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NM_000112.4(SLC26A2):c.438dup (p.Ala147fs) AND Atelosteogenesis type II

Germline classification:
Likely pathogenic (1 submission)
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:
RCV004576972.1

Allele description [Variation Report for NM_000112.4(SLC26A2):c.438dup (p.Ala147fs)]

NM_000112.4(SLC26A2):c.438dup (p.Ala147fs)

Gene:
SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000112.4(SLC26A2):c.438dup (p.Ala147fs)
HGVS:
  • NC_000005.10:g.149978090dup
  • NG_007147.2:g.19208dup
  • NM_000112.4:c.438dupMANE SELECT
  • NP_000103.2:p.Ala147fs
  • LRG_684:g.19208dup
  • NC_000005.9:g.149357646_149357647insT
  • NC_000005.9:g.149357653dup
  • NM_000112.3:c.438dupT
Protein change:
A147fs
Links:
dbSNP: rs769859976
NCBI 1000 Genomes Browser:
rs769859976
Molecular consequence:
  • NM_000112.4:c.438dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV005060900Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV005060900.1

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

Description

The observed frameshift c.438dup(p.Ala147CysfsTer28) variant in SLC26A2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is present with an allele frequency of 0.0008% in gnomAD Exomes database. This variant has been submitted to the ClinVar database as Pathogenic. This variant causes a frameshift starting with codon Alanine 147, changes this amino acid to Cysteine residue, and creates a premature Stop codon at position 28 of the new reading frame, denoted p.Ala147CysfsTer28. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. Functional studies are required to prove pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic. In absence of another reportable variant in SLC26A2 gene, the molecular diagnosis is not confirmed.

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

Last Updated: Sep 29, 2024