COPG1

COPI coat complex subunit gamma 1, the group of MicroRNA protein coding host genes|Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|COPI coat complex

Basic information

Region (hg38): 3:129249606-129277773

Previous symbols: [ "COPG" ]

Links

ENSG00000181789 ∙ NCBI:22820 ∙ OMIM:615525 ∙ HGNC:2236 ∙ Uniprot:Q9Y678 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-severe combined immunodeficiency due to COPG1 deficiency (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 128	AR	Allergy/Immunology/Infectious	Individuals have recurrent infections, including respiratory infections, and awareness may allow preventative measures and early and aggressive treatment of infections	Allergy/Immunology/Infectious	33529166

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COPG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPG1 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	5	4	10
missense			64		1	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					7	7
Total	0	0	65	5	12

Variants in COPG1

This is a list of pathogenic ClinVar variants found in the COPG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129249723-T-C		not specified	Uncertain significance (Dec 07, 2023)
3-129252270-T-C		not specified	Benign (Jan 24, 2024)
3-129252285-G-A		not specified	Uncertain significance (May 24, 2024)
3-129252287-G-A		not specified	Uncertain significance (Mar 15, 2024)
3-129252302-C-T		not specified	Uncertain significance (Apr 07, 2022)
3-129252353-A-C		not specified	Uncertain significance (Nov 29, 2023)
3-129252630-A-T		not specified	Uncertain significance (Jun 16, 2023)
3-129252635-G-C		not specified	Uncertain significance (May 28, 2024)
3-129252642-C-T		not specified	Uncertain significance (Nov 17, 2022)
3-129252643-G-A			Likely benign (Jul 01, 2023)
3-129252885-C-T		not specified	Uncertain significance (May 17, 2023)
3-129252889-G-A			Uncertain significance (Mar 01, 2023)
3-129252904-C-T		not specified	Uncertain significance (Jan 22, 2025)
3-129252908-C-T			Benign (Feb 27, 2018)
3-129252924-A-C		not specified	Uncertain significance (Jul 17, 2023)
3-129254710-C-T			Likely benign (Aug 01, 2023)
3-129254714-G-C		not specified	Uncertain significance (Dec 20, 2023)
3-129254986-G-T		not specified	Uncertain significance (Mar 02, 2023)
3-129255046-G-T		not specified	Uncertain significance (Feb 25, 2025)
3-129255049-T-A		not specified	Uncertain significance (Dec 05, 2022)
3-129255135-A-C		not specified	Benign (Jan 24, 2024)
3-129256124-G-T		not specified	Uncertain significance (Dec 11, 2024)
3-129257476-G-A		not specified	Uncertain significance (Dec 30, 2024)
3-129257532-G-A		not specified	Uncertain significance (Nov 22, 2023)
3-129257548-C-T		not specified	Uncertain significance (Oct 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COPG1	protein_coding	protein_coding	ENST00000314797	24	28166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.175	0.825	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	400	535	0.748	0.0000320	5759
Missense in Polyphen		118	196.86	0.5994		2060
Synonymous	0.793	190	204	0.929	0.0000126	1686
Loss of Function	4.77	11	45.9	0.240	0.00000221	553

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. Required for limiting lipid storage in lipid droplets. Involved in lipid homeostasis by regulating the presence of perilipin family members PLIN2 and PLIN3 at the lipid droplet surface and promoting the association of adipocyte triglyceride lipase (PNPLA2) with the lipid droplet surface to mediate lipolysis (By similarity). {ECO:0000250, ECO:0000269|PubMed:20674546}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Glycosphingolipid biosynthesis - neolactoseries;Post-translational protein modification;Metabolism of proteins;Tyrosine metabolism;Proteoglycan biosynthesis;Androgen and estrogen biosynthesis and metabolism;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Purine metabolism;Pyrimidine metabolism;Glycosphingolipid metabolism;Phosphatidylinositol phosphate metabolism;Prostaglandin formation from arachidonate;Methionine and cysteine metabolism;Aminosugars metabolism;Galactose metabolism;O-Glycan biosynthesis;C21-steroid hormone biosynthesis and metabolism;Glycerophospholipid metabolism;Vitamin B9 (folate) metabolism;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;N-Glycan biosynthesis;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.717
• ghis: 0.529

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Copg1
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

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;protein secretion;establishment of Golgi localization;organelle transport along microtubule
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;membrane;COPI vesicle coat;transport vesicle
• Molecular function: structural molecule activity;protein binding