PSMB5
proteasome 20S subunit beta 5, the group of Proteasome
Basic information
Region (hg38): 14:23016543-23035230
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 PSMB5 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 | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in PSMB5
This is a list of pathogenic ClinVar variants found in the PSMB5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-23026165-C-T | not specified | Uncertain significance (May 22, 2023) | ||
| 14-23026166-G-A | not specified | Uncertain significance (Nov 22, 2022) | ||
| 14-23026279-C-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 14-23026285-T-C | not specified | Uncertain significance (Mar 20, 2024) | ||
| 14-23026292-C-T | not specified | Uncertain significance (Apr 21, 2022) | ||
| 14-23026365-G-A | not specified | Likely benign (Nov 18, 2023) | ||
| 14-23033380-T-C | not specified | Uncertain significance (Jan 24, 2024) | ||
| 14-23033419-T-G | not specified | Uncertain significance (May 20, 2024) | ||
| 14-23033599-T-C | Uncertain significance (Apr 01, 2020) | |||
| 14-23033653-C-A | not specified | Uncertain significance (May 14, 2024) | ||
| 14-23033667-T-C | not specified | Uncertain significance (Sep 12, 2023) | ||
| 14-23033671-G-C | not specified | Uncertain significance (Aug 01, 2022) | ||
| 14-23034803-G-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 14-23034835-C-A | not specified | Uncertain significance (Oct 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PSMB5 | protein_coding | protein_coding | ENST00000361611 | 3 | 18688 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.959 | 0.0410 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 123 | 160 | 0.769 | 0.00000928 | 1676 |
| Missense in Polyphen | 35 | 68.255 | 0.51278 | 731 | ||
| Synonymous | 0.270 | 61 | 63.7 | 0.957 | 0.00000334 | 579 |
| Loss of Function | 2.93 | 0 | 9.98 | 0.00 | 6.51e-7 | 108 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the 20S core proteasome complex involved in the proteolytic degradation of most intracellular proteins. This complex plays numerous essential roles within the cell by associating with different regulatory particles. Associated with two 19S regulatory particles, forms the 26S proteasome and thus participates in the ATP-dependent degradation of ubiquitinated proteins. The 26S proteasome plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins that could impair cellular functions, and by removing proteins whose functions are no longer required. Associated with the PA200 or PA28, the 20S proteasome mediates ubiquitin-independent protein degradation. This type of proteolysis is required in several pathways including spermatogenesis (20S-PA200 complex) or generation of a subset of MHC class I-presented antigenic peptides (20S-PA28 complex). Within the 20S core complex, PSMB5 displays a chymotrypsin-like activity. {ECO:0000269|PubMed:15244466, ECO:0000269|PubMed:18502982, ECO:0000269|PubMed:18565852, ECO:0000269|PubMed:27176742, ECO:0000269|PubMed:8610016}.;
- Pathway
- Proteasome - Homo sapiens (human);Proteasome Degradation;TLR NFkB;proteasome complex;antigen processing and presentation;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;TNFalpha;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.354
Intolerance Scores
- loftool
- 0.294
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.862
- hipred
- Y
- hipred_score
- 0.840
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Psmb5
- Phenotype
Gene ontology
- Biological process
- proteolysis;response to oxidative stress;proteasomal protein catabolic process;proteasomal ubiquitin-independent protein catabolic process;viral process;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
- Cellular component
- proteasome complex;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;proteasome core complex;proteasome core complex, beta-subunit complex;extracellular exosome
- Molecular function
- endopeptidase activity;threonine-type endopeptidase activity;protein binding;peptidase activity