COPS2

COP9 signalosome subunit 2, the group of COP9 signalosome

Basic information

Region (hg38): 15:49106067-49155661

Links

ENSG00000166200 ∙ NCBI:9318 ∙ OMIM:604508 ∙ HGNC:30747 ∙ Uniprot:P61201 ∙ 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 COPS2 gene.

• Inborn genetic diseases (4 variants)
• not provided (3 variants)

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				1	1	2
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	4	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)
15-49128693-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: gnomAD

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: dbNSFP

• 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

• 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