GeneBe

COPS8

COP9 signalosome subunit 8, the group of COP9 signalosome

Basic information

Region (hg38): 2:237085882-237100474

Links

ENSG00000198612 ∙ NCBI:10920 ∙ OMIM:616011 ∙ HGNC:24335 ∙ Uniprot:Q99627 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COPS8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPS8 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
12
clinvar
 12
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 12 0 0

Variants in COPS8

This is a list of pathogenic ClinVar variants found in the COPS8 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-237085987-A-G not specified Uncertain significance (Apr 25, 2022)2344060
2-237086023-G-A not specified Uncertain significance (Feb 03, 2022)2275871
2-237087170-T-C not specified Uncertain significance (Sep 29, 2023)3076288
2-237088627-A-G not specified Uncertain significance (Jan 26, 2022)2273845
2-237088652-C-G not specified Uncertain significance (Dec 13, 2023)3076289
2-237089865-A-C not specified Uncertain significance (Jul 14, 2023)2611728
2-237089903-A-T not specified Uncertain significance (Jun 24, 2022)2295805
2-237094104-C-T not specified Uncertain significance (Mar 17, 2023)2522017
2-237094113-G-A not specified Uncertain significance (Jul 13, 2022)2301489
2-237094114-C-G not specified Uncertain significance (Jun 24, 2022)2215271
2-237094125-C-A not specified Uncertain significance (Jan 31, 2022)2349416
2-237094179-G-A not specified Uncertain significance (Oct 05, 2023)3076290

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COPS8protein_codingprotein_codingENST00000354371 815155
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.7250.275125734031257370.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.919871150.7590.000005701346
Missense in Polyphen1528.0770.53425350
Synonymous0.04374242.40.9910.00000246404
Loss of Function2.82213.00.1545.50e-7155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005550.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.000008850.00000879
Middle Eastern0.00005550.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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/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. {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
0.186

Intolerance Scores

loftool
0.223
rvis_EVS
0.06
rvis_percentile_EVS
58.26

Haploinsufficiency Scores

pHI
0.253
hipred
Y
hipred_score
0.656
ghis
0.604

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.801

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cops8
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; immune system phenotype; growth/size/body region phenotype; cellular phenotype;

Gene ontology

Biological process
protein deneddylation;nucleotide-excision repair, DNA damage recognition;transcription-coupled nucleotide-excision repair;protein phosphorylation;activation of NF-kappaB-inducing kinase activity;negative regulation of cell population proliferation;COP9 signalosome assembly;post-translational protein modification
Cellular component
nucleus;nucleoplasm;cytosol;COP9 signalosome;perinuclear region of cytoplasm;extracellular exosome
Molecular function
protein binding