COPS6
COP9 signalosome subunit 6, the group of JAMM/MPN+ metallopeptidase family|COP9 signalosome
Basic information
Region (hg38): 7:100088969-100092187
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 COPS6 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 | 9 | |||||
| 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 | 0 | 0 |
Variants in COPS6
This is a list of pathogenic ClinVar variants found in the COPS6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-100089010-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
| 7-100089043-G-A | not specified | Uncertain significance (Aug 01, 2022) | ||
| 7-100089353-T-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 7-100089355-A-C | not specified | Uncertain significance (Jul 12, 2023) | ||
| 7-100089732-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 7-100090476-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 7-100091134-A-C | Malignant tumor of prostate | Uncertain significance (-) | ||
| 7-100091291-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 7-100091312-G-A | not specified | Uncertain significance (Mar 26, 2024) | ||
| 7-100091459-A-G | not specified | Uncertain significance (Mar 01, 2023) | ||
| 7-100091682-G-A | not specified | Uncertain significance (Sep 22, 2021) | ||
| 7-100091692-C-G | not specified | Uncertain significance (Mar 07, 2023) | ||
| 7-100091721-G-A | not specified | Uncertain significance (Oct 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COPS6 | protein_coding | protein_coding | ENST00000303904 | 10 | 3247 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.987 | 0.0133 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 101 | 191 | 0.530 | 0.0000108 | 2160 |
| Missense in Polyphen | 28 | 74.335 | 0.37667 | 812 | ||
| Synonymous | -1.04 | 86 | 74.6 | 1.15 | 0.00000474 | 620 |
| Loss of Function | 3.65 | 1 | 17.5 | 0.0573 | 8.85e-7 | 200 |
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) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. Has some glucocorticoid receptor- responsive activity. Stabilizes COP1 through reducing COP1 auto- ubiquitination and decelerating COP1 turnover rate, hence regulates the ubiquitination of COP1 targets. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:21625211, ECO:0000269|PubMed:9535219}.;
- Pathway
- Nucleotide-binding Oligomerization Domain (NOD) pathway;DNA Repair;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Clathrin-mediated endocytosis;Neddylation;Cargo recognition for clathrin-mediated endocytosis;DNA Damage Recognition in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Formation of TC-NER Pre-Incision Complex;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- loftool
- 0.247
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.463
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.645
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cops6
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- cops6
- Affected structure
- pharyngeal arch cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- protein deneddylation;nucleotide-excision repair, DNA damage recognition;transcription-coupled nucleotide-excision repair;viral process;post-translational protein modification
- Cellular component
- nucleoplasm;cytosol;COP9 signalosome
- Molecular function
- protein binding