COG7

component of oligomeric golgi complex 7, the group of Components of oligomeric golgi complex

Basic information

Region (hg38): 16:23388493-23453189

Links

ENSG00000168434 ∙ NCBI:91949 ∙ OMIM:606978 ∙ HGNC:18622 ∙ Uniprot:P83436 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• COG7-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• COG7-congenital disorder of glycosylation (Moderate), mode of inheritance: AR
• COG7-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• COG7-congenital disorder of glycosylation (Definitive), mode of inheritance: AR
• COG7-congenital disorder of glycosylation (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIe	AR	Hematologic	Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Biochemical; Cardiovascular; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic	15107842; 17356545; 19577670
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COG7 gene.

• COG7 congenital disorder of glycosylation (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COG7 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			3	111	1	115
missense		2	180	3	1	186
nonsense	2		2			4
start loss	1	1				2
frameshift	1	1	4			6
inframe indel						0
splice donor/acceptor (+/-2bp)	1		2			3
splice region	1	1	9	20		31
non coding			6	81	26	113
Total	5	4	197	195	28

Highest pathogenic variant AF is 0.00000657

Variants in COG7

This is a list of pathogenic ClinVar variants found in the COG7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23388624-CT-C		Congenital disorder of glycosylation	Benign (Aug 06, 2019)
16-23388624-C-CT			Likely benign (Oct 12, 2019)
16-23388642-TG-T		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
16-23388727-C-T		COG7 congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
16-23388733-T-C		COG7 congenital disorder of glycosylation	Benign (Jun 29, 2018)
16-23388873-G-A		COG7 congenital disorder of glycosylation	Benign (Jun 29, 2018)
16-23388890-G-C		COG7 congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
16-23388906-G-A		not specified	Likely benign (Jan 27, 2016)
16-23388911-G-T		not specified • COG7 congenital disorder of glycosylation	Benign/Likely benign (Jan 12, 2018)
16-23388920-T-A			Uncertain significance (-)
16-23388929-C-G		COG7 congenital disorder of glycosylation	Likely benign (May 27, 2022)
16-23388929-C-T		COG7 congenital disorder of glycosylation	Likely benign (May 29, 2022)
16-23388931-C-A		not specified	Uncertain significance (Aug 21, 2024)
16-23388931-C-T		COG7 congenital disorder of glycosylation	Uncertain significance (Apr 06, 2020)
16-23388936-C-T		COG7 congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Apr 27, 2023)
16-23388937-G-A		COG7 congenital disorder of glycosylation	Uncertain significance (May 03, 2022)
16-23388940-T-C		COG7 congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
16-23388941-G-C		COG7 congenital disorder of glycosylation	Likely benign (Mar 25, 2020)
16-23388942-G-A		COG7 congenital disorder of glycosylation	Uncertain significance (Apr 19, 2022)
16-23388946-C-A		COG7 congenital disorder of glycosylation	Uncertain significance (Jul 11, 2023)
16-23388949-C-T			Uncertain significance (Oct 27, 2017)
16-23388950-G-A		not specified • COG7 congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Jan 31, 2024)
16-23388952-T-C		COG7 congenital disorder of glycosylation	Uncertain significance (Sep 01, 2021)
16-23388954-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2023)
16-23388963-C-T		COG7 congenital disorder of glycosylation	Uncertain significance (Mar 02, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COG7	protein_coding	protein_coding	ENST00000307149	17	64688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-7	1.00	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.757	382	426	0.897	0.0000247	5069
Missense in Polyphen		72	107.16	0.67188		1367
Synonymous	0.375	177	183	0.965	0.0000118	1510
Loss of Function	3.26	18	40.4	0.446	0.00000213	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000730	0.000730
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000343	0.000343
Middle Eastern	0.000218	0.000217
South Asian	0.000751	0.000752
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal Golgi function. {ECO:0000250}.
• Disease: DISEASE: Congenital disorder of glycosylation 2E (CDG2E) [MIM:608779]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:15107842}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.743
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.49

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.554
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cog7

Gene ontology

• Biological process: protein glycosylation;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;protein localization to organelle;protein localization to Golgi apparatus;protein stabilization
• Cellular component: Golgi membrane;nucleolus;Golgi apparatus;Golgi transport complex;trans-Golgi network membrane
• Molecular function: protein binding