Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001089.3(ABCA3):c.863G>A (p.Arg288Lys)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 1, 2021)
Last evaluated:
Feb 26, 2020
Accession:
VCV000227155.9
Variation ID:
227155
Description:
single nucleotide variant
Help

NM_001089.3(ABCA3):c.863G>A (p.Arg288Lys)

Allele ID
230628
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2319591 (GRCh38) GRCh38 UCSC
16: 2369592 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2319591C>T
NC_000016.9:g.2369592C>T
NG_011790.1:g.26156G>A
NM_001089.3:c.863G>A MANE Select NP_001080.2:p.Arg288Lys missense
Protein change
R288K
Other names
-
Canonical SPDI
NC_000016.10:2319590:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00567
Exome Aggregation Consortium (ExAC) 0.00593
The Genome Aggregation Database (gnomAD) 0.00980
1000 Genomes Project 0.00220
Trans-Omics for Precision Medicine (TOPMed) 0.00569
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00608
Links
ClinGen: CA7841496
dbSNP: rs117603931
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Feb 26, 2020 RCV000514255.6
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Sep 24, 2019 RCV000850152.3
Likely benign 1 criteria provided, single submitter Jan 15, 2015 RCV000219053.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ABCA3 - - GRCh38
GRCh37
364 402

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 15, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269961.2
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Comment:
p.Arg288Lys in exon 8 of ABCA3: This variant is not expected to have clinical si gnificance because it has been identified in 0.95% (642/67532) of … (more)
Likely benign
(Feb 27, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000609652.1
Submitted: (Oct 05, 2017)
Evidence details
Uncertain significance
(Sep 24, 2019)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV000992326.2
Submitted: (Nov 14, 2019)
Evidence details
Comment:
This ABCA3 variant (rs117603931) reaches polymorphic frequency (greater or equal than 1%) within the European (non-Finnish) subpopulation in large population datasets (gnomAD: 1324/129014 total alleles; … (more)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001037379.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001273222.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Feb 26, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001817061.1
Submitted: (Sep 01, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 30413314, 24871971, 29255193, 26928390, 23166334, 27374344, 27516224, 16728712, 20981092, 22995991, 22304854, 25073622)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
An informatics approach to analyzing the incidentalome. Berg JS Genetics in medicine : official journal of the American College of Medical Genetics 2013 PMID: 22995991
Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome. Wambach JA Pediatrics 2012 PMID: 23166334
A child with severe pneumomediastinum and ABCA3 gene mutation: a puzzling connection. Copertino M Archivos de bronconeumologia 2012 PMID: 22304854
ABCA3 mutation and pulmonary hypertension: a link with alveolar capillary dysplasia? Danhaive O The Journal of pediatrics 2008 PMID: 18492541
Alteration of the pulmonary surfactant system in full-term infants with hereditary ABCA3 deficiency. Brasch F American journal of respiratory and critical care medicine 2006 PMID: 16728712

Text-mined citations for rs117603931...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021