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.

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.

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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in PSMD9

This is a list of pathogenic ClinVar variants found in the PSMD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121888894-C-T		not specified	Uncertain significance (Apr 01, 2024)
12-121888899-G-A		not specified	Uncertain significance (Mar 17, 2023)
12-121894748-A-G		not specified	Likely benign (Jul 12, 2022)
12-121894749-T-C		not specified	Uncertain significance (Feb 28, 2024)
12-121894799-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-121894817-C-T		not specified	Uncertain significance (Aug 20, 2024)
12-121899694-A-G		not specified	Uncertain significance (Mar 07, 2024)
12-121899702-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-121899718-C-T		not specified	Uncertain significance (Mar 27, 2023)
12-121899721-G-A		not specified	Uncertain significance (Jul 16, 2024)
12-121899757-G-T		not specified	Uncertain significance (Apr 20, 2023)
12-121899816-A-G		not specified	Uncertain significance (Nov 15, 2024)
12-121899825-G-A		not specified	Uncertain significance (May 12, 2024)
12-121899835-C-T		not specified	Uncertain significance (May 14, 2024)
12-121903064-A-C		not specified	Uncertain significance (Jun 30, 2023)
12-121915858-G-T		not specified	Uncertain significance (Feb 28, 2023)
12-121915859-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-121915871-A-C		not specified	Uncertain significance (Aug 12, 2024)
12-121915872-C-T		not specified	Uncertain significance (Nov 19, 2024)
12-121915881-G-A		not specified	Uncertain significance (Mar 20, 2024)
12-121915885-G-C		not specified	Likely benign (May 05, 2023)
12-121915929-G-C		not specified	Uncertain significance (Apr 07, 2023)

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