COPB1
COPI coat complex subunit beta 1, the group of Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|COPI coat complex
Basic information
Region (hg38): 11:14443440-14500027
Previous symbols: [ "COPB" ]
Links
Phenotypes
GenCC
Source:
- Baralle-Macken syndrome (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Baralle-Macken syndrome | AD | Allergy/Immunology/Infectious | Among other features, individuals have been described with immunodeficiency, and awareness may allow preventive measures and early and aggressive treatment of infections | Allergy/Immunology/Infectious; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Ophthalmologic | 33632302 |
ClinVar
This is a list of variants' phenotypes submitted to
- Immunodeficiency;Microcephaly;Cataract;Intellectual disability, severe (1 variants)
- Baralle-Macken syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPB1 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 | 8 | |||||
| missense | 40 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 1 | 0 | 40 | 8 | 1 |
Variants in COPB1
This is a list of pathogenic ClinVar variants found in the COPB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-14458612-T-G | not specified | Uncertain significance (Sep 22, 2023) | ||
| 11-14458653-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 11-14460272-T-C | not specified | Uncertain significance (May 21, 2024) | ||
| 11-14460281-T-C | not specified | Uncertain significance (May 30, 2024) | ||
| 11-14461277-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 11-14464921-A-C | not specified | Uncertain significance (Jul 06, 2021) | ||
| 11-14464956-C-T | Baralle-Macken syndrome | Uncertain significance (Jul 03, 2023) | ||
| 11-14464983-G-A | not specified | Uncertain significance (May 10, 2022) | ||
| 11-14464997-A-G | not specified | Uncertain significance (Nov 27, 2023) | ||
| 11-14465005-C-T | Likely benign (Jun 01, 2022) | |||
| 11-14466307-A-G | Likely benign (Oct 01, 2022) | |||
| 11-14466378-C-T | not specified | Uncertain significance (Jun 11, 2024) | ||
| 11-14468724-T-C | Short stature;Failure to thrive;Delayed speech and language development;Skeletal dysplasia | Pathogenic (Apr 20, 2022) | ||
| 11-14468728-T-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 11-14469353-C-T | not specified | Uncertain significance (May 13, 2024) | ||
| 11-14469357-T-G | not specified | Uncertain significance (Sep 17, 2021) | ||
| 11-14469389-A-T | not specified | Uncertain significance (Jul 27, 2021) | ||
| 11-14469406-T-C | not specified | Uncertain significance (Nov 29, 2021) | ||
| 11-14469480-A-G | Likely benign (May 01, 2023) | |||
| 11-14474533-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 11-14474554-T-G | not specified | Uncertain significance (Apr 26, 2023) | ||
| 11-14474565-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 11-14474578-A-C | not specified | Uncertain significance (Apr 05, 2023) | ||
| 11-14474581-A-C | Microcephaly;Cataract;Intellectual disability, severe;Immunodeficiency • Baralle-Macken syndrome | Pathogenic (Mar 14, 2024) | ||
| 11-14474596-G-A | not specified | Uncertain significance (Jun 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COPB1 | protein_coding | protein_coding | ENST00000249923 | 21 | 56588 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000644 | 125733 | 0 | 4 | 125737 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.38 | 354 | 505 | 0.702 | 0.0000255 | 6276 |
| Missense in Polyphen | 127 | 225.84 | 0.56234 | 2785 | ||
| Synonymous | 0.764 | 162 | 175 | 0.927 | 0.00000883 | 1810 |
| Loss of Function | 5.85 | 5 | 49.4 | 0.101 | 0.00000279 | 614 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000547 | 0.0000544 |
| Finnish | 0.0000465 | 0.0000462 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000547 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. Plays a functional role in facilitating the transport of kappa- type opioid receptor mRNAs into axons and enhances translation of these proteins. Required for limiting lipid storage in lipid droplets. Involved in lipid homeostasis by regulating the presence of perilipin family members PLIN2 and PLIN3 at the lipid droplet surface and promoting the association of adipocyte surface triglyceride lipase (PNPLA2) with the lipid droplet to mediate lipolysis (By similarity). Involved in the Golgi disassembly and reassembly processes during cell cycle. Involved in autophagy by playing a role in early endosome function. Plays a role in organellar compartmentalization of secretory compartments including endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC), Golgi, trans-Golgi network (TGN) and recycling endosomes, and in biosynthetic transport of CAV1. Promotes degradation of Nef cellular targets CD4 and MHC class I antigens by facilitating their trafficking to degradative compartments. {ECO:0000250, ECO:0000269|PubMed:18385291, ECO:0000269|PubMed:18725938, ECO:0000269|PubMed:19364919, ECO:0000269|PubMed:20056612}.;
- Pathway
- Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Glycosphingolipid biosynthesis - neolactoseries;Post-translational protein modification;Metabolism of proteins;Tyrosine metabolism;Proteoglycan biosynthesis;Androgen and estrogen biosynthesis and metabolism;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Purine metabolism;Innate Immune System;Immune System;Pyrimidine metabolism;Glycosphingolipid metabolism;Phosphatidylinositol phosphate metabolism;Prostaglandin formation from arachidonate;Methionine and cysteine metabolism;Aminosugars metabolism;Galactose metabolism;O-Glycan biosynthesis;C21-steroid hormone biosynthesis and metabolism;Glycerophospholipid metabolism;Vitamin B9 (folate) metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;N-Glycan biosynthesis;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- 0.0571
- rvis_EVS
- -1.11
- rvis_percentile_EVS
- 6.72
Haploinsufficiency Scores
- pHI
- 0.524
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.684
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.756
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Copb1
- Phenotype
Zebrafish Information Network
- Gene name
- copb1
- Affected structure
- muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- structure
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;viral process;neutrophil degranulation
- Cellular component
- Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;Golgi-associated vesicle;cytosol;plasma membrane;membrane;COPI vesicle coat;transport vesicle;secretory granule membrane;intracellular membrane-bounded organelle;tertiary granule membrane;ficolin-1-rich granule membrane
- Molecular function
- structural molecule activity;protein binding