COPZ2

COPI coat complex subunit zeta 2, the group of COPI coat complex|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:48026167-48038030

Links

ENSG00000005243 ∙ NCBI:51226 ∙ OMIM:615526 ∙ HGNC:19356 ∙ Uniprot:Q9P299 ∙ 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 COPZ2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPZ2 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	1		2
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	1	0

Variants in COPZ2

This is a list of pathogenic ClinVar variants found in the COPZ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48032160-C-T		not specified	Uncertain significance (Jun 11, 2021)
17-48037713-C-G		not specified	Likely benign (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COPZ2	protein_coding	protein_coding	ENST00000006101	10	11860

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.46e-8	0.157	124621	0	19	124640	0.0000762

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.117	102	98.7	1.03	0.00000556	1334
Missense in Polyphen		35	32.767	1.0681		348
Synonymous	1.90	24	39.1	0.614	0.00000252	374
Loss of Function	0.0322	11	11.1	0.990	4.72e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000914	0.0000885
Middle Eastern	0.000226	0.000223
South Asian	0.0000327	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. The zeta subunit may be involved in regulating the coat assembly and, hence, the rate of biosynthetic protein transport due to its association-dissociation properties with the coatomer complex (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.322
• hipred: N
• hipred_score: 0.244
• ghis: 0.629

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0610

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Copz2

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cis-Golgi network;cytosol;COPI vesicle coat;transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane