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NM_001089.3(ABCA3):c.4085C>T (p.Ala1362Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 20, 2020)
Last evaluated:
May 20, 2019
Accession:
VCV000694630.3
Variation ID:
694630
Description:
single nucleotide variant
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NM_001089.3(ABCA3):c.4085C>T (p.Ala1362Val)

Allele ID
682734
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2281460 (GRCh38) GRCh38 UCSC
16: 2331461 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.9:g.2331461G>A
NC_000016.10:g.2281460G>A
NM_001089.3:c.4085C>T MANE Select NP_001080.2:p.Ala1362Val missense
NG_011790.1:g.64287C>T
Protein change
A1362V
Other names
-
Canonical SPDI
NC_000016.10:2281459:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00029
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Exome Aggregation Consortium (ExAC) 0.00022
The Genome Aggregation Database (gnomAD), exomes 0.00027
The Genome Aggregation Database (gnomAD) 0.00010
1000 Genomes Project 0.00080
Links
dbSNP: rs145251229
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 19, 2018 RCV000902436.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 20, 2019 RCV000856676.2
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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
(May 20, 2019)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV000999222.1
Submitted: (Jun 07, 2019)
Evidence details
Comment:
This previously reported ABCA3 variant (rs145251229) has been identified in large population datasets and the minor allele frequency is neither low enough to consider the … (more)
Likely benign
(Nov 19, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001046858.1
Submitted: (Mar 14, 2019)
Evidence details
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001278810.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
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)

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
Hereditary interstitial lung diseases manifesting in early childhood in Japan. Akimoto T Pediatric research 2014 PMID: 25105258

Text-mined citations for rs145251229...

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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 Feb 27, 2021