COPB2 (coat protein complex I subunit beta 2)

Gene

• Entrez ID: 9276
• Gene name: Coat protein complex I subunit beta 2
• Gene symbol: COPB2
• Synonyms (NCBI Gene): MCPH19, OPDD, beta'-COP
• Chromosome: 3
• Chromosome location: 3q23
• Summary: The Golgi coatomer complex (see MIM 601924) constitutes the coat of nonclathrin-coated vesicles and is essential for Golgi budding and vesicular trafficking. It consists of 7 protein subunits, including COPB2.[supplied by OMIM, Jul 2002]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1229568621	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT036883	hsa-miR-877-3p	CLASH	23622248
MIRT694310	hsa-miR-8066	HITS-CLIP	23313552
MIRT694309	hsa-miR-101-5p	HITS-CLIP	23313552
MIRT694308	hsa-miR-300	HITS-CLIP	23313552
MIRT694307	hsa-miR-381-3p	HITS-CLIP	23313552
MIRT694306	hsa-miR-4666a-3p	HITS-CLIP	23313552
MIRT694305	hsa-miR-549a	HITS-CLIP	23313552
MIRT694304	hsa-miR-520d-5p	HITS-CLIP	23313552
MIRT694303	hsa-miR-524-5p	HITS-CLIP	23313552
MIRT694302	hsa-let-7a-3p	HITS-CLIP	23313552
MIRT694301	hsa-let-7b-3p	HITS-CLIP	23313552
MIRT694300	hsa-let-7f-1-3p	HITS-CLIP	23313552
MIRT694299	hsa-miR-98-3p	HITS-CLIP	23313552
MIRT694298	hsa-miR-4789-5p	HITS-CLIP	23313552
MIRT694297	hsa-let-7f-2-3p	HITS-CLIP	23313552
MIRT694296	hsa-miR-1185-1-3p	HITS-CLIP	23313552
MIRT694295	hsa-miR-1185-2-3p	HITS-CLIP	23313552
MIRT694294	hsa-miR-8070	HITS-CLIP	23313552
MIRT694293	hsa-miR-510-3p	HITS-CLIP	23313552
MIRT440912	hsa-miR-376a-5p	HITS-CLIP	24374217
MIRT440912	hsa-miR-376a-5p	HITS-CLIP	24374217
MIRT733137	hsa-miR-335-3p	FACS, Luciferase reporter assay, qRT-PCR, Western blotting	32004259
MIRT694310	hsa-miR-8066	HITS-CLIP	23313552
MIRT694309	hsa-miR-101-5p	HITS-CLIP	23313552
MIRT694308	hsa-miR-300	HITS-CLIP	23313552
MIRT694307	hsa-miR-381-3p	HITS-CLIP	23313552
MIRT694306	hsa-miR-4666a-3p	HITS-CLIP	23313552
MIRT694305	hsa-miR-549a	HITS-CLIP	23313552
MIRT694304	hsa-miR-520d-5p	HITS-CLIP	23313552
MIRT694303	hsa-miR-524-5p	HITS-CLIP	23313552
MIRT694302	hsa-let-7a-3p	HITS-CLIP	23313552
MIRT694301	hsa-let-7b-3p	HITS-CLIP	23313552
MIRT694300	hsa-let-7f-1-3p	HITS-CLIP	23313552
MIRT694299	hsa-miR-98-3p	HITS-CLIP	23313552
MIRT694298	hsa-miR-4789-5p	HITS-CLIP	23313552
