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 (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

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 (670 variants)
Inborn_genetic_diseases (115 variants)
not_provided (87 variants)
not_specified (48 variants)
COG5-related_disorder (26 variants)
Craniosynostosis_syndrome (1 variants)
Congenital_disorder_of_glycosylation (1 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. These statistics are base on transcript: NM_000006348.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	165 clinvar	2 clinvar	172
missense	3 clinvar	2 clinvar	314 clinvar	14 clinvar		333
nonsense	22 clinvar	3 clinvar		1 clinvar		26
start loss		1	3			4
frameshift	16 clinvar	3 clinvar	2 clinvar			21
splice donor/acceptor (+/-2bp)		15 clinvar				15
Total	41	24	324	180	2

Highest pathogenic variant AF is 0.0000464777

Loading clinvar variants...

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
Phenotype

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