COG3

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

Basic information

Region (hg38): 13:45464897-45536701

Links

ENSG00000136152 ∙ NCBI:83548 ∙ OMIM:606975 ∙ HGNC:18619 ∙ Uniprot:Q96JB2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

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.

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.

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						0
missense			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in COG3

This is a list of pathogenic ClinVar variants found in the COG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-45465041-C-T		not specified	Uncertain significance (May 26, 2022)
13-45465046-G-C		not specified	Uncertain significance (Sep 26, 2023)
13-45465115-C-T		not specified	Uncertain significance (Jun 10, 2024)
13-45465131-C-T		not specified	Uncertain significance (Dec 20, 2023)
13-45465145-G-C		Congenital disorder of glycosylation, type IIbb	Pathogenic (Oct 19, 2023)
13-45465149-G-A		not specified	Uncertain significance (Mar 20, 2024)
13-45465155-C-G		not specified	Uncertain significance (Mar 15, 2024)
13-45465160-T-C		Congenital disorder of glycosylation, type IIbb	Pathogenic (Oct 19, 2023)
13-45465167-T-C		not specified	Uncertain significance (Sep 16, 2021)
13-45476207-A-G		not specified	Uncertain significance (Feb 05, 2024)
13-45476249-G-A		not specified	Uncertain significance (Jul 15, 2021)
13-45476270-G-A		Congenital disorder of glycosylation, type IIbb	Uncertain significance (Mar 19, 2024)
13-45479026-C-A		not specified	Uncertain significance (Aug 17, 2022)
13-45479039-T-C		not specified	Uncertain significance (Jun 17, 2024)
13-45479059-A-G		not specified	Uncertain significance (Jan 10, 2023)
13-45483294-A-G		not specified	Uncertain significance (Aug 01, 2022)
13-45483329-A-T		not specified	Uncertain significance (Dec 03, 2021)
13-45486497-T-A		not specified	Uncertain significance (Feb 13, 2024)
13-45486556-C-G		not specified	Uncertain significance (Feb 17, 2022)
13-45490945-G-A		not specified	Uncertain significance (Nov 15, 2023)
13-45491449-C-G		not specified	Uncertain significance (Mar 07, 2024)
13-45492234-C-T		not specified	Uncertain significance (Dec 12, 2022)
13-45493454-A-G		not specified	Uncertain significance (Oct 17, 2023)
13-45493474-G-A		not specified	Uncertain significance (Jul 25, 2023)
13-45496269-C-T		not specified	Uncertain significance (Apr 22, 2022)

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

• 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