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NM_000112.4(SLC26A2):c.2032_2033delinsCT (p.Gly678Leu) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 19, 2022
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:
RCV001869490.3

Allele description [Variation Report for NM_000112.4(SLC26A2):c.2032_2033delinsCT (p.Gly678Leu)]

NM_000112.4(SLC26A2):c.2032_2033delinsCT (p.Gly678Leu)

Gene:
SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000112.4(SLC26A2):c.2032_2033delinsCT (p.Gly678Leu)
HGVS:
  • NC_000005.10:g.149981625_149981626delinsCT
  • NG_007147.2:g.22743_22744delinsCT
  • NM_000112.4:c.2032_2033delinsCTMANE SELECT
  • NP_000103.2:p.Gly678Leu
  • LRG_684t1:c.2032_2033delinsCT
  • LRG_684:g.22743_22744delinsCT
  • NC_000005.9:g.149361188_149361189delinsCT
  • NM_000112.3:c.2032_2033delinsCT
Protein change:
G678L
Links:
dbSNP: rs2113699627
NCBI 1000 Genomes Browser:
rs2113699627
Molecular consequence:
  • NM_000112.4:c.2032_2033delinsCT - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002200346Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 19, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002200346.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces glycine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 678 of the SLC26A2 protein (p.Gly678Leu). This variant is present in population databases (no rsID available, gnomAD 0.07%). This missense change has been observed in individual(s) with clinical features of SLC26A2-related conditions (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1331381). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). This variant disrupts the p.Gly678 amino acid residue in SLC26A2. Other variant(s) that disrupt this residue have been observed in individuals with SLC26A2-related conditions (PMID: 8528239), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 20, 2024