COPE
COPI coat complex subunit epsilon, the group of COPI coat complex
Basic information
Region (hg38): 19:18899514-18919387
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 COPE 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 | 18 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 0 | 0 |
Variants in COPE
This is a list of pathogenic ClinVar variants found in the COPE region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-18899715-A-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 19-18899908-T-C | not specified | Uncertain significance (Feb 14, 2024) | ||
| 19-18903297-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 19-18903311-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 19-18904797-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 19-18905577-G-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 19-18905604-G-C | not specified | Uncertain significance (Mar 01, 2024) | ||
| 19-18905618-G-T | not specified | Uncertain significance (Mar 16, 2022) | ||
| 19-18907015-C-G | not specified | Uncertain significance (Jun 28, 2023) | ||
| 19-18907033-C-T | not specified | Uncertain significance (Sep 14, 2023) | ||
| 19-18907102-C-T | not specified | Uncertain significance (Dec 07, 2023) | ||
| 19-18910992-T-C | not specified | Uncertain significance (Aug 03, 2022) | ||
| 19-18911008-G-A | not specified | Uncertain significance (Apr 25, 2023) | ||
| 19-18911031-G-A | not specified | Uncertain significance (May 07, 2024) | ||
| 19-18911049-T-C | not specified | Uncertain significance (Apr 17, 2023) | ||
| 19-18912997-G-A | not specified | Uncertain significance (Aug 17, 2021) | ||
| 19-18913013-C-T | not specified | Uncertain significance (Jan 17, 2023) | ||
| 19-18913025-C-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 19-18919276-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
| 19-18919323-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 19-18919344-G-C | not specified | Uncertain significance (Jun 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COPE | protein_coding | protein_coding | ENST00000262812 | 10 | 19884 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.692 | 0.307 | 125729 | 0 | 9 | 125738 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.285 | 179 | 190 | 0.942 | 0.0000115 | 1986 |
| Missense in Polyphen | 36 | 51.968 | 0.69273 | 626 | ||
| Synonymous | -1.01 | 101 | 88.9 | 1.14 | 0.00000618 | 599 |
| Loss of Function | 3.14 | 3 | 17.0 | 0.177 | 8.07e-7 | 191 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000127 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000272 | 0.0000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000328 | 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. The 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 with 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 (By similarity). {ECO:0000250}.;
- Pathway
- 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;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
- 0.154
Intolerance Scores
- loftool
- 0.571
- rvis_EVS
- 0.07
- rvis_percentile_EVS
- 58.96
Haploinsufficiency Scores
- pHI
- 0.230
- hipred
- Y
- hipred_score
- 0.774
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.937
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cope
- Phenotype
Gene ontology
- Biological process
- endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;protein transport
- Cellular component
- Golgi membrane;nucleoplasm;endoplasmic reticulum membrane;Golgi apparatus;cytosol;COPI vesicle coat;transport vesicle
- Molecular function
- structural molecule activity;protein binding