COG3

component of oligomeric golgi complex 3, the group of Components of oligomeric golgi complex

Basic information

Region (hg38): 13:45464898-45536701

Links

ENSG00000136152

∙ NCBI:83548 ∙ OMIM:606975 ∙ HGNC:18619 ∙ Uniprot:Q96JB2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital disorder of glycosylation, type IIbb (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIbb	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	37711075

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COG3 gene.

not_specified (77 variants)
Congenital_disorder_of_glycosylation,_type_IIbb (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COG3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031431.4. 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						0
missense	2 clinvar		76 clinvar	2 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	0	76	2	0

Highest pathogenic variant AF is 0.000029749324

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COG3	protein_coding	protein_coding	ENST00000349995	23	71706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000705	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	331	422	0.785	0.0000204	5404
Missense in Polyphen		86	130.19	0.66059		1670
Synonymous	0.949	151	167	0.906	0.00000867	1537
Loss of Function	5.84	5	49.2	0.102	0.00000230	628

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000881	0.0000881
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.000324	0.000323
European (Non-Finnish)	0.0000540	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in ER-Golgi transport. {ECO:0000269|PubMed:11929878}.;
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: 0.119

Intolerance Scores

loftool
rvis_EVS: -0.27
rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

pHI: 0.258
hipred: Y
hipred_score: 0.580
ghis: 0.605

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cog3
Phenotype: vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: protein glycosylation;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;Golgi organization;protein localization to organelle;protein stabilization
Cellular component: Golgi membrane;Golgi apparatus;cis-Golgi network;cytosol;plasma membrane;Golgi transport complex;Golgi cisterna membrane;trans-Golgi network membrane
Molecular function: protein binding;protein transporter activity