NM_020751.3(COG6):c.697G>A (p.Glu233Lys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 5, 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:: RCV002528278.3

Allele description [Variation Report for NM_020751.3(COG6):c.697G>A (p.Glu233Lys)]

NM_020751.3(COG6):c.697G>A (p.Glu233Lys)

Gene:

COG6:component of oligomeric golgi complex 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q14.11

Genomic location:

Preferred name:

NM_020751.3(COG6):c.697G>A (p.Glu233Lys)

HGVS:

NC_000013.11:g.39682173G>A
NG_028352.1:g.31547G>A
NM_001145079.2:c.697G>A
NM_020751.3:c.697G>AMANE SELECT
NP_001138551.1:p.Glu233Lys
NP_065802.1:p.Glu233Lys
NC_000013.10:g.40256310G>A
NM_020751.2:c.697G>A
NR_026745.1:n.862G>A

Protein change:

E233K

Links:

dbSNP: rs745501973

NCBI 1000 Genomes Browser:

rs745501973

Molecular consequence:

NM_001145079.2:c.697G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020751.3:c.697G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_026745.1:n.862G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: COG6-congenital disorder of glycosylation
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIl; CDG IIl; Congenital disorder of glycosylation type 2L; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013810; MedGen: C3553230; OMIM: 614576

Name:: Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome
Synonyms:: Shaheen syndrome
Identifiers:: MONDO: MONDO:0014131; MedGen: C3809160; Orphanet: 363523; OMIM: 615328

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003458546	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30426380, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003458546

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 5, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Comparison of clinical parameters with whole exome sequencing analysis results of autosomal recessive patients; a center experience.

Elmas M, Yıldız H, Erdoğan M, Gogus B, Avcı K, Solak M.

Mol Biol Rep. 2019 Feb;46(1):287-299. doi: 10.1007/s11033-018-4470-7. Epub 2018 Nov 13.

PubMed [citation]

PMID:: 30426380

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, SCV003458546.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This missense change has been observed in individual(s) with clinical features of COG6-related conditions (PMID: 30426380). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 452649). This variant is present in population databases (rs745501973, gnomAD 0.007%), including at least one homozygous and/or hemizygous individual. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 233 of the COG6 protein (p.Glu233Lys).

#	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: Dec 14, 2024

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