NM_006348.5(COG5):c.59C>T (p.Ala20Val) AND COG5-congenital disorder of glycosylation

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 8, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001945023.4

Allele description [Variation Report for NM_006348.5(COG5):c.59C>T (p.Ala20Val)]

NM_006348.5(COG5):c.59C>T (p.Ala20Val)

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.59C>T (p.Ala20Val)

HGVS:

NC_000007.14:g.107563838G>A
NG_028095.2:g.5677C>T
NM_001161520.2:c.59C>T
NM_001379511.1:c.59C>T
NM_001379512.1:c.59C>T
NM_001379513.1:c.59C>T
NM_001379514.1:c.59C>T
NM_001379515.1:c.59C>T
NM_001379516.1:c.59C>T
NM_006348.5:c.59C>TMANE SELECT
NM_181733.4:c.59C>T
NP_001154992.2:p.Ala20Val
NP_001366440.1:p.Ala20Val
NP_001366441.1:p.Ala20Val
NP_001366442.1:p.Ala20Val
NP_001366443.1:p.Ala20Val
NP_001366444.1:p.Ala20Val
NP_001366445.1:p.Ala20Val
NP_006339.4:p.Ala20Val
NP_859422.3:p.Ala20Val
NC_000007.13:g.107204283G>A

Protein change:

A20V

Links:

dbSNP: rs368239973

NCBI 1000 Genomes Browser:

rs368239973

Molecular consequence:

NM_001161520.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379511.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379512.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379513.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379514.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379515.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379516.1:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006348.5:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181733.4:c.59C>T - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002180089	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 8, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002791143	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 29, 2021)	unknown	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

SCV002180089

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 8, 2022)

germline

clinical testing

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

SCV002791143

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 29, 2021)

unknown

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
not provided	unknown	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002180089.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 51 of the COG5 protein (p.Ala51Val). This variant is present in population databases (rs368239973, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with COG5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1413450). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002791143.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine