COPS7B

COP9 signalosome subunit 7B, the group of COP9 signalosome

Basic information

Region (hg38): 2:231781671-231809254

Links

ENSG00000144524 ∙ NCBI:64708 ∙ OMIM:616010 ∙ HGNC:16760 ∙ Uniprot:Q9H9Q2 ∙ 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 COPS7B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPS7B 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in COPS7B

This is a list of pathogenic ClinVar variants found in the COPS7B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-231788655-G-A		not specified	Uncertain significance (Nov 05, 2021)
2-231791796-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-231794266-A-T		not specified	Uncertain significance (Mar 03, 2025)
2-231796121-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-231796130-A-C		not specified	Uncertain significance (Feb 07, 2025)
2-231796159-A-T		not specified	Uncertain significance (Mar 25, 2024)
2-231796217-C-G		not specified	Uncertain significance (Jun 06, 2023)
2-231796268-A-C		not specified	Uncertain significance (Dec 19, 2022)
2-231798888-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-231798921-A-G		not specified	Uncertain significance (Feb 27, 2023)
2-231807514-G-C		not specified	Uncertain significance (May 01, 2024)
2-231807517-A-G		not specified	Uncertain significance (Jun 12, 2023)
2-231807536-A-G		not specified	Uncertain significance (Jan 31, 2024)
2-231807549-G-C		not specified	Uncertain significance (Aug 28, 2023)
2-231807598-A-G		not specified	Uncertain significance (Jan 17, 2023)
2-231807614-A-C		not specified	Uncertain significance (Nov 09, 2023)
2-231807638-G-A		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COPS7B	protein_coding	protein_coding	ENST00000350033	6	27583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.601	0.399	125735	0	4	125739	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	108	145	0.746	0.00000794	1704
Missense in Polyphen		23	50.991	0.45106		619
Synonymous	0.274	57	59.7	0.955	0.00000333	523
Loss of Function	2.99	3	15.9	0.189	9.29e-7	168

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)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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, JUN, I-kappa-B-alpha/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}.
• 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: 0.0819

Intolerance Scores

• loftool: 0.622
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.495
• hipred: Y
• hipred_score: 0.673
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cops7b

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