COG7 (component of oligomeric golgi complex 7)

Gene

• Entrez ID: 91949
• Gene name: Component of oligomeric golgi complex 7
• Gene symbol: COG7
• Synonyms (NCBI Gene): CDG2E
• Chromosome: 16
• Chromosome location: 16p12.2
• Summary: The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the co

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs115605801	T>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs149163316	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs201446992	A>G	Likely-pathogenic	Splice donor variant
rs370447404	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs548129734	G>A,C	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs769603091	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs797044712	->A	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1057519232	->A	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1555493029	C>A	Pathogenic	Splice acceptor variant
rs1555496968	T>C	Pathogenic	Intron variant
rs1555497568	T>G	Pathogenic	Intron variant, 5 prime UTR variant
rs1555497604	A>G	Likely-pathogenic	Missense variant, initiator codon variant, non coding transcript variant, 5 prime UTR variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT518040	hsa-miR-4438	PAR-CLIP	23446348
MIRT518039	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT518038	hsa-miR-5095	PAR-CLIP	23446348
MIRT518037	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT518036	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT518040	hsa-miR-4438	PAR-CLIP	23446348
MIRT518039	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT518038	hsa-miR-5095	PAR-CLIP	23446348
MIRT518037	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT518036	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT902312	hsa-miR-1244	CLIP-seq
MIRT902313	hsa-miR-128	CLIP-seq
MIRT902314	hsa-miR-1305	CLIP-seq
MIRT902315	hsa-miR-199a-3p	CLIP-seq
MIRT902316	hsa-miR-199b-3p	CLIP-seq
MIRT902317	hsa-miR-27a	CLIP-seq
MIRT902318	hsa-miR-27b	CLIP-seq
MIRT902319	hsa-miR-3129-5p	CLIP-seq
MIRT902320	hsa-miR-33a	CLIP-seq
MIRT902321	hsa-miR-33b	CLIP-seq
MIRT902322	hsa-miR-498	CLIP-seq
MIRT902323	hsa-miR-513a-5p	CLIP-seq
MIRT902312	hsa-miR-1244	CLIP-seq
MIRT902313	hsa-miR-128	CLIP-seq
MIRT902315	hsa-miR-199a-3p	CLIP-seq
MIRT902316	hsa-miR-199b-3p	CLIP-seq
MIRT902317	hsa-miR-27a	CLIP-seq
MIRT902318	hsa-miR-27b	CLIP-seq
MIRT902319	hsa-miR-3129-5p	CLIP-seq
MIRT902320	hsa-miR-33a	CLIP-seq
MIRT902321	hsa-miR-33b	CLIP-seq
MIRT902323	hsa-miR-513a-5p	CLIP-seq
MIRT902312	hsa-miR-1244	CLIP-seq
MIRT902314	hsa-miR-1305	CLIP-seq
MIRT2203424	hsa-miR-3156-5p	CLIP-seq
MIRT902322	hsa-miR-498	CLIP-seq
MIRT2506396	hsa-miR-2053	CLIP-seq
MIRT2506397	hsa-miR-3149	CLIP-seq
MIRT2506398	hsa-miR-3194-3p	CLIP-seq
MIRT2506399	hsa-miR-4775	CLIP-seq
MIRT2506400	hsa-miR-4797-5p	CLIP-seq
MIRT2506401	hsa-miR-569	CLIP-seq
MIRT2506402	hsa-miR-590-3p	CLIP-seq
MIRT2506403	hsa-miR-720	CLIP-seq

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, 19536132, 21903422, 25416956, 26871637, 31515488, 32296183, 33961781
GO:0005730	Component	Nucleolus	IDA
GO:0005794	Component	Golgi apparatus	IDA	11980916
GO:0005794	Component	Golgi apparatus	IEA
GO:0006486	Process	Protein glycosylation	IMP	15107842, 16420527
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006886	Process	Intracellular protein transport	IMP	15107842
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IMP	16420527, 16510524
GO:0007030	Process	Golgi organization	IBA
GO:0007030	Process	Golgi organization	IMP	27066481
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0017119	Component	Golgi transport complex	IBA
GO:0017119	Component	Golgi transport complex	IDA	15047703
GO:0017119	Component	Golgi transport complex	IEA
GO:0017119	Component	Golgi transport complex	NAS	27066481
GO:0032588	Component	Trans-Golgi network membrane	TAS
GO:0033365	Process	Protein localization to organelle	IMP	16420527
GO:0034067	Process	Protein localization to Golgi apparatus	IMP	16510524
GO:0050821	Process	Protein stabilization	IMP	16420527, 16510524
GO:0070085	Process	Glycosylation	IMP	27066481

