COG1 (component of oligomeric golgi complex 1)

Gene

• Entrez ID: 9382
• Gene name: Component of oligomeric golgi complex 1
• Gene symbol: COG1
• Synonyms (NCBI Gene): CDG2G, LDLB
• Chromosome: 17
• Chromosome location: 17q25.1
• Summary: The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. It is thought that this protein is required for steps in the normal medial and trans Golgi-ass

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs185592690	C>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs201263432	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs747606976	C>-,CC,CCC	Pathogenic	Coding sequence variant, frameshift variant
rs1555725221	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555725363	->CCTGGTAATAAAATGAC	Likely-pathogenic	Stop gained, inframe insertion, coding sequence variant
rs1568296260	G>A	Pathogenic	Intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT045480	hsa-miR-149-5p	CLASH	23622248
MIRT042242	hsa-miR-484	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	NAS	27066481
GO:0000139	Component	Golgi membrane	TAS
GO:0000301	Process	Retrograde transport, vesicle recycling within Golgi	IMP	27066481
GO:0005515	Function	Protein binding	IPI	15047703, 33961781
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	11980916
GO:0005794	Component	Golgi apparatus	IEA
GO:0006891	Process	Intra-Golgi vesicle-mediated transport	IEA
GO:0006891	Process	Intra-Golgi vesicle-mediated transport	NAS	11980916
GO:0007030	Process	Golgi organization	IMP	27066481
GO:0007030	Process	Golgi organization	NAS	11980916
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0017119	Component	Golgi transport complex	IDA	15047703
GO:0017119	Component	Golgi transport complex	IEA
GO:0017119	Component	Golgi transport complex	NAS	11980916, 27066481
GO:0032588	Component	Trans-Golgi network membrane	TAS
GO:0070085	Process	Glycosylation	IMP	27066481

Other IDs

• MIM: 606973
• HGNC: 6545
• e!Ensembl: ENSG00000166685

Protein

• UniProt ID: Q8WTW3
• Protein name: Conserved oligomeric Golgi complex subunit 1 (COG complex subunit 1) (Component of oligomeric Golgi complex 1)
• Protein function: Required for normal Golgi function.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08700	Vps51	13 → 93		Family

• Sequence:

  MATAATSPALKRLDLRDPAALFETHGAEEIRGLERQVRAEIEHKKEELRQMVGERYRDLI
  EAADTIGQMRRCAVGLVDAVKATDQYCARLRQAGSAAPRPPRAQQPQQPSQEKFYSMAAQ
  IKLLLEIPEKIWSSMEASQCLHATQLYLLCCHLHSLLQLDSSSSRYSPVLSRFPILIRQV
  AAASHFRSTILHESKMLLKCQGVSDQAVAEALCSIMLLEESSPRQALTDFLLARKATIQK
  LLNQPHHGAGIKAQICSLVELLATTLKQAHALFYTLPEGLLPDPALPCGLLFSTLETITG
  QHPAGKGTGVLQEEMKLCSWFKHLPASIVEFQPTLRTLAHPISQEYLKDTLQKWIHMCNE
  DIKNGITNLLMYVKSMKGLAGIRDAMWELLTNESTNHSWDVLCRRLLEKPLLFWEDMMQQ
  LFLDRLQTLTKEGFDSISSSSKELLVSALQELESSTSNSPSNKHIHFEYNMSLFLWSESP
  NDLPSDAAWVSVANRGQFASSGLSMKAQAISPCVQNFCSALDSKLKVKLDDLLAYLPSDD
  SSLPKDVSPTQAKSSAFDRYADAGTVQEMLRTQSVACIKHIVDCIRAELQSIEEGVQGQQ
  DALNSAKLHSVLFMARLCQSLGELCPHLKQCILGKSESSEKPAREFRALRKQGKVKTQEI
  IPTQAKWQEVKEVLLQQSVMGYQVWSSAVVKVLIHGFTQSLLLDDAGSVLATATSWDELE
  IQEEAESGSSVTSKIRLPAQPSWYVQSFLFSLCQEINRVGGHALPKVTLQEMLKSCMVQV
  VAAYEKLSEEKQIKKEGAFPVTQNRALQLLYDLRYLNIVLTAKGDEVKSGRSKPDSRIEK
  VTDHLEALIDPFDLDVFTPHLNSNLHRLVQRTSVLFGLVTGTENQLAPRSSTFNSQEPHN
  ILPLASSQIRFGLLPLSMTSTRKAKSTRNIETKAQVVPPARSTAGDPTVPGSLFRQLVSE
  EDNTSAPSLFKLGWLSSMTK

• Sequence length: 980

Pathways

Reactome:

COPI-mediated anterograde transport
Intra-Golgi traffic
Retrograde transport at the Trans-Golgi-Network

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
COG1 congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs2145097019, rs1568296260, rs773341615, rs758521897, rs2061375797, rs2061310130, rs771513054, rs2511081455, rs747606976, rs1227032564	RCV002022121 RCV000003840 RCV002650955 RCV002801336 RCV002858696 RCV002876073 RCV003008412 RCV003610058 RCV000990056 RCV001202775	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephrotic syndrome	Pathogenic	rs1568296260	RCV001849253	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG1-CDG	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG1-CONGENITAL DISORDER OF GLYCOSYLATION	—	ClinGen, GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG1-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE 2G	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIG	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Burkitt Lymphoma	Burkitt`s Lymphoma	BEFREE	24504345		★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	34539936	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebrocostomandibular Syndrome	Cerebrocostomandibular Syndrome	BEFREE	19008299		★☆☆☆☆ Found in Text Mining only
Cerebrocostomandibular-Like Syndrome	Cerebrocostomandibular-Like Syndrome	BEFREE	19008299		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	24504345		★☆☆☆☆ Found in Text Mining only
COG1-CDG	Congenital Disorder Of Glycosylation	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type 2G	Congenital disorder of glycosylation	Pubtator	16537452	Inhibit	★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type 2G	Congenital disorder of glycosylation	Pubtator	16537452	Associate	★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type II	Congenital disorder of glycosylation	Pubtator	16537452	Associate	★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation, type 2G	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	19008299, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation, type 2G	Congenital disorder of glycosylation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation, type 2G	Congenital disorder of glycosylation	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ii	Congenital disorder of glycosylation	BEFREE	16537452		★☆☆☆☆ Found in Text Mining only
Congenital fusion of ribs	Rib fusion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital kyphoscoliosis	Congenital kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Defect of vertebral segmentation	Abnormal spinal segmentation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	37488513	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hematologic Neoplasms	Hematologic Neoplasms	BEFREE	24504345		★☆☆☆☆ Found in Text Mining only
Hydronephrosis	Hydronephrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★☆☆☆☆ Found in Text Mining only
Idiopathic pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Moderate intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nervous System Diseases	Nervous system disease	Pubtator	19690088	Associate	★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pierre Robin Syndrome	Pierre-Robin Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rhizomelia	Rhizomelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Temporal cortical atrophy	Temporal cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only