PSMD7

proteasome 26S subunit, non-ATPase 7, the group of Proteasome|JAMM/MPN+ metallopeptidase family

Basic information

Region (hg38): 16:74296813-74306288

Links

ENSG00000103035 ∙ NCBI:5713 ∙ OMIM:157970 ∙ HGNC:9565 ∙ Uniprot:P51665 ∙ 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 PSMD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD7 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	2
missense			9			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	9	1	1

Variants in PSMD7

This is a list of pathogenic ClinVar variants found in the PSMD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-74300118-C-T			Likely benign (May 01, 2022)
16-74301101-T-C			Benign (Jul 11, 2018)
16-74301558-G-A		not specified	Uncertain significance (May 24, 2023)
16-74301587-G-A		not specified	Uncertain significance (Jun 05, 2023)
16-74301636-G-A		not specified	Uncertain significance (Sep 26, 2023)
16-74304340-C-A		not specified	Uncertain significance (Dec 19, 2022)
16-74305341-G-T		not specified	Uncertain significance (May 30, 2024)
16-74305369-A-G		not specified	Uncertain significance (Jul 06, 2021)
16-74305375-T-G		not specified	Uncertain significance (Jun 13, 2024)
16-74305379-T-A		not specified	Uncertain significance (Mar 31, 2023)
16-74305422-A-G		not specified	Uncertain significance (Jul 12, 2022)
16-74305672-A-G		not specified	Uncertain significance (Jan 17, 2023)
16-74305694-G-T		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD7	protein_coding	protein_coding	ENST00000219313	7	9514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.264	0.735	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	132	177	0.745	0.00000968	2145
Missense in Polyphen		13	44.315	0.29336		577
Synonymous	-2.03	95	72.9	1.30	0.00000438	590
Loss of Function	2.84	4	16.4	0.243	8.95e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000365	0.0000352
Middle Eastern	0.00	0.00
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)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.456
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.799
• hipred: Y
• hipred_score: 0.765
• ghis: 0.669

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmd7
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: psmd7
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;neutrophil degranulation;post-translational protein modification
• Cellular component: proteasome complex;extracellular region;nucleus;nucleoplasm;cytosol;proteasome regulatory particle;membrane;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: protein binding;protein homodimerization activity