NM_033409.4(SLC52A3):c.765C>T (p.Leu255=) AND not specified

Germline classification:: Benign (5 submissions)
Last evaluated:: Aug 23, 2017
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:: RCV000252910.15

Allele description [Variation Report for NM_033409.4(SLC52A3):c.765C>T (p.Leu255=)]

NM_033409.4(SLC52A3):c.765C>T (p.Leu255=)

Gene:

SLC52A3:solute carrier family 52 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_033409.4(SLC52A3):c.765C>T (p.Leu255=)

HGVS:

NC_000020.11:g.763806G>A
NG_027687.2:g.17180C>T
NM_001370085.1:c.765C>T
NM_001370086.1:c.765C>T
NM_033409.4:c.765C>TMANE SELECT
NP_001357014.1:p.Leu255=
NP_001357015.1:p.Leu255=
NP_212134.3:p.Leu255=
LRG_1394t1:c.765C>T
LRG_1394:g.17180C>T
LRG_1394p1:p.Leu255=
NC_000020.10:g.744450G>A
NG_027687.1:g.9779C>T
NM_033409.3:c.765C>T
p.Leu255Leu

Links:

dbSNP: rs3746805

NCBI 1000 Genomes Browser:

rs3746805

Molecular consequence:

NM_001370085.1:c.765C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370086.1:c.765C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_033409.4:c.765C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

182

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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receptor-interacting serine-threonine kinase 4, partial [Crystallaria asprella]
receptor-interacting serine-threonine kinase 4, partial [Crystallaria asprella]
gi|482711055|gb|AGK34063.1|

Protein
early growth response 1, partial [Stellifer ericymba]
early growth response 1, partial [Stellifer ericymba]
gi|808040337|gb|AKC94559.1|

Protein
Stellifer rastrifer isolate CN440 early growth response 1 (EGR1) gene, partial c...
Stellifer rastrifer isolate CN440 early growth response 1 (EGR1) gene, partial cds
gi|808040342|gb|KP722874.1|

Nucleotide
early growth response 1, partial [Pteroscion peli]
early growth response 1, partial [Pteroscion peli]
gi|808040323|gb|AKC94552.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000315227	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000731907	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Aug 23, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001740231	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001924122	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001956486	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

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	clinical testing
not provided	germline	not provided	182	182	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV000315227.1

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000731907.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	182	not provided	not provided	clinical testing	PubMed (1)

Description

p.Leu255Leu in exon 3 of SLC52A3: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 53.54% (6191/11564 ) of Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.b roadinstitute.org; dbSNP rs3746805).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		182	not provided	182	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001740231.3

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

#	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

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001924122.1

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

#	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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001956486.1

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

#	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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