PSMB1
proteasome 20S subunit beta 1, the group of Proteasome
Basic information
Region (hg38): 6:170535120-170553307
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with microcephaly, hypotonia, and absent language (Limited), mode of inheritance: AR
- neurodevelopmental disorder with microcephaly, hypotonia, and absent language (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurodevelopmental disorder with microcephaly, hypotonia, and absent language | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic | 32129449 |
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 PSMB1 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 | 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 | 0 | 0 |
Variants in PSMB1
This is a list of pathogenic ClinVar variants found in the PSMB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-170537323-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 6-170543693-C-G | not specified | Uncertain significance (Jul 05, 2023) | ||
| 6-170543726-T-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 6-170543727-A-G | Neurodevelopmental disorder with microcephaly, hypotonia, and absent language | Pathogenic (Sep 15, 2022) | ||
| 6-170549009-T-C | not specified | Uncertain significance (Dec 13, 2021) | ||
| 6-170549027-T-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 6-170549033-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 6-170549036-T-C | not specified | Uncertain significance (Dec 03, 2021) | ||
| 6-170549081-G-C | not specified | Uncertain significance (Jun 18, 2024) | ||
| 6-170549100-T-C | not specified | Uncertain significance (Aug 01, 2022) | ||
| 6-170549112-T-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 6-170553175-G-A | not specified | Uncertain significance (May 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PSMB1 | protein_coding | protein_coding | ENST00000262193 | 6 | 18225 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0300 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.875 | 109 | 138 | 0.790 | 0.00000737 | 1554 |
| Missense in Polyphen | 18 | 45.186 | 0.39835 | 494 | ||
| Synonymous | -0.374 | 58 | 54.5 | 1.06 | 0.00000308 | 486 |
| Loss of Function | 3.05 | 0 | 10.8 | 0.00 | 5.20e-7 | 139 |
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). {ECO:0000269|PubMed:15244466, ECO:0000269|PubMed:27176742, ECO:0000269|PubMed:8610016}.;
- Pathway
- Proteasome - Homo sapiens (human);Proteasome Degradation;TLR NFkB;Neutrophil degranulation;proteasome complex;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;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.335
Intolerance Scores
- loftool
- 0.137
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.56
Haploinsufficiency Scores
- pHI
- 0.922
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.576
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
- Psmb1
- Phenotype
Zebrafish Information Network
- Gene name
- psmb1
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
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;neutrophil degranulation;post-translational protein modification
- Cellular component
- proteasome complex;extracellular region;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome core complex;proteasome core complex, beta-subunit complex;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
- Molecular function
- endopeptidase activity;threonine-type endopeptidase activity;protein binding