NM_001089.3(ABCA3):c.1136G>A (p.Gly379Asp) AND Surfactant metabolism dysfunction, pulmonary, 3

Clinical significance:Uncertain significance (Last evaluated: Jun 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001257422.1

Allele description [Variation Report for NM_001089.3(ABCA3):c.1136G>A (p.Gly379Asp)]

NM_001089.3(ABCA3):c.1136G>A (p.Gly379Asp)

Gene:
ABCA3:ATP binding cassette subfamily A member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001089.3(ABCA3):c.1136G>A (p.Gly379Asp)
HGVS:
  • NC_000016.10:g.2308599C>T
  • NG_011790.1:g.37148G>A
  • NM_001089.3:c.1136G>AMANE SELECT
  • NP_001080.2:p.Gly379Asp
  • NC_000016.9:g.2358600C>T
  • p.Gly379Asp
Protein change:
G379D
Molecular consequence:
  • NM_001089.3:c.1136G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
Unknown function
Observations:
1

Condition(s)

Name:
Surfactant metabolism dysfunction, pulmonary, 3 (SMDP3)
Synonyms:
INTERSTITIAL LUNG DISEASE DUE TO ABCA3 DEFICIENCY; PULMONARY ALVEOLAR PROTEINOSIS, CONGENITAL, 3
Identifiers:
MONDO: MONDO:0012582; MedGen: C1970456; OMIM: 610921

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001429634Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Geneticscriteria provided, single submitter
Uncertain significance
(Jun 1, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Hindugermlineyes1not 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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV001429634.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Hindu1not providednot providedclinical testing PubMed (1)

Description

A homozygous missense variation in exon 11 of the ABCA3 gene that results in the amino acid substitution of Aspartic acid for Glycine at codon 379 was detected. The observed variant c.1136G>A (p.Gly379Asp) has not been reported in the 1000 genomes and ExAC databases. The variant lies in the ABC-2 transporter domain of the protein. The in silico predictions of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by SIFT and MutationTaster2. The reference codon is conserved across mammals. In summary, the variant meets our criteria to be classified as variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 1, 2020

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