COPS9

COP9 signalosome subunit 9

Basic information

Region (hg38): 2:240126563-240136807

Previous symbols: [ "MYEOV2" ]

Links

ENSG00000172428NCBI:150678OMIM:619349HGNC:21314Uniprot:Q8WXC6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COPS9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPS9 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
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 0 0

Variants in COPS9

This is a list of pathogenic ClinVar variants found in the COPS9 region.

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

Position Type Phenotype Significance ClinVar
2-240129912-T-C not specified Uncertain significance (Aug 13, 2021)2354372

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COPS9protein_codingprotein_codingENST00000307266 510245
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001340.672125739091257480.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2621541451.060.000008411625
Missense in Polyphen55.03450.9931445
Synonymous-0.4846358.31.080.00000366498
Loss of Function0.69356.980.7173.88e-771

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001740.000174
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Isoform 1: 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. Plays a role in cell proliferation. {ECO:0000269|PubMed:26456823}.;

Intolerance Scores

loftool
rvis_EVS
0.51
rvis_percentile_EVS
80.01

Haploinsufficiency Scores

pHI
0.136
hipred
N
hipred_score
0.123
ghis
0.510

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Cops9
Phenotype

Gene ontology

Biological process
positive regulation of cell population proliferation;cellular response to UV
Cellular component
nuclear chromatin;nucleus;nucleoplasm;cytoplasm;COP9 signalosome
Molecular function
protein binding