MIRT694297	hsa-let-7f-2-3p	HITS-CLIP	23313552
MIRT694296	hsa-miR-1185-1-3p	HITS-CLIP	23313552
MIRT694295	hsa-miR-1185-2-3p	HITS-CLIP	23313552
MIRT694294	hsa-miR-8070	HITS-CLIP	23313552
MIRT694293	hsa-miR-510-3p	HITS-CLIP	23313552
MIRT1967962	hsa-miR-128	CLIP-seq
MIRT1967963	hsa-miR-369-3p	CLIP-seq
MIRT1967964	hsa-miR-374a	CLIP-seq
MIRT1967965	hsa-miR-374b	CLIP-seq
MIRT1967966	hsa-miR-3908	CLIP-seq
MIRT1967967	hsa-miR-3942-5p	CLIP-seq
MIRT1967968	hsa-miR-410	CLIP-seq
MIRT1967969	hsa-miR-4318	CLIP-seq
MIRT1967970	hsa-miR-4703-5p	CLIP-seq
MIRT1967971	hsa-miR-4766-3p	CLIP-seq
MIRT1967972	hsa-miR-4778-3p	CLIP-seq
MIRT1967973	hsa-miR-570	CLIP-seq
MIRT2203871	hsa-miR-330-3p	CLIP-seq
MIRT2203872	hsa-miR-3545-5p	CLIP-seq
MIRT2203873	hsa-miR-3688-3p	CLIP-seq
MIRT1967963	hsa-miR-369-3p	CLIP-seq
MIRT1967964	hsa-miR-374a	CLIP-seq
MIRT1967965	hsa-miR-374b	CLIP-seq
MIRT1967966	hsa-miR-3908	CLIP-seq
MIRT1967967	hsa-miR-3942-5p	CLIP-seq
MIRT2203874	hsa-miR-3978	CLIP-seq
MIRT1967968	hsa-miR-410	CLIP-seq
MIRT2203875	hsa-miR-4310	CLIP-seq
MIRT1967969	hsa-miR-4318	CLIP-seq
MIRT2203876	hsa-miR-4422	CLIP-seq
MIRT2203877	hsa-miR-4694-3p	CLIP-seq
MIRT1967970	hsa-miR-4703-5p	CLIP-seq
MIRT1967971	hsa-miR-4766-3p	CLIP-seq
MIRT2203878	hsa-miR-522	CLIP-seq
MIRT2203879	hsa-miR-548c-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0005198	Function	Structural molecule activity	IEA
GO:0005515	Function	Protein binding	IPI	21988832, 25609649, 34504087, 35140242
GO:0005737	Component	Cytoplasm	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006886	Process	Intracellular protein transport	IBA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	IBA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IMP	34450031
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	TAS	11030615
GO:0006891	Process	Intra-Golgi vesicle-mediated transport	IBA
GO:0006891	Process	Intra-Golgi vesicle-mediated transport	IDA	8335000
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0030117	Component	Membrane coat	IEA
GO:0030126	Component	COPI vesicle coat	IBA
GO:0030126	Component	COPI vesicle coat	IDA	8335000, 14729954
GO:0030133	Component	Transport vesicle	TAS
GO:0030663	Component	COPI-coated vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA

