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NM_000017.4(ACADS):c.1058C>T (p.Ser353Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(4);Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jul 4, 2021)
Last evaluated:
Oct 19, 2018
Accession:
VCV000003836.11
Variation ID:
3836
Description:
single nucleotide variant
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NM_000017.4(ACADS):c.1058C>T (p.Ser353Leu)

Allele ID
18875
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.31
Genomic location
12: 120739168 (GRCh38) GRCh38 UCSC
12: 121176971 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P16219:p.Ser353Leu
NC_000012.11:g.121176971C>T
NC_000012.12:g.120739168C>T
... more HGVS
Protein change
S353L, S349L
Other names
S329L
p.S353L:TCG>TTG
Canonical SPDI
NC_000012.12:120739167:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00017
The Genome Aggregation Database (gnomAD) 0.00022
The Genome Aggregation Database (gnomAD), exomes 0.00020
Exome Aggregation Consortium (ExAC) 0.00012
Links
ClinGen: CA252888
UniProtKB: P16219#VAR_013570
OMIM: 606885.0012
dbSNP: rs28941773
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Dec 12, 2017 RCV000185693.4
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Oct 19, 2018 RCV000004040.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ACADS - - GRCh38
GRCh37
237 254

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001148848.6
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Apr 24, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: germline
Invitae
Accession: SCV000756743.2
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces serine with leucine at codon 353 of the ACADS protein (p.Ser353Leu). The serine residue is highly conserved and there is a … (more)
Likely pathogenic
(Dec 12, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000883331.1
Submitted: (Oct 10, 2018)
Evidence details
Comment:
The ACADS p.Ser353Leu variant (rs28941773) has been reported in two individuals with a diagnosis of short-chain acyl-CoA dehydrogenase (SCAD) deficiency who also had a common … (more)
Likely pathogenic
(Jan 12, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000238614.11
Submitted: (Jul 13, 2017)
Evidence details
Comment:
The S353L missense variant in the ACADS gene has been reported previously as S329L in a patient with 10% of control short chain acyl-CoA dehydrogenase … (more)
Likely pathogenic
(Dec 03, 2017)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: inherited
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000746500.1
Submitted: (Dec 03, 2017)
Evidence details
Pathogenic
(Oct 19, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000914566.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The ACADS c.1058C>T (p.Ser353Leu) missense variant has been reported in two studies in which it is identified in at least seven probands with short-chain acyl-coA … (more)
Likely pathogenic
(Jun 21, 2018)
no assertion criteria provided
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: unknown
Counsyl
Accession: SCV000678148.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (3)
Pathogenic
(Jan 01, 2001)
no assertion criteria provided
Method: literature only
SCAD DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000024206.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
High prevalence of short-chain acyl-CoA dehydrogenase deficiency in the Netherlands, but no association with epilepsy of unknown origin in childhood. van Maldegem BT Neuropediatrics 2011 PMID: 21500142
Fasting and fat-loading tests provide pathophysiological insight into short-chain acyl-coenzyme a dehydrogenase deficiency. van Maldegem BT The Journal of pediatrics 2010 PMID: 19800078
The ACADS gene variation spectrum in 114 patients with short-chain acyl-CoA dehydrogenase (SCAD) deficiency is dominated by missense variations leading to protein misfolding at the cellular level. Pedersen CB Human genetics 2008 PMID: 18523805
Clinical, biochemical, and genetic heterogeneity in short-chain acyl-coenzyme A dehydrogenase deficiency. van Maldegem BT JAMA 2006 PMID: 16926354
Role of common gene variations in the molecular pathogenesis of short-chain acyl-CoA dehydrogenase deficiency. Corydon MJ Pediatric research 2001 PMID: 11134486

Text-mined citations for rs28941773...

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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 07, 2021