PSMD13

proteasome 26S subunit, non-ATPase 13, the group of Proteasome

Basic information

Region (hg38): 11:236965-252984

Links

ENSG00000185627 ∙ NCBI:5719 ∙ OMIM:603481 ∙ HGNC:9558 ∙ Uniprot:Q9UNM6 ∙ 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 PSMD13 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD13 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		1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in PSMD13

This is a list of pathogenic ClinVar variants found in the PSMD13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-237030-C-T		PSMD13-related disorder	Likely benign (Feb 21, 2019)
11-244431-A-C		not specified	Uncertain significance (Oct 06, 2021)
11-244462-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-244741-G-A		not specified	Uncertain significance (May 24, 2023)
11-244754-T-C		not specified	Uncertain significance (Feb 27, 2024)
11-247283-A-G		not specified	Uncertain significance (Nov 18, 2023)
11-247341-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-247345-C-G		not specified	Uncertain significance (Nov 19, 2021)
11-247387-C-T		not specified	Likely benign (Jul 12, 2023)
11-247412-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-248972-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-251914-C-T		not specified	Uncertain significance (Jun 03, 2022)
11-252524-G-A		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD13	protein_coding	protein_coding	ENST00000431206	11	16438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000987	125475	0	1	125476	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.634	188	214	0.878	0.0000117	2478
Missense in Polyphen		30	54.059	0.55495		673
Synonymous	0.472	78	83.5	0.934	0.00000475	717
Loss of Function	4.40	1	24.5	0.0409	0.00000142	254

LoF frequencies by population

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

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;Neutrophil degranulation;B cell receptor signaling;Post-translational protein modification;Metabolism of proteins;DroToll-like;Notch;Hedgehog;Innate Immune System;Immune System;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;TNFalpha;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Intolerance Scores

• loftool: 0.0938
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.04

Haploinsufficiency Scores

• pHI: 0.933
• hipred: Y
• hipred_score: 0.748
• ghis: 0.540

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd13

Zebrafish Information Network

• Gene name: psmd13
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;meiosis I;protein deubiquitination;proteasome assembly;neutrophil degranulation;post-translational protein modification
• Cellular component: proteasome complex;extracellular region;nucleus;nucleoplasm;cytosol;proteasome regulatory particle;proteasome regulatory particle, lid subcomplex;membrane;proteasome accessory complex;secretory granule lumen;ficolin-1-rich granule lumen
• Molecular function: structural molecule activity