COPA
Basic information
Region (hg38): 1:160288594-160343566
Links
Phenotypes
GenCC
Source:
- autoimmune interstitial lung disease-arthritis syndrome (Strong), mode of inheritance: AD
- autoimmune interstitial lung disease-arthritis syndrome (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Autoinflammation and autoimmunity, systemic, with immune dysregulation | AD | Allergy/Immunology/Infectious | Individuals may manifest with multisystemic autoimmune conditions, as well as recurrent infections, and medical management has been described such that early awareness may allow prompt treatment | Allergy/Immunology/Infectious | 25894502; 38175705 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 variants)
- Autoimmune interstitial lung disease-arthritis syndrome (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPA 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 | 146 | 15 | 167 | |||
missense | 252 | 46 | 10 | 315 | ||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 7 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 27 | 42 | 5 | 74 | ||
non coding | 17 | 133 | 20 | 171 | ||
Total | 4 | 4 | 289 | 325 | 45 |
Variants in COPA
This is a list of pathogenic ClinVar variants found in the COPA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-160290161-C-T | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Dec 05, 2024) | ||
1-160290168-G-A | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Mar 01, 2023) | ||
1-160290169-C-T | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Mar 16, 2019) | ||
1-160290176-CTG-C | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Aug 17, 2024) | ||
1-160290179-A-G | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Aug 23, 2022) | ||
1-160290180-T-C | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Jan 03, 2024) | ||
1-160290182-C-T | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Oct 17, 2022) | ||
1-160290224-A-G | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Feb 19, 2024) | ||
1-160290224-AAAAC-A | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Apr 15, 2023) | ||
1-160290236-G-A | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Sep 11, 2023) | ||
1-160290236-G-C | Autoimmune interstitial lung disease-arthritis syndrome | Benign (Oct 30, 2024) | ||
1-160290443-T-C | not specified | Benign (Nov 12, 2023) | ||
1-160290481-AC-GA | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Dec 20, 2022) | ||
1-160290483-A-G | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Mar 01, 2024) | ||
1-160290492-T-C | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Jul 27, 2023) | ||
1-160290497-T-C | Uncertain significance (Sep 18, 2024) | |||
1-160290508-A-G | Uncertain significance (Dec 06, 2023) | |||
1-160290511-T-C | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Jun 16, 2024) | ||
1-160290542-C-A | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Feb 02, 2024) | ||
1-160290548-G-A | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Nov 19, 2024) | ||
1-160290549-T-G | Autoimmune interstitial lung disease-arthritis syndrome | Likely benign (Mar 01, 2024) | ||
1-160290555-C-A | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Sep 01, 2021) | ||
1-160290566-G-C | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Dec 25, 2023) | ||
1-160290574-C-T | Autoimmune interstitial lung disease-arthritis syndrome • Inborn genetic diseases | Conflicting classifications of pathogenicity (Sep 06, 2024) | ||
1-160290575-G-A | Autoimmune interstitial lung disease-arthritis syndrome | Uncertain significance (Apr 10, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
COPA | protein_coding | protein_coding | ENST00000368069 | 33 | 54128 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.48e-10 | 125742 | 0 | 6 | 125748 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.56 | 441 | 707 | 0.624 | 0.0000395 | 8082 |
Missense in Polyphen | 63 | 165.65 | 0.38031 | 1804 | ||
Synonymous | 2.55 | 197 | 248 | 0.794 | 0.0000122 | 2395 |
Loss of Function | 7.64 | 3 | 73.9 | 0.0406 | 0.00000404 | 822 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000129 | 0.000129 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000949 | 0.00000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
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 (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Autoimmune interstitial lung, joint, and kidney disease (AILJK) [MIM:616414]: An autoimmune disease characterized by inflammatory arthritis, interstitial lung disease, and immune complex-mediated renal disease. {ECO:0000269|PubMed:25894502}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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;adp-ribosylation factor;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;Arf1 pathway;COPI-dependent Golgi-to-ER retrograde traffic;C-MYB transcription factor network;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
- 0.184
Intolerance Scores
- loftool
- 0.312
- rvis_EVS
- -0.98
- rvis_percentile_EVS
- 8.85
Haploinsufficiency Scores
- pHI
- 0.129
- hipred
- Y
- hipred_score
- 0.689
- ghis
- 0.630
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.687
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Copa
- Phenotype
Zebrafish Information Network
- Gene name
- copa
- 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;regulation of signaling receptor activity;pancreatic juice secretion
- Cellular component
- Golgi membrane;extracellular space;cytoplasm;endoplasmic reticulum membrane;cytosol;membrane;COPI vesicle coat;transport vesicle;extracellular exosome
- Molecular function
- hormone activity;structural molecule activity