Intellectual disability
Gene: COG6

COG6 (component of oligomeric golgi complex 6)
EnsemblGeneIds (GRCh38): ENSG00000133103
EnsemblGeneIds (GRCh37): ENSG00000133103
OMIM: 606977, Gene2Phenotype
COG6 is in 7 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Comment on list classification: New gene added by external expert and reviewed by curation team: appropriate phenotype, sufficient cases and external expert review all support gene-disease association and relevance to this panel to rate gene to Green.
Created: 25 Feb 2019, 4:21 p.m.

Created: 25 Feb 2019, 4:21 p.m.

Panel version: 2.754

Konstantinos Varvagiannis (Other)

Green List (high evidence)

DD/ID is an almost universal feature of individuals with biallelic COG6 mutations, whether this is associated with a type II transferrin IEF pattern (as in Congenital disorder of glycosylation, type IIl, 614576) or not (as in Shaheen syndrome, 615328).

More than 15 patients from several different families have been reported to date.

PMID: 26260076 is a collaborative study reporting on new patients as well as on individuals previously described up to 2015 by Lubbehusen et al. (2010 - PMID: 20605848), Huybrechts et al. (2012 - PMID: 23430903) as well as Shaheen et al. (2013 - PMID: 23606727).

As summarized in table 1 of the article, developmental disability was a feature in 8/10, although for a further 2/10 this was probably not relevant (both deceased too early).

The following articles are additional reports although there might be some overlap (applicable for the Saudi patients) : PMIDs: 28139241 (individuals with diagnosis of CDG from Spain), 28742265 (cohort of CDG patients from Saudi Arabia), 29445937 (case report of Saudi subject), 29709711 (Chinese individual with COG6-CDG).

All types of variants have been observed including missense, stopgain and frameshift ones, as well as variants leading to aberrant splicing [eg. positions -2, -9, -24]. The deep intronic variant (position -24) in the individuals reported by Shaheen and others is considered a founder mutation in the Saudi population.

Individuals homozygous for the latter variant have detectable levels of the normal transcript, although 75% of the produced transcript (upon RT-PCR analysis) correspond to retention of 37 intronic nucleotides leading to frameshift and introduction of a premature stop codon. This was also confirmed with Western blot.

Given the detectable levels of the normal transcript, it has been proposed that Shaheen syndrome represents the mildest end of the spectrum COG6-related disorders.

COG6 is included in gene panels for intellectual disability offered by different diagnostic laboratories.

As a result this gene can be considered for inclusion in this panel as green.
Sources: Literature, Expert Review
Created: 26 Nov 2018, 1:26 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Congenital disorder of glycosylation, type IIl, 614576; Shaheen syndrome, 615328

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 26 Nov 2018, 1:26 p.m.

Panel version: 2.555

Details

Mode of Inheritance

BIALLELIC, autosomal or pseudoautosomal

Sources

Expert Review Green

Phenotypes

Congenital disorder of glycosylation, type IIl, 614576
Shaheen syndrome, 615328

OMIM

606977

Clinvar variants

Variants in COG6

Penetrance

Complete

Publications

Panels with this gene

History Filter Activity

25 Feb 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: cog6 has been classified as Green List (High Evidence).

26 Nov 2018, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: COG6 was added gene: COG6 was added to Intellectual disability. Sources: Literature,Expert Review Mode of inheritance for gene: COG6 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: COG6 were set to 26260076; 20605848; 23430903; 23606727; 28139241; 28742265; 29445937; 29709711 Phenotypes for gene: COG6 were set to Congenital disorder of glycosylation, type IIl, 614576; Shaheen syndrome, 615328 Penetrance for gene: COG6 were set to Complete Review for gene: COG6 was set to GREEN gene: COG6 was marked as current diagnostic

Intellectual disability Gene: COG6