COPB1

COPI coat complex subunit beta 1, the group of Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|COPI coat complex

Basic information

Region (hg38): 11:14443440-14500027

Previous symbols: [ "COPB" ]

Links

ENSG00000129083

∙ NCBI:1315 ∙ OMIM:600959 ∙ HGNC:2231 ∙ Uniprot:P53618 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Baralle-Macken syndrome (Limited), mode of inheritance: Unknown
Baralle-Macken syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Baralle-Macken syndrome	AD	Allergy/Immunology/Infectious	Among other features, individuals have been described with immunodeficiency, and awareness may allow preventive measures and early and aggressive treatment of infections	Allergy/Immunology/Infectious; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Ophthalmologic	33632302

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COPB1 gene.

not_specified (79 variants)
not_provided (12 variants)
Baralle-Macken_syndrome (6 variants)
Intellectual_disability,_severe (2 variants)
Cataract (2 variants)
Microcephaly (2 variants)
Short_stature (1 variants)
Skeletal_dysplasia (1 variants)
Immunodeficiency (1 variants)
Delayed_speech_and_language_development (1 variants)
Failure_to_thrive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COPB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001144061.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				11 clinvar		11
missense	2 clinvar		78 clinvar	1 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		2 clinvar				2
Total	2	2	78	12	0

Highest pathogenic variant AF is 0.00092306617

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COPB1	protein_coding	protein_coding	ENST00000249923	21	56588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000644	125733	0	4	125737	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.38	354	505	0.702	0.0000255	6276
Missense in Polyphen		127	225.84	0.56234		2785
Synonymous	0.764	162	175	0.927	0.00000883	1810
Loss of Function	5.85	5	49.4	0.101	0.00000279	614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000327	0.0000327
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. Plays a functional role in facilitating the transport of kappa- type opioid receptor mRNAs into axons and enhances translation of these proteins. 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 surface triglyceride lipase (PNPLA2) with the lipid droplet to mediate lipolysis (By similarity). Involved in the Golgi disassembly and reassembly processes during cell cycle. Involved in autophagy by playing a role in early endosome function. Plays a role in organellar compartmentalization of secretory compartments including endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC), Golgi, trans-Golgi network (TGN) and recycling endosomes, and in biosynthetic transport of CAV1. Promotes degradation of Nef cellular targets CD4 and MHC class I antigens by facilitating their trafficking to degradative compartments. {ECO:0000250, ECO:0000269|PubMed:18385291, ECO:0000269|PubMed:18725938, ECO:0000269|PubMed:19364919, ECO:0000269|PubMed:20056612}.;
Pathway: Neutrophil degranulation;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;Innate Immune System;Immune System;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: 0.258

Intolerance Scores

loftool: 0.0571
rvis_EVS: -1.11
rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

pHI: 0.524
hipred: Y
hipred_score: 0.825
ghis: 0.684

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.756

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Copb1
Phenotype

Zebrafish Information Network

Gene name: copb1
Affected structure: muscle cell
Phenotype tag: abnormal
Phenotype quality: structure

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;viral process;neutrophil degranulation
Cellular component: Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;Golgi-associated vesicle;cytosol;plasma membrane;membrane;COPI vesicle coat;transport vesicle;secretory granule membrane;intracellular membrane-bounded organelle;tertiary granule membrane;ficolin-1-rich granule membrane
Molecular function: structural molecule activity;protein binding