Other IDs

• MIM: 606978
• HGNC: 18622
• e!Ensembl: ENSG00000168434

Protein

• UniProt ID: P83436
• Protein name: Conserved oligomeric Golgi complex subunit 7 (COG complex subunit 7) (Component of oligomeric Golgi complex 7)
• Protein function: Required for normal Golgi function.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF10191	COG7	2 → 767	Golgi complex component 7 (COG7)	Family

• Sequence:

  MDFSKFLADDFDVKEWINAAFRAGSKEAASGKADGHAATLVMKLQLFIQEVNHAVEETSH
  QALQNMPKVLRDVEALKQEASFLKEQMILVKEDIKKFEQDTSQSMQVLVEIDQVKSRMQL
  AAESLQEADKWSTLSADIEETFKTQDIAVISAKLTGMQNSLMMLVDTPDYSEKCVHLEAL
  KNRLEALASPQIVAAFTSQAVDQSKVFVKVFTEIDRMPQLLAYYYKCHKVQLLAAWQELC
  QSDLSLDRQLTGLYDALLGAWHTQIQWATQVFQKPHEVVMVLLIQTLGALMPSLPSCLSN
  GVERAGPEQELTRLLEFYDATAHFAKGLEMALLPHLHEHNLVKVTELVDAVYDPYKPYQL
  KYGDMEESNLLIQMSAVPLEHGEVIDCVQELSHSVNKLFGLASAAVDRCVRFTNGLGTCG
  LLSALKSLFAKYVSDFTSTLQSIRKKCKLDHIPPNSLFQEDWTAFQNSIRIIATCGELLR
  HCGDFEQQLANRILSTAGKYLSDSCSPRSLAGFQESILTDKKNSAKNPWQEYNYLQKDNP
  AEYASLMEILYTLKEKGSSNHNLLAAPRAALTRLNQQAHQLAFDSVFLRIKQQLLLISKM
  DSWNTAGIGETLTDELPAFSLTPLEYISNIGQYIMSLPLNLEPFVTQEDSALELALHAGK
  LPFPPEQGDELPELDNMADNWLGSIARATMQTYCDAILQIPELSPHSAKQLATDIDYLIN
  VMDALGLQPSRTLQHIVTLLKTRPEDYRQVSKGLPRRLATTVATMRSVNY

• Sequence length: 770

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
COG7 congenital disorder of glycosylation	Likely pathogenic; Pathogenic	rs768615420, rs1036433681, rs1051352713, rs945537370, rs1555497568, rs1555496968, rs797044712, rs2506642569, rs2506592783, rs2506584752, rs2506639430, rs1963666828, rs780863769, rs2506567482, rs1963459711, rs1963314793, rs2506619664, rs1555493029, rs1555497604	RCV001821868 RCV001821869 RCV001815626 RCV003089136 RCV000003835 RCV000003836 RCV001852190 RCV002805642 RCV002828325 RCV002857191 RCV003029764 RCV003059190 RCV003233294 RCV003504081 RCV003609309 RCV003610188 RCV003610189 RCV000662352 RCV000662353	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG7-CDG	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG7-CONGENITAL DISORDER OF GLYCOSYLATION	—	ClinGen, GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COG7-related disorder	Benign; Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation	Uncertain significance; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION TYPE 2E	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIE	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
COG7-CDG	Congenital Disorder Of Glycosylation	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 2E	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	15107842, 17356545, 19577670, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 2E	Congenital disorder of glycosylation	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 2E	Congenital disorder of glycosylation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	16510524, 23228021	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	21431621, 23228021, 23865579, 28883096		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Heart Defects	Congenital heart defects	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Nonbullous Ichthyosiform Erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydronephrosis	Hydronephrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrichosis	HYPERTRICHOSIS	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	17356545		★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nervous System Diseases	Nervous system disease	Pubtator	19690088	Associate	★☆☆☆☆ Found in Text Mining only
Neurogenic Urinary Bladder	Neurogenic Urinary Bladder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Profound global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only