NM_005660.3(SLC35A2):c.1069G>C (p.Gly357Arg) AND SLC35A2-congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 14, 2023
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:: RCV003741345.2

Allele description [Variation Report for NM_005660.3(SLC35A2):c.1069G>C (p.Gly357Arg)]

NM_005660.3(SLC35A2):c.1069G>C (p.Gly357Arg)

Gene:

SLC35A2:solute carrier family 35 member A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.23

Genomic location:

Preferred name:

NM_005660.3(SLC35A2):c.1069G>C (p.Gly357Arg)

HGVS:

NC_000023.11:g.48904840C>G
NG_015967.1:g.11923C>G
NG_015967.2:g.11912C>G
NG_034300.1:g.12119G>C
NM_001032289.3:c.479G>C
NM_001042498.3:c.1069G>C
NM_001282647.2:c.479G>C
NM_001282648.2:c.407G>C
NM_001282649.2:c.886G>C
NM_001282650.2:c.1108G>C
NM_001282651.2:c.1153G>C
NM_005660.3:c.1069G>CMANE SELECT
NP_001027460.1:p.Arg160Pro
NP_001035963.1:p.Gly357Arg
NP_001269576.1:p.Arg160Pro
NP_001269577.1:p.Arg136Pro
NP_001269578.1:p.Gly296Arg
NP_001269579.1:p.Gly370Arg
NP_001269580.1:p.Gly385Arg
NP_005651.1:p.Gly357Arg
NC_000023.10:g.48762117C>G

Protein change:

G296R

Molecular consequence:

NM_001032289.3:c.479G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001042498.3:c.1069G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282647.2:c.479G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282648.2:c.407G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282649.2:c.886G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282650.2:c.1108G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282651.2:c.1153G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005660.3:c.1069G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: SLC35A2-congenital disorder of glycosylation
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIm; CDG IIm; CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIm, SOMATIC MOSAIC; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010478; MedGen: C3806688; Orphanet: 356961; OMIM: 300896

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004509084	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 14, 2023)	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

SCV004509084

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 14, 2023)

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, SCV004509084.1

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC35A2 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. This variant has not been reported in the literature in individuals affected with SLC35A2-related conditions. This variant is present in population databases (rs782347244, gnomAD 0.008%), including at least one homozygous and/or hemizygous individual. This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 357 of the SLC35A2 protein (p.Gly357Arg).

#	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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