NM_018714.3(COG1):c.1282-3T>C AND COG1 congenital disorder of glycosylation

Clinical significance:Uncertain significance (Last evaluated: Jan 21, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000315945.3

Allele description [Variation Report for NM_018714.3(COG1):c.1282-3T>C]

NM_018714.3(COG1):c.1282-3T>C

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.1282-3T>C
HGVS:
  • NC_000017.11:g.73201106T>C
  • NG_008971.1:g.13073T>C
  • NM_018714.3:c.1282-3T>CMANE SELECT
  • NC_000017.10:g.71197245T>C
  • NM_018714.2:c.1282-3T>C
Links:
dbSNP: rs188853520
NCBI 1000 Genomes Browser:
rs188853520
Molecular consequence:
  • NM_018714.3:c.1282-3T>C - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000406287Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV001522988Baylor Geneticscriteria provided, single submitter
Uncertain significance
(Jan 21, 2019)
unknownclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000406287.3

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

Description

This variant was observed in the ICSL laboratory 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, this variant 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, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From Baylor Genetics, SCV001522988.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Mar 28, 2021

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