PSMD9

proteasome 26S subunit, non-ATPase 9, the group of Proteasome|PDZ domain containing

Basic information

Region (hg38): 12:121888732-121918297

Links

ENSG00000110801 ∙ NCBI:5715 ∙ OMIM:603146 ∙ HGNC:9567 ∙ Uniprot:O00233 ∙ 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 PSMD9 gene.

• not_specified (38 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002813.7. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			36	4		40
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	40	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD9	protein_coding	protein_coding	ENST00000541212	6	29567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000486	0.425	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.505	124	141	0.880	0.00000819	1454
Missense in Polyphen		33	49.813	0.66247		502
Synonymous	0.389	52	55.7	0.934	0.00000326	423
Loss of Function	0.510	9	10.8	0.833	4.68e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000808	0.0000703
Middle Eastern	0.000118	0.000109
South Asian	0.000164	0.000163
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). During the base subcomplex assembly is part of an intermediate PSMD9:PSMC6:PSMC3 module, also known as modulator trimer complex; PSMD9 is released during the further base assembly process. {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: 0.145

Intolerance Scores

• loftool: 0.870
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.951

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd9

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;positive regulation of insulin secretion;post-translational protein modification;positive regulation of transcription, DNA-templated;negative regulation of insulin secretion;proteasome regulatory particle assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, base subcomplex
• Molecular function: transcription coactivator activity;protein binding;bHLH transcription factor binding