Other IDs

• MIM: 606990
• HGNC: 2232
• e!Ensembl: ENSG00000184432

Protein

• UniProt ID: P35606
• Protein name: Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP) (p102)
• Protein 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 ne
• PDB: 8D30, 8D41
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00400	WD40	89 → 127	WD domain, G-beta repeat	Repeat
  PF00400	WD40	132 → 171	WD domain, G-beta repeat	Repeat
  PF00400	WD40	175 → 215	WD domain, G-beta repeat	Repeat
  PF00400	WD40	219 → 257	WD domain, G-beta repeat	Repeat
  PF04053	Coatomer_WDAD	319 → 763	Coatomer WD associated region	Family

• Sequence:

  MPLRLDIKRKLTARSDRVKSVDLHPTEPWMLASLYNGSVCVWNHETQTLVKTFEVCDLPV
  RAAKFVARKNWVVTGADDMQIRVFNYNTLERVHMFEAHSDYIRCIAVHPTQPFILTSSDD
  MLIKLWDWDKKWSCSQVFEGHTHYVMQIVINPKDNNQFASASLDRTIKVWQLGSSSPNFT
  LEGHEKGVNCIDYYSGGDKPYLISGADDRLVKIWDYQNKTCVQTLEGHAQNVSCASFHPE
  LPIIITGSEDGTVRIWHSSTYRLESTLNYGMERVWCVASLRGSNNVALGYDEGSIIVKLG
  REEPAMSMDANGKIIWAKHSEVQQANLKAMGDAEIKDGERLPLAVKDMGSCEIYPQTIQH
  NPNGRFVVVCGDGEYIIYTAMALRNKSFGSAQEFAWAHDSSEYAIRESNSIVKIFKNFKE
  KKSFKPDFGAESIYGGFLLGVRSVNGLAFYDWDNTELIRRIEIQPKHIFWSDSGELVCIA
  TEESFFILKYLSEKVLAAQETHEGVTEDGIEDAFEVLGEIQEIVKTGLWVGDCFIYTSSV
  NRLNYYVGGEIVTIAHLDRTMYLLGYIPKDNRLYLGDKELNIISYSLLVSVLEYQTAVMR
  RDFSMADKVLPTIPKEQRTRVAHFLEKQGFKQQALTVSTDPEHRFELALQLGELKIAYQL
  AVEAESEQKWKQLAELAISKCQFGLAQECLHHAQDYGGLLLLATASGNANMVNKLAEGAE
  RDGKNNVAFMSYFLQGKVDACLELLIRTGRLPEAAFLARTYLPSQVSRVVKLWRENLSKV
  NQKAAESLADPTEYENLFPGLKEAFVVEEWVKETHADLWPAKQYPLVTPNEERNVMEEGK
  DFQPSRSTAQQELDGKPASPTPVIVASHTANKEEKSLLELEVDLDNLELEDIDTTDINLD
  EDILDD

• Sequence length: 906

Pathways

Reactome:

COPI-mediated anterograde transport
COPI-dependent Golgi-to-ER retrograde traffic

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Microcephaly 19, primary, autosomal recessive	Pathogenic	rs1229568621	RCV000516154	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteoporosis, childhood- or juvenile-onset, with developmental delay	Pathogenic; Likely pathogenic	rs2107801858, rs2107807701, rs2472899515	RCV002248440 RCV002248441 RCV003142298	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOSOMAL RECESSIVE PRIMARY MICROCEPHALY	—	Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BONE FRAGILITY WITH CONTRACTURES, ARTERIAL RUPTURE, AND DEAFNESS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COPB2-related disorder	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS-PSEUDOGLIOMA SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous cell lung carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	29674272		★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	28087520		★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	28087520		★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Primary Microcephaly	Microcephaly	ORPHANET_DG	29036432		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive primary microcephaly	Microcephaly	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	31119859	Stimulate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	31926110	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33824874, 40191726	Associate	★☆☆☆☆ Found in Text Mining only
Central visual impairment	Central Visual Impairment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	29509246		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	29509246	Associate	★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	34676262	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	31631786		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	28415695, 33211699	Associate	★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathy	Diabetic Nephropathy	BEFREE	30150789		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Familial lichen amyloidosis	Lichen amyloidosis	BEFREE	29129687		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	31710183	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glomerulosclerosis (disorder)	Glomerulosclerosis	BEFREE	30150789		★☆☆☆☆ Found in Text Mining only
Graves Ophthalmopathy	Graves ophthalmopathy	Pubtator	38536014	Stimulate	★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Juvenile osteoporosis	Osteoporosis	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	34676262	Associate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31119859	Stimulate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	27986120, 29129687		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	30968146		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28415695, 30968146		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	29036432		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
MICROCEPHALY 19, PRIMARY, AUTOSOMAL RECESSIVE	Microcephaly	UNIPROT_DG	29036432		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	BEFREE	21326860		★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	Pubtator	21326860	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28415695, 29674272, 30968146		★☆☆☆☆ Found in Text Mining only
Neuronal heterotopia	Neuronal Heterotopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	28415695	Associate	★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	27986120, 29129687		★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	BEFREE	10953354		★☆☆☆☆ Found in Text Mining only
Scleroderma	Scleroderma	BEFREE	10702668		★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	35715770	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	30968146		★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	10702668		★☆☆☆☆ Found in Text Mining only
Unilateral agenesis of kidney	Renal aplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	34676262	Associate	★☆☆☆☆ Found in Text Mining only
Vesico-Ureteral Reflux	Vesicoureteral Reflux	HPO_DG			★☆☆☆☆ Found in Text Mining only
Vitamin D Deficiency	Vitamin d deficiency	Pubtator	23527013	Associate	★☆☆☆☆ Found in Text Mining only