NM_018714.3(COG1):c.2626_2629dup (p.Gly877fs) AND COG1 congenital disorder of glycosylation

Clinical significance:Uncertain significance (Last evaluated: Dec 25, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000778510.1

Allele description [Variation Report for NM_018714.3(COG1):c.2626_2629dup (p.Gly877fs)]

NM_018714.3(COG1):c.2626_2629dup (p.Gly877fs)

Gene:
COG1:component of oligomeric golgi complex 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
17q25.1
Genomic location:
Preferred name:
NM_018714.3(COG1):c.2626_2629dup (p.Gly877fs)
HGVS:
  • NC_000017.11:g.73206714_73206717dup
  • NG_008971.1:g.18681_18684dup
  • NM_018714.3:c.2626_2629dupMANE SELECT
  • NP_061184.1:p.Gly877fs
  • NC_000017.10:g.71202853_71202856dup
  • NM_018714.2:c.2626_2629dupTTTG
Protein change:
G877fs
Links:
dbSNP: rs1568298983
NCBI 1000 Genomes Browser:
rs1568298983
Molecular consequence:
  • NM_018714.3:c.2626_2629dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000914784Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Dec 25, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000914784.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant results in a frameshift and is predicted to result in premature termination of the protein. It was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018) and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene and cDNA change, and amino acid change. No publications were found based on this search. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for this disease.

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

Last Updated: Nov 27, 2021

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