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NM_018714.3(COG1):c.2365G>A (p.Glu789Lys) AND COG1 congenital disorder of glycosylation

Clinical significance:Conflicting interpretations of pathogenicity, Uncertain significance(1); Likely benign(1) (Last evaluated: Nov 29, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000966463.8

Allele description [Variation Report for NM_018714.3(COG1):c.2365G>A (p.Glu789Lys)]

NM_018714.3(COG1):c.2365G>A (p.Glu789Lys)

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.2365G>A (p.Glu789Lys)
HGVS:
  • NC_000017.11:g.73203776G>A
  • NG_008971.1:g.15743G>A
  • NM_018714.3:c.2365G>AMANE SELECT
  • NP_061184.1:p.Glu789Lys
  • NC_000017.10:g.71199915G>A
  • NC_000017.10:g.71199915G>A
  • NM_018714.2:c.2365G>A
Protein change:
E789K
Links:
dbSNP: rs201867802
NCBI 1000 Genomes Browser:
rs201867802
Molecular consequence:
  • NM_018714.3:c.2365G>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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001113788Invitaecriteria provided, single submitter
Likely benign
(Nov 29, 2021)
germlineclinical testing

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

SCV001281462Illumina Laboratory Services,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing.

Jones MA, Rhodenizer D, da Silva C, Huff IJ, Keong L, Bean LJ, Coffee B, Collins C, Tanner AK, He M, Hegde MR.

Mol Genet Metab. 2013 Sep-Oct;110(1-2):78-85. doi: 10.1016/j.ymgme.2013.05.012. Epub 2013 May 28.

PubMed [citation]
PMID:
23806237

Details of each submission

From Invitae, SCV001113788.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services,Illumina, SCV001281462.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 23, 2022

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