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NM_001089.3(ABCA3):c.839G>A (p.Arg280His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 27, 2020
Accession:
VCV000228421.4
Variation ID:
228421
Description:
single nucleotide variant
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NM_001089.3(ABCA3):c.839G>A (p.Arg280His)

Allele ID
230629
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2319615 (GRCh38) GRCh38 UCSC
16: 2369616 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2319615C>T
NC_000016.9:g.2369616C>T
NM_001089.3:c.839G>A MANE Select NP_001080.2:p.Arg280His missense
NG_011790.1:g.26132G>A
Protein change
R280H
Other names
-
Canonical SPDI
NC_000016.10:2319614:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00081
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
Exome Aggregation Consortium (ExAC) 0.00100
The Genome Aggregation Database (gnomAD) 0.00092
1000 Genomes Project 0.00020
Links
ClinGen: CA7841503
dbSNP: rs143008553
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Aug 27, 2020 RCV000308878.3
Uncertain significance 1 criteria provided, single submitter Dec 9, 2015 RCV000219325.1
Likely benign 1 criteria provided, single submitter Aug 20, 2020 RCV001477709.1
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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

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 09, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000271479.2
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The p.Arg280His variant in ABCA3 has been reported in 1 individual with adult id iopathic interstitial pneumonia (Van Moorsel, 2010). It has been identified in … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000396148.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Aug 27, 2020)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001431524.1
Submitted: (Sep 02, 2020)
Evidence details
Publications
PubMed (3)
Likely benign
(Aug 20, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001681956.1
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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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

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Title Author Journal Year Link
Lung disease caused by <i>ABCA3</i> mutations. Kröner C Thorax 2017 PMID: 27516224
Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome. Wambach JA Pediatrics 2012 PMID: 23166334
Surfactant protein C mutations are the basis of a significant portion of adult familial pulmonary fibrosis in a dutch cohort. van Moorsel CH American journal of respiratory and critical care medicine 2010 PMID: 20656946

Text-mined citations for rs143008553...

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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 Jul 07, 2021