NM_033409.4(SLC52A3):c.865G>A (p.Glu289Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 21, 2024
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:: RCV001586041.5

Allele description [Variation Report for NM_033409.4(SLC52A3):c.865G>A (p.Glu289Lys)]

NM_033409.4(SLC52A3):c.865G>A (p.Glu289Lys)

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.865G>A (p.Glu289Lys)

HGVS:

NC_000020.11:g.763706C>T
NG_027687.2:g.17280G>A
NM_001370085.1:c.865G>A
NM_001370086.1:c.865G>A
NM_033409.4:c.865G>AMANE SELECT
NP_001357014.1:p.Glu289Lys
NP_001357015.1:p.Glu289Lys
NP_212134.3:p.Glu289Lys
LRG_1394t1:c.865G>A
LRG_1394:g.17280G>A
LRG_1394p1:p.Glu289Lys
NC_000020.10:g.744350C>T
NG_027687.1:g.9879G>A
NM_033409.3:c.865G>A

Protein change:

E289K

Links:

dbSNP: rs142265627

NCBI 1000 Genomes Browser:

rs142265627

Molecular consequence:

NM_001370085.1:c.865G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370086.1:c.865G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033409.4:c.865G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens cDNA clone IMAGE:40116185, containing frame-shift errors
Homo sapiens cDNA clone IMAGE:40116185, containing frame-shift errors
gi|144719326|gb|BC139750.1|

Nucleotide
Lyrm1 LYR motif containing 1 [Rattus norvegicus]
Lyrm1 LYR motif containing 1 [Rattus norvegicus]
Gene ID:365361

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001820564	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 21, 2024)	germline	clinical testing	Citation Link,
SCV005194843	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV001820564

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 21, 2024)

germline

clinical testing

Citation Link,

SCV005194843

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	clinical testing, not provided

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

Details of each submission

From GeneDx, SCV001820564.2

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

Description

In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 23506902)

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005194843.1

#	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: Oct 8, 2024

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