NM_000112.4(SLC26A2):c.2065A>T (p.Thr689Ser) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Nov 29, 2023
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:: RCV000588132.20

Allele description [Variation Report for NM_000112.4(SLC26A2):c.2065A>T (p.Thr689Ser)]

NM_000112.4(SLC26A2):c.2065A>T (p.Thr689Ser)

Gene:

SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_000112.4(SLC26A2):c.2065A>T (p.Thr689Ser)

HGVS:

NC_000005.10:g.149981658A>T
NG_007147.2:g.22776A>T
NM_000112.4:c.2065A>TMANE SELECT
NP_000103.2:p.Thr689Ser
NP_000103.2:p.Thr689Ser
LRG_684t1:c.2065A>T
LRG_684:g.22776A>T
LRG_684p1:p.Thr689Ser
NC_000005.9:g.149361221A>T
NM_000112.3:c.2065A>T
P50443:p.Thr689Ser

Protein change:

T689S

Links:

UniProtKB: P50443#VAR_020402; dbSNP: rs3776070

NCBI 1000 Genomes Browser:

rs3776070

Molecular consequence:

NM_000112.4:c.2065A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000695418	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Feb 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000884513	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 29, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000695418

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Feb 29, 2016)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000884513

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 29, 2023)

germline

clinical testing

Citation Link

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

Identification of sequence polymorphisms in two sulfation-related genes, PAPSS2 and SLC26A2, and an association analysis with knee osteoarthritis.

Ikeda T, Mabuchi A, Fukuda A, Hiraoka H, Kawakami A, Yamamoto S, Machida H, Takatori Y, Kawaguchi H, Nakamura K, Ikegawa S.

J Hum Genet. 2001;46(9):538-43.

PubMed [citation]

PMID:: 11558903

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695418.1

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

Description

Variant summary: The c.2065A>T in SLC26A2 gene is a missense change that involves a non-conserved nucleotide and 5/5 in silico algorithms predict benign outcome. The variant is present in the control population dataset of ExAC at frequency of 17%. The observed frequency exceeds the maximum expected allele frequency for a pathogenic SLC26A2 variant of 0.29%, suggesting that it is a benign polymorphism. The variant of interest has been reported by reputable databases/clinical laboratories as Benign and widely recognized as benign polymorphism in the field (GeneReviews). Taking together, based on the prevalence in general population the variant was classified as Benign.

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884513.9

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

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine