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NM_000112.4(SLC26A2):c.485_486del (p.Val162fs) AND Sulfate transporter-related osteochondrodysplasia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 9, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000780713.2

Allele description [Variation Report for NM_000112.4(SLC26A2):c.485_486del (p.Val162fs)]

NM_000112.4(SLC26A2):c.485_486del (p.Val162fs)

Gene:
SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000112.4(SLC26A2):c.485_486del (p.Val162fs)
HGVS:
  • NC_000005.10:g.149978135TG[1]
  • NG_007147.2:g.19253TG[1]
  • NM_000112.4:c.485_486delMANE SELECT
  • NP_000103.2:p.Val162fs
  • LRG_684t1:c.485_486del
  • LRG_684:g.19253TG[1]
  • NC_000005.9:g.149357698TG[1]
  • NC_000005.9:g.149357698_149357699del
  • NM_000112.3:c.485_486del
  • NM_000112.3:c.485_486delTG
Protein change:
V162fs
Links:
dbSNP: rs763198695
NCBI 1000 Genomes Browser:
rs763198695
Molecular consequence:
  • NM_000112.4:c.485_486del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Sulfate transporter-related osteochondrodysplasia
Synonyms:
DTDST-related dysplasias
Identifiers:
MedGen: CN120497

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000918220Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Sep 9, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Autosomal recessive multiple epiphyseal dysplasia in a Korean girl caused by novel compound heterozygous mutations in the DTDST (SLC26A2) gene.

Cho TJ, Kim OH, Lee HR, Shin SJ, Yoo WJ, Park WY, Park SS, Cho SI, Choi IH.

J Korean Med Sci. 2010 Jul;25(7):1105-8. doi: 10.3346/jkms.2010.25.7.1105. Epub 2010 Jun 16.

PubMed [citation]
PMID:
20592910
PMCID:
PMC2890895

Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing.

Bae JS, Kim NK, Lee C, Kim SC, Lee HR, Song HR, Park KB, Kim HW, Lee SH, Kim HY, Lee SC, Jeong C, Park MS, Yoo WJ, Chung CY, Choi IH, Kim OH, Park WY, Cho TJ.

Genet Med. 2016 Jun;18(6):563-9. doi: 10.1038/gim.2015.129. Epub 2015 Sep 24.

PubMed [citation]
PMID:
26402641
See all PubMed Citations (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918220.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Variant summary: SLC26A2 c.485_486delTG (p.Val162GlyfsX12) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-06 in 247972 control chromosomes. c.485_486delTG has been reported in the literature in at-least one individual affected with Sulfate Transporter-Related Osteochondrodysplasia and has been subsequently cited by others (example, Cho_2010, Kim_2011, Bae_2016, Kausar_2019) consistent with the mutational spectrum of SLC26A2 related skeletal dysplasias. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024