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NM_006348.5(COG5):c.1A>G (p.Met1Val) AND COG5-congenital disorder of glycosylation

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 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:
RCV001909243.3

Allele description [Variation Report for NM_006348.5(COG5):c.1A>G (p.Met1Val)]

NM_006348.5(COG5):c.1A>G (p.Met1Val)

Gene:
COG5:component of oligomeric golgi complex 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_006348.5(COG5):c.1A>G (p.Met1Val)
HGVS:
  • NC_000007.14:g.107563896T>C
  • NG_028095.2:g.5619A>G
  • NM_001161520.2:c.1A>G
  • NM_001379511.1:c.1A>G
  • NM_001379512.1:c.1A>G
  • NM_001379513.1:c.1A>G
  • NM_001379514.1:c.1A>G
  • NM_001379515.1:c.1A>G
  • NM_001379516.1:c.1A>G
  • NM_006348.3:c.94A>G
  • NM_006348.5:c.1A>GMANE SELECT
  • NM_181733.4:c.1A>G
  • NP_001154992.2:p.Met1Val
  • NP_001366440.1:p.Met1Val
  • NP_001366441.1:p.Met1Val
  • NP_001366442.1:p.Met1Val
  • NP_001366443.1:p.Met1Val
  • NP_001366444.1:p.Met1Val
  • NP_001366445.1:p.Met1Val
  • NP_006339.4:p.Met1Val
  • NP_859422.3:p.Met1Val
  • NC_000007.13:g.107204341T>C
Protein change:
M1V
Links:
dbSNP: rs1804241289
NCBI 1000 Genomes Browser:
rs1804241289
Molecular consequence:
  • NM_001161520.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379511.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379512.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379513.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379514.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379515.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001379516.1:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_006348.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_181733.4:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001161520.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379511.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379512.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379513.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379514.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379515.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379516.1:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006348.5:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181733.4:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
COG5-congenital disorder of glycosylation
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIi; Congenital disorder of glycosylation type 2i; CDG IIi; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013325; MedGen: C3150876; Orphanet: 263487; OMIM: 613612

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002184966Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 12, 2022) 		germlineclinical testing

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

Help

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002184966.3

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 32 of the COG5 protein (p.Met32Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with COG5-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.

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

Last Updated: Sep 29, 2024