PSMD7
proteasome 26S subunit, non-ATPase 7, the group of Proteasome|JAMM/MPN+ metallopeptidase family
Basic information
Region (hg38): 16:74296814-74306288
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 2 | |||||
| missense | 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) | ||
| 16-74302225-T-C | not specified | Uncertain significance (Jul 27, 2024) | ||
| 16-74302263-G-T | not specified | Uncertain significance (Aug 04, 2024) | ||
| 16-74304303-G-A | not specified | Uncertain significance (Nov 24, 2024) | ||
| 16-74304340-C-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 16-74305335-A-T | not specified | Uncertain significance (Aug 05, 2024) | ||
| 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) | ||
| 16-74305645-G-A | not specified | Uncertain significance (Aug 10, 2024) | ||
| 16-74305672-A-G | not specified | Uncertain significance (Jan 17, 2023) | ||
| 16-74305684-A-G | not specified | Uncertain significance (Nov 15, 2024) | ||
| 16-74305694-G-T | not specified | Uncertain significance (Aug 02, 2022) |
GnomAD
Source:
| 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:
- 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