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NM_001089.3(ABCA3):c.5C>A (p.Ala2Asp) AND Interstitial lung disease due to ABCA3 deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 6, 2019
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:
RCV001257124.1

Allele description [Variation Report for NM_001089.3(ABCA3):c.5C>A (p.Ala2Asp)]

NM_001089.3(ABCA3):c.5C>A (p.Ala2Asp)

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.5C>A (p.Ala2Asp)
HGVS:
  • NC_000016.10:g.2326462G>T
  • NG_011790.1:g.19285C>A
  • NM_001089.3:c.5C>AMANE SELECT
  • NP_001080.2:p.Ala2Asp
  • NC_000016.9:g.2376463G>T
  • NC_000016.9:g.2376463G>T
  • NM_001089.2:c.5C>A
Protein change:
A2D
Links:
dbSNP: rs148662935
NCBI 1000 Genomes Browser:
rs148662935
Molecular consequence:
  • NM_001089.3:c.5C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Interstitial lung disease due to ABCA3 deficiency
Synonyms:
PULMONARY ALVEOLAR PROTEINOSIS, CONGENITAL, 3; Surfactant metabolism dysfunction, pulmonary, 3
Identifiers:
MONDO: MONDO:0012582; MedGen: C1970456; OMIM: 610921

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001433648Johns Hopkins Genomics, Johns Hopkins University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 6, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 Johns Hopkins Genomics, Johns Hopkins University, SCV001433648.1

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

Description

ABCA3 c.5C>A has not been reported in ClinVar nor the literature, to our knowledge. This variant (rs148662935) has been identified in a large population dataset and the minor allele frequency is neither low enough to consider the variant rare (<0.1%) nor high enough to consider it a population polymorphism (>1%) within the African subpopulation (gnomAD: 73/24134 alleles; 0.3025%, no homozygotes). Of three bioinformatics tools queried, one predicts that the substitution would be damaging, while two predict that it would be tolerated. Additionally, the alanine residue at this position is evolutionarily conserved across primates and most high-order species assessed6. Bioinformatic analysis predicts that this missense variant would not affect normal exon 4 splicing, although this has not been confirmed experimentally to our knowledge. Due to lack of functional data, we consider the clinical significance of c.5C>A to be uncertain at this time.

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

Last Updated: Feb 20, 2024