COPS7A

COP9 signalosome subunit 7A, the group of COP9 signalosome

Basic information

Region (hg38): 12:6724014-6731875

Links

ENSG00000111652

∙ NCBI:50813 ∙ OMIM:616009 ∙ HGNC:16758 ∙ Uniprot:Q9UBW8 ∙ 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 COPS7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPS7A 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 COPS7A

This is a list of pathogenic ClinVar variants found in the COPS7A region.

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

Position	Phenotype	Significance	ClinVar
12-6724750-C-T	not specified	Uncertain significance (Feb 03, 2022)	2275416
12-6724765-G-A	not specified	Uncertain significance (Jun 10, 2022)	2295183
12-6724772-G-A	not specified	Uncertain significance (Aug 20, 2024)	3496006
12-6724801-A-T	not specified	Uncertain significance (Aug 10, 2021)	2349701
12-6727957-G-A	not specified	Uncertain significance (Jun 28, 2024)	3496004
12-6729310-C-T	not specified	Uncertain significance (Dec 03, 2024)	3496007
12-6729397-C-T	not specified	Uncertain significance (Oct 01, 2024)	3496003
12-6729398-G-A	not specified	Uncertain significance (Feb 28, 2024)	3076282
12-6729410-G-T	not specified	Uncertain significance (Jan 03, 2025)	3076283
12-6730427-T-G	not specified	Uncertain significance (Oct 19, 2024)	3496001
12-6730717-G-T	not specified	Uncertain significance (Aug 01, 2024)	3496005
12-6730786-C-T	not specified	Uncertain significance (Oct 24, 2023)	3076284

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COPS7A	protein_coding	protein_coding	ENST00000543155	7	8135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0436	0.951	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	103	165	0.624	0.0000101	1753
Missense in Polyphen		21	42.935	0.48911		512
Synonymous	-0.319	71	67.7	1.05	0.00000387	589
Loss of Function	2.45	5	15.4	0.326	8.07e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

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, 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: 0.123

Intolerance Scores

loftool: 0.132
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.538
hipred: Y
hipred_score: 0.765
ghis: 0.615

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.920

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cops7a
Phenotype

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