variants in PSMD8

This is a list of pathogenic ClinVar variants found in the PSMD8 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38374657-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-38374773-C-T		not specified	Likely benign (Sep 29, 2022)
19-38374779-G-A			Benign (Feb 08, 2018)
19-38374782-T-G		not specified	Uncertain significance (Mar 20, 2024)
19-38374786-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-38374839-C-G		not specified	Uncertain significance (Jun 07, 2024)
19-38374860-G-C		not specified	Uncertain significance (May 24, 2023)
19-38374945-A-C		not specified	Uncertain significance (Mar 06, 2023)
19-38374946-G-A			Benign (Jun 19, 2017)
19-38376391-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-38376451-A-G		not specified	Uncertain significance (May 12, 2024)
19-38380925-A-G			Benign (Feb 08, 2018)
19-38383286-A-G		not specified	Uncertain significance (Dec 27, 2022)
19-38383367-C-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD8	protein_coding	protein_coding	ENST00000215071	7	9289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0688	0.929	125569	0	14	125583	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	173	192	0.902	0.0000102	2188
Missense in Polyphen		28	50.722	0.55202		641
Synonymous	0.0780	78	78.9	0.989	0.00000421	687
Loss of Function	2.64	5	16.6	0.300	8.96e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000315	0.0000315
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000979	0.0000925
European (Non-Finnish)	0.0000633	0.0000617
Middle Eastern	0.000109	0.000109
South Asian	0.0000372	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. {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;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)

Intolerance Scores

• loftool: 0.273
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.941
• hipred: Y
• hipred_score: 0.806
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd8

Gene ontology

• Biological process: protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: proteasome complex;nucleus;nucleoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, lid subcomplex;proteasome accessory complex