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NM_001089.3(ABCA3):c.1502C>A (p.Ala501Glu)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 21, 2020
Accession:
VCV000178700.4
Variation ID:
178700
Description:
single nucleotide variant
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NM_001089.3(ABCA3):c.1502C>A (p.Ala501Glu)

Allele ID
176147
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2300114 (GRCh38) GRCh38 UCSC
16: 2350115 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2300114G>T
NC_000016.9:g.2350115G>T
NM_001089.3:c.1502C>A MANE Select NP_001080.2:p.Ala501Glu missense
NG_011790.1:g.45633C>A
Protein change
A501E
Other names
-
Canonical SPDI
NC_000016.10:2300113:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00339 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00323
Trans-Omics for Precision Medicine (TOPMed) 0.00233
1000 Genomes Project 0.00339
Links
ClinGen: CA182810
dbSNP: rs141621969
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Aug 21, 2020 RCV001517013.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 11, 2015 RCV000155457.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations May 28, 2019 RCV000758248.3
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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
Likely benign
(Dec 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000520868.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Feb 11, 2019)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV000886888.1
Submitted: (Mar 05, 2019)
Evidence details
Uncertain significance
(Nov 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000205148.4
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The Ala501Glu variant of ABCA3 has been previously identified in one individual with severe pulmonary hypertension and histological/ultrastructural analyses con sistent with ABCA3 deficiency (Danhaive … (more)
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Surfactant metabolism dysfunction, pulmonary, 3
Allele origin: unknown
Mendelics
Accession: SCV001139800.1
Submitted: (Oct 22, 2019)
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: SCV001279948.1
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)
Benign
(Aug 21, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001725398.1
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
ABCA3 mutation and pulmonary hypertension: a link with alveolar capillary dysplasia? Danhaive O The Journal of pediatrics 2008 PMID: 18492541

Text-mined citations for rs141621969...

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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