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NM_000112.4(SLC26A2):c.1714del (p.Leu572fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 19, 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:
RCV001382138.7

Allele description [Variation Report for NM_000112.4(SLC26A2):c.1714del (p.Leu572fs)]

NM_000112.4(SLC26A2):c.1714del (p.Leu572fs)

Gene:
SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000112.4(SLC26A2):c.1714del (p.Leu572fs)
HGVS:
  • NC_000005.10:g.149981307del
  • NG_007147.2:g.22425del
  • NM_000112.4:c.1714delMANE SELECT
  • NP_000103.2:p.Leu572fs
  • LRG_684:g.22425del
  • NC_000005.9:g.149360869del
  • NC_000005.9:g.149360870del
Protein change:
L572fs
Links:
dbSNP: rs2113699101
NCBI 1000 Genomes Browser:
rs2113699101
Molecular consequence:
  • NM_000112.4:c.1714del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Achondrogenesis, type IB (ACG1B)
Synonyms:
Achondrogenesis Fraccaro type
Identifiers:
MONDO: MONDO:0010966; MedGen: C0265274; Orphanet: 932; Orphanet: 93298; OMIM: 600972
Name:
Atelosteogenesis type II (AO2)
Synonyms:
NEONATAL OSSEOUS DYSPLASIA I; Neonatal osseous dysplasia 1; Atelosteogenesis type 2
Identifiers:
MONDO: MONDO:0009727; MedGen: C1850554; Orphanet: 56304; OMIM: 256050
Name:
Multiple epiphyseal dysplasia type 4 (EDM4)
Synonyms:
Multiple epiphyseal dysplasia, autosomal recessive; Multiple epiphyseal dysplasia with clubfoot; Multiple epiphyseal dysplasia with double-layered patella; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009189; MedGen: C1847593; Orphanet: 93307; OMIM: 226900
Name:
Diastrophic dysplasia (DTD)
Synonyms:
Diastrophic dwarfism
Identifiers:
MONDO: MONDO:0009107; MedGen: C0220726; Orphanet: 628; OMIM: 222600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001580769Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jul 19, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

The diastrophic dysplasia gene encodes a novel sulfate transporter: positional cloning by fine-structure linkage disequilibrium mapping.

Hästbacka J, de la Chapelle A, Mahtani MM, Clines G, Reeve-Daly MP, Daly M, Hamilton BA, Kusumi K, Trivedi B, Weaver A, et al.

Cell. 1994 Sep 23;78(6):1073-87.

PubMed [citation]
PMID:
7923357

Achondrogenesis type IB is caused by mutations in the diastrophic dysplasia sulphate transporter gene.

Superti-Furga A, Hästbacka J, Wilcox WR, Cohn DH, van der Harten HJ, Rossi A, Blau N, Rimoin DL, Steinmann B, Lander ES, Gitzelmann R.

Nat Genet. 1996 Jan;12(1):100-2. No abstract available.

PubMed [citation]
PMID:
8528239
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001580769.4

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

Description

This variant has not been reported in the literature in individuals with SLC26A2-related conditions. This sequence change results in a premature translational stop signal in the SLC26A2 gene (p.Leu572Phefs*13). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 168 amino acids of the SLC26A2 protein. This variant is not present in population databases (ExAC no frequency). This variant disrupts the C-terminus of the SLC26A2 protein. Other variant(s) that disrupt this region (p.Lys575Serfs*10) have been determined to be pathogenic (PMID: 7923357, 8528239, 8571951, Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024