PSMD10

proteasome 26S subunit, non-ATPase 10, the group of Ankyrin repeat domain containing|Proteasome

Basic information

Region (hg38): X:108084207-108091549

Links

ENSG00000101843

∙ NCBI:5716 ∙ OMIM:300880 ∙ HGNC:9555 ∙ Uniprot:O75832 ∙ 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 PSMD10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD10 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 clinvar	1 clinvar	2
missense			6 clinvar		1 clinvar	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	2

Variants in PSMD10

This is a list of pathogenic ClinVar variants found in the PSMD10 region.

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

Position	Phenotype	Significance	ClinVar
X-108084978-C-T		Benign (Mar 29, 2018)	726032
X-108085003-A-T	not specified	Uncertain significance (Mar 01, 2024)	3220424
X-108085073-T-G	not specified	Uncertain significance (Jan 08, 2024)	3220423
X-108085108-C-T	not specified	Uncertain significance (Mar 21, 2023)	2527644
X-108087715-G-A		Benign (May 23, 2018)	744170
X-108087791-G-A	not specified	Uncertain significance (Dec 20, 2023)	3220421
X-108087800-T-A	not specified	Uncertain significance (Jun 12, 2023)	2559708
X-108087803-T-C	not specified	Uncertain significance (Jun 28, 2022)	2298437
X-108091512-C-A		Likely benign (Feb 01, 2023)	2661160

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD10	protein_coding	protein_coding	ENST00000217958	5	7412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.501	0.481	125743	3	0	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.883	60	82.6	0.727	0.00000578	1471
Missense in Polyphen		12	26.291	0.45643		486
Synonymous	0.323	30	32.3	0.928	0.00000235	445
Loss of Function	1.91	1	6.07	0.165	3.80e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000721	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.0000721	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as a chaperone during the assembly of the 26S proteasome, specifically of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD10:PSMC4:PSMC5:PAAF1 module which probably assembles with a PSMD5:PSMC2:PSMC1:PSMD2 module. Independently of the proteasome, regulates EGF-induced AKT activation through inhibition of the RHOA/ROCK/PTEN pathway, leading to prolonged AKT activation. Plays an important role in RAS-induced tumorigenesis.;
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: 0.125

Intolerance Scores

loftool: 0.391
rvis_EVS: -0.1
rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

pHI: 0.978
hipred: Y
hipred_score: 0.800
ghis: 0.693

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Psmd10
Phenotype

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;apoptotic process;cytoplasmic sequestering of NF-kappaB;protein deubiquitination;positive regulation of cell growth;positive regulation of protein ubiquitination;negative regulation of NF-kappaB transcription factor activity;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of apoptotic process;negative regulation of MAPK cascade;negative regulation of DNA damage response, signal transduction by p53 class mediator;post-translational protein modification;positive regulation of cyclin-dependent protein serine/threonine kinase activity;proteasome regulatory particle assembly;negative regulation of release of cytochrome c from mitochondria
Cellular component: proteasome complex;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, base subcomplex;intermediate filament cytoskeleton
Molecular function: protein binding;transcription factor binding