NM_001089.3(ABCA3):c.1474dup (p.Tyr492fs) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 25, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001008382.1

Allele description [Variation Report for NM_001089.3(ABCA3):c.1474dup (p.Tyr492fs)]

NM_001089.3(ABCA3):c.1474dup (p.Tyr492fs)

Gene:
ABCA3:ATP binding cassette subfamily A member 3 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001089.3(ABCA3):c.1474dup (p.Tyr492fs)
HGVS:
  • NC_000016.10:g.2300142dup
  • NG_011790.1:g.45605dup
  • NM_001089.3:c.1474dupMANE SELECT
  • NP_001080.2:p.Tyr492fs
  • NC_000016.9:g.2350143dup
  • NM_001089.2:c.1474dupT
Protein change:
Y492fs
Links:
dbSNP: rs756855585
NCBI 1000 Genomes Browser:
rs756855585
Molecular consequence:
  • NM_001089.3:c.1474dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001168150GeneDxcriteria provided, single submitter
Likely pathogenic
(Sep 25, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168150.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1474dupT variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is observed in 2/9850 (0.0203%) alleles from individuals of Ashkenazi Jewish background in large population cohorts (Lek et al., 2016). It causes a frameshift starting with codon Tyrosine 492, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 18 of the new reading frame, denoted p.Tyr492LeufsX18. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we consider this variant to be likely pathogenic.

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

Last Updated: Feb 27, 2021

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