COPS2
COP9 signalosome subunit 2, the group of COP9 signalosome
Basic information
Region (hg38): 15:49106068-49155661
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 COPS2 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 | 2 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 9 | 2 | 1 |
Variants in COPS2
This is a list of pathogenic ClinVar variants found in the COPS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-49127966-A-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 15-49128023-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 15-49128026-G-C | not specified | Uncertain significance (Mar 28, 2023) | ||
| 15-49128027-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 15-49128083-C-A | not specified | Uncertain significance (May 14, 2024) | ||
| 15-49128693-A-G | Likely benign (Jul 03, 2018) | |||
| 15-49133795-T-C | not specified | Uncertain significance (Dec 04, 2023) | ||
| 15-49133803-C-T | Benign (Dec 31, 2019) | |||
| 15-49133964-A-G | not specified | Uncertain significance (Nov 13, 2023) | ||
| 15-49137205-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 15-49144992-T-A | Likely benign (Jul 21, 2018) | |||
| 15-49155536-C-T | not specified | Uncertain significance (Nov 22, 2023) | ||
| 15-49155569-T-A | not specified | Uncertain significance (Dec 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COPS2 | protein_coding | protein_coding | ENST00000299259 | 13 | 49591 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000281 | 125586 | 0 | 1 | 125587 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.13 | 48 | 221 | 0.217 | 0.0000104 | 3011 |
| Missense in Polyphen | 1 | 38.989 | 0.025648 | 579 | ||
| Synonymous | 0.752 | 69 | 77.4 | 0.891 | 0.00000386 | 749 |
| Loss of Function | 5.04 | 0 | 29.6 | 0.00 | 0.00000168 | 366 |
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 | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Essential 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/ICSBP, 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. Involved in early stage of neuronal differentiation via its interaction with NIF3L1. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:9535219}.;
- 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
- 0.156
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.807
- hipred
- Y
- hipred_score
- 0.755
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.873
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Cops2
- Phenotype
- cellular phenotype; reproductive system 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); embryo phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;protein deneddylation;nucleotide-excision repair, DNA damage recognition;transcription-coupled nucleotide-excision repair;transcription by RNA polymerase II;protein phosphorylation;signal transduction;cell population proliferation;neuron differentiation;skeletal muscle cell differentiation;post-translational protein modification;negative regulation of transcription, DNA-templated;negative regulation of nucleic acid-templated transcription
- Cellular component
- nucleoplasm;cytoplasm;cytosol;COP9 signalosome
- Molecular function
- transcription corepressor activity;protein binding