NM_001013251.3(SLC3A2):c.1013G>T (p.Arg338Met) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Dec 31, 2019
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:: RCV000896397.5

Allele description [Variation Report for NM_001013251.3(SLC3A2):c.1013G>T (p.Arg338Met)]

NM_001013251.3(SLC3A2):c.1013G>T (p.Arg338Met)

Gene:

SLC3A2:solute carrier family 3 member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q12.3

Genomic location:

Preferred name:

NM_001013251.3(SLC3A2):c.1013G>T (p.Arg338Met)

HGVS:

NC_000011.10:g.62885478G>T
NM_001012662.3:c.1319G>T
NM_001012664.3:c.1130G>T
NM_001013251.3:c.1013G>TMANE SELECT
NM_002394.6:c.1316G>T
NP_001012680.1:p.Arg440Met
NP_001012682.1:p.Arg377Met
NP_001013269.1:p.Arg338Met
NP_002385.3:p.Arg439Met
NC_000011.9:g.62652950G>T
NM_001012662.2:c.1319G>T
NR_037193.2:n.907G>T

Protein change:

R338M

Links:

dbSNP: rs116829615

NCBI 1000 Genomes Browser:

rs116829615

Molecular consequence:

NM_001012662.3:c.1319G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001012664.3:c.1130G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001013251.3:c.1013G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002394.6:c.1316G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_037193.2:n.907G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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glycosyltransferase, partial [Caristius macropus]
glycosyltransferase, partial [Caristius macropus]
gi|531992956|gb|AGT60500.1|

Protein
RecName: Full=Glycosyltransferase 8 domain-containing protein 2
RecName: Full=Glycosyltransferase 8 domain-containing protein 2
gi|81884050|sp|Q640P4.1|GL8D2_MOUSE

Protein
PREDICTED: Homo sapiens uncharacterized lncRNA (LOC105370182), transcript varian...
PREDICTED: Homo sapiens uncharacterized lncRNA (LOC105370182), transcript variant X3, ncRNA
gi|2217479654|ref|XR_007084060.1|

Nucleotide
Mus musculus RUN and SH3 domain containing 1 (Rusc1), transcript variant 2, mRNA
Mus musculus RUN and SH3 domain containing 1 (Rusc1), transcript variant 2, mRNA
gi|2715693097|ref|NM_001083807.2|

Nucleotide
myc proto-oncogene protein [Marmota monax]
myc proto-oncogene protein [Marmota monax]
gi|2187334657|ref|XP_046320899.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001040485	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 31, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005210849	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001040485

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 31, 2019)

germline

clinical testing

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

SCV005210849

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	not provided
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

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, SCV001040485.2

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005210849.1

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

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

Last Updated: Sep 29, 2024

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