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NM_000112.3(SLC26A2):c.2065A>T (p.Thr689Ser)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Oct 10, 2018)
Last evaluated:
May 1, 2017
Accession:
VCV000065560.1
Variation ID:
65560
Description:
single nucleotide variant
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NM_000112.3(SLC26A2):c.2065A>T (p.Thr689Ser)

Allele ID
76468
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q32
Genomic location
5: 149981658 (GRCh38) GRCh38 UCSC
5: 149361221 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.149361221A>T
NC_000005.10:g.149981658A>T
NM_000112.3:c.2065A>T NP_000103.2:p.Thr689Ser missense
... more HGVS
Protein change
T689S
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.19289 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.19816
The Genome Aggregation Database (gnomAD) 0.18737
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.19383
The Genome Aggregation Database (gnomAD), exomes 0.17166
1000 Genomes Project 0.19289
Links
UniProtKB: P50443#VAR_020402
dbSNP: rs3776070
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Apr 8, 2016 RCV000176981.3
Benign 2 criteria provided, multiple submitters, no conflicts May 1, 2017 RCV000588132.1
Benign 2 criteria provided, single submitter Jun 14, 2016 RCV000055762.2
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000269354.1
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000334149.1
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000363939.1
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000388712.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC26A2 - - GRCh38
GRCh37
206 219

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302311.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Achondrogenesis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000454841.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Sulfate Transporter-Related Osteochondrodysplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000454838.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Diastrophic Dysplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000454842.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Atelosteogenesis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000454839.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Multiple Epiphyseal Dysplasia, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000454840.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Feb 29, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Integrated Genetics/Laboratory Corporation of America
Accession: SCV000695418.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
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 ... (more)
Benign
(Oct 14, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000228781.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Benign
(May 01, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000884513.1
Submitted: (Oct 10, 2018)
Evidence details
Benign
(Apr 08, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000516357.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at ... (more)
non-pathogenic
(Jul 18, 2013)
no assertion criteria provided
Method: curation
Diastrophic Dysplasia
Allele origin: not provided
GeneReviews
Accession: SCV000086702.1
Submitted: (Apr 30, 2013)
Evidence details
Comment:
Converted during submission to Benign.

Citations for this variant

Title Author Journal Year Link
Diastrophic Dysplasia Bonafé L - 2013 PMID: 20301524
Identification of sequence polymorphisms in two sulfation-related genes, PAPSS2 and SLC26A2, and an association analysis with knee osteoarthritis. Ikeda T Journal of human genetics 2001 PMID: 11558903
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC26A2 - - - -

Record last updated Jun 13, 2019