NM_015386.3(COG4):c.1798G>A (p.Val600Met) AND COG4-congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 3, 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:: RCV000824114.7

Allele description [Variation Report for NM_015386.3(COG4):c.1798G>A (p.Val600Met)]

NM_015386.3(COG4):c.1798G>A (p.Val600Met)

Gene:

COG4:component of oligomeric golgi complex 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_015386.3(COG4):c.1798G>A (p.Val600Met)

HGVS:

NC_000016.10:g.70483882C>T
NG_027529.1:g.44673G>A
NM_001195139.2:c.1723G>A
NM_001365426.1:c.1372G>A
NM_015386.3:c.1798G>AMANE SELECT
NP_001182068.2:p.Val575Met
NP_001352355.1:p.Val458Met
NP_056201.2:p.Val600Met
NC_000016.9:g.70517785C>T
NM_015386.2:c.1798G>A
NR_158212.1:n.1757G>A

Protein change:

V458M

Links:

dbSNP: rs767599010

NCBI 1000 Genomes Browser:

rs767599010

Molecular consequence:

NM_001195139.2:c.1723G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365426.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015386.3:c.1798G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_158212.1:n.1757G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: COG4-congenital disorder of glycosylation
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIj; CDG IIj; Congenital disorder of glycosylation type 2J; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013281; MedGen: C4303552; Orphanet: 263501; OMIM: 613489

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000964997	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 3, 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

SCV000964997

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 3, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000964997.4

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

Description

ClinVar contains an entry for this variant (Variation ID: 665763). 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. 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: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with COG4-related conditions. This variant is present in population databases (rs767599010, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 600 of the COG4 protein (p.Val600Met).

#	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: Sep 29, 2024

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