NM_018714.3(COG1):c.988G>A (p.Glu330Lys) AND COG1 congenital disorder of glycosylation

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 12, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000819653.6

Allele description

NM_018714.3(COG1):c.988G>A (p.Glu330Lys)

Genes:

LOC126862634:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:71195948-71197147 [Gene]
COG1:component of oligomeric golgi complex 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_018714.3(COG1):c.988G>A (p.Glu330Lys)

HGVS:

NC_000017.11:g.73199939G>A
NG_008971.1:g.11906G>A
NM_018714.3:c.988G>AMANE SELECT
NP_061184.1:p.Glu330Lys
NC_000017.10:g.71196078G>A
NM_018714.2:c.988G>A

Protein change:

E330K

Links:

dbSNP: rs779924491

NCBI 1000 Genomes Browser:

rs779924491

Molecular consequence:

NM_018714.3:c.988G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: COG1 congenital disorder of glycosylation (CDG2G)
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIg; CDG IIg; CDGII/COG1 CEREBROCOSTOMANDIBULAR-LIKE SYNDROME; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012637; MedGen: C2931011; Orphanet: 263508; OMIM: 611209

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000960324	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000960324

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 12, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000960324.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is present in population databases (rs779924491, gnomAD 0.006%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt COG1 protein function. ClinVar contains an entry for this variant (Variation ID: 662087). This variant has not been reported in the literature in individuals affected with COG1-related conditions. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 330 of the COG1 protein (p.Glu330Lys).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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