PSMB6
proteasome 20S subunit beta 6, the group of Proteasome
Basic information
Region (hg38): 17:4796144-4798502
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 PSMB6 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 | 12 | |||||
| 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 | 3 | 0 |
Variants in PSMB6
This is a list of pathogenic ClinVar variants found in the PSMB6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-4796219-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 17-4796731-A-G | not specified | Uncertain significance (Dec 07, 2023) | ||
| 17-4796737-A-G | not specified | Uncertain significance (May 15, 2023) | ||
| 17-4796755-G-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 17-4797476-C-G | not specified | Uncertain significance (Dec 09, 2023) | ||
| 17-4797488-G-A | not specified | Likely benign (Apr 25, 2022) | ||
| 17-4797804-G-C | not specified | Uncertain significance (Nov 08, 2024) | ||
| 17-4798026-G-C | not specified | Uncertain significance (Oct 29, 2024) | ||
| 17-4798028-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 17-4798039-G-A | not specified | Uncertain significance (Aug 10, 2024) | ||
| 17-4798057-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-4798076-C-T | not specified | Uncertain significance (Mar 16, 2024) | ||
| 17-4798109-G-A | not specified | Uncertain significance (Aug 27, 2024) | ||
| 17-4798138-C-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 17-4798396-G-A | not specified | Likely benign (Nov 17, 2023) | ||
| 17-4798399-G-A | not specified | Likely benign (Jul 25, 2023) | ||
| 17-4798403-C-A | not specified | Uncertain significance (Jun 17, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PSMB6 | protein_coding | protein_coding | ENST00000270586 | 6 | 2352 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0158 | 0.961 | 125738 | 0 | 7 | 125745 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.46 | 99 | 149 | 0.664 | 0.00000838 | 1502 |
| Missense in Polyphen | 11 | 44.71 | 0.24603 | 487 | ||
| Synonymous | -0.264 | 58 | 55.5 | 1.04 | 0.00000318 | 500 |
| Loss of Function | 1.99 | 5 | 12.6 | 0.397 | 6.91e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000310 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000165 | 0.000163 |
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, PSMB6 displays a peptidylglutamyl-hydrolizing activity also termed postacidic or caspase-like activity, meaning that the peptides bond hydrolysis occurs directly after acidic residues. {ECO:0000269|PubMed:15244466, 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;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- loftool
- 0.335
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.840
- hipred
- Y
- hipred_score
- 0.754
- ghis
- 0.571
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.884
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Psmb6
- Phenotype
Gene ontology
- Biological process
- 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;cytosol;proteasome core complex;proteasome core complex, beta-subunit complex;extracellular exosome
- Molecular function
- endopeptidase activity;threonine-type endopeptidase activity;cadherin binding