COG5

component of oligomeric golgi complex 5, the group of Components of oligomeric golgi complex

Basic information

Region (hg38): 7:107201372-107564261

Previous symbols: [ "GOLTC1" ]

Links

ENSG00000164597 ∙ NCBI:10466 ∙ OMIM:606821 ∙ HGNC:14857 ∙ Uniprot:Q9UP83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• COG5-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• COG5-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• COG5-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
• COG5-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• COG5-congenital disorder of glycosylation (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIi	AR	Hematologic	Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Audiologic/Otolaryngologic; Biochemical; Hematologic; Neurologic; Ophthalmologic	19690088; 23228021; 31572517; 32174980
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COG5 gene.

• COG5-congenital disorder of glycosylation (29 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COG5 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			1	138	3	142
missense		1	276	2	2	281
nonsense	18	3				21
start loss		1	2			3
frameshift	11	3	1			15
inframe indel			3			3
splice donor/acceptor (+/-2bp)		11				11
splice region			22	26	6	54
non coding		2	77	119	62	260
Total	29	21	360	259	67

Highest pathogenic variant AF is 0.0000330

Variants in COG5

This is a list of pathogenic ClinVar variants found in the COG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-107201418-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-107201425-A-T		not specified	Uncertain significance (Jan 30, 2024)
7-107201426-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-107201774-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107201796-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
7-107201879-C-T		COG5-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Jan 01, 2023)
7-107202032-A-G		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202048-C-A		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202067-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
7-107202090-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202176-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202238-A-ATCTT		Congenital disorder of glycosylation	Likely benign (Jun 14, 2016)
7-107202273-A-G		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202405-G-A		COG5-congenital disorder of glycosylation	Likely benign (Jan 12, 2018)
7-107202519-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202518-G-GAA		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
7-107202530-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
7-107202649-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202651-G-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202654-G-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202688-G-C		COG5-congenital disorder of glycosylation	Benign (Jan 13, 2018)
7-107202838-A-G		COG5-congenital disorder of glycosylation	Likely benign (Jan 12, 2018)
7-107202882-A-G		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
7-107202894-G-A		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
7-107202899-T-G		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COG5	protein_coding	protein_coding	ENST00000297135	22	362960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.77e-20	0.356	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.483	492	463	1.06	0.0000231	5568
Missense in Polyphen		104	118.25	0.87953		1447
Synonymous	-2.00	192	160	1.20	0.00000786	1691
Loss of Function	1.75	37	50.4	0.734	0.00000258	585

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.000870	0.000870
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.000870	0.000870
South Asian	0.000460	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal Golgi function. {ECO:0000250}.
• Disease: DISEASE: Congenital disorder of glycosylation 2I (CDG2I) [MIM:613612]: 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. Congenital disorder of glycosylation type 2I is characterized by mild neurological impairments. {ECO:0000269|PubMed:19690088}. 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: 0.100

Intolerance Scores

• loftool: 0.980
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.32

Haploinsufficiency Scores

• pHI: 0.693
• hipred: N
• hipred_score: 0.277
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cog5

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;intra-Golgi vesicle-mediated transport;protein transport
• Cellular component: Golgi membrane;nucleoplasm;Golgi apparatus;cytosol;membrane;Golgi transport complex;trans-Golgi network membrane
• Molecular function: molecular_function;protein binding