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NM_000018.4(ACADVL):c.1600G>A (p.Glu534Lys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(8);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000021018.14
Variation ID:
21018
Description:
single nucleotide variant
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NM_000018.4(ACADVL):c.1600G>A (p.Glu534Lys)

Allele ID
33870
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p13.1
Genomic location
17: 7224388 (GRCh38) GRCh38 UCSC
17: 7127707 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P49748:p.Glu534Lys
NC_000017.11:g.7224388G>A
NC_000017.10:g.7127707G>A
... more HGVS
Protein change
E534K, E458K, E512K, E557K
Other names
p.E534K:GAG>AAG
NM_000018.3(ACADVL):c.1600G>A(p.Glu534Lys)
NM_001033859.2(ACADVL):c.1534G>A(p.Glu512Lys)
NM_001270447.1(ACADVL):c.1669G>A(p.Glu557Lys)
NM_001270448.1(ACADVL):c.1372G>A(p.Glu458Lys)
Canonical SPDI
NC_000017.11:7224387:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00639 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00926
The Genome Aggregation Database (gnomAD), exomes 0.00204
1000 Genomes Project 0.00639
The Genome Aggregation Database (gnomAD) 0.00864
Exome Aggregation Consortium (ExAC) 0.00257
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01030
Links
ClinGen: CA285289
UniProtKB: P49748#VAR_010105
dbSNP: rs2230180
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Nov 5, 2019 RCV000077907.9
Conflicting interpretations of pathogenicity 7 criteria provided, conflicting interpretations Dec 4, 2020 RCV000020074.14
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ACADVL - - GRCh38
GRCh37
884 960

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: unknown
Mendelics
Accession: SCV001140232.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Nov 07, 2019)
criteria provided, single submitter
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000602373.3
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: germline
Invitae
Accession: SCV000654939.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Oct 10, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000238672.6
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)
Uncertain significance
(May 31, 2018)
criteria provided, single submitter
Method: curation
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803496.1
Submitted: (Jun 13, 2018)
Evidence details
Comment:
This variant is interpreted as a Uncertain Significance - Conflicting Evidence, for Very long chain acyl-coa dehydrogenase deficiency, in Autosomal Recessive manner. The following ACMG … (more)
Benign
(Feb 26, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000109736.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001281708.1
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)
Benign
(Nov 05, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001362324.1
Submitted: (Mar 06, 2020)
Evidence details
Comment:
Variant summary: ACADVL c.1600G>A (p.Glu534Lys) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Benign
(Nov 01, 2019)
criteria provided, single submitter
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: germline
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Accession: SCV001365184.2
Submitted: (Jul 13, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The NM_000018.3:c.1600G>A (NP_000009.1:p.Glu534Lys) [GRCH38: NC_000017.11:g.7224388G>A] variant in ACADVL gene is interpretated to be Benign based on ACMG guidelines (PMID: 25741868). This variant has been reported. … (more)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Very long chain acyl-CoA dehydrogenase deficiency
Allele origin: germline
Natera, Inc.
Accession: SCV001459260.1
Submitted: (Dec 28, 2020)
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
Recurrent ACADVL molecular findings in individuals with a positive newborn screen for very long chain acyl-coA dehydrogenase (VLCAD) deficiency in the United States. Miller MJ Molecular genetics and metabolism 2015 PMID: 26385305
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Bell CJ Science translational medicine 2011 PMID: 21228398
Molecular heterogeneity in very-long-chain acyl-CoA dehydrogenase deficiency causing pediatric cardiomyopathy and sudden death. Mathur A Circulation 1999 PMID: 10077518
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ACADVL - - - -

Text-mined citations for rs2230180...

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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 Sep 12, 2021