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NM_000017.4(ACADS):c.319C>T (p.Arg107Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(8);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
11 (Most recent: Apr 29, 2019)
Last evaluated:
Apr 27, 2019
Accession:
VCV000003826.4
Variation ID:
3826
Description:
single nucleotide variant
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NM_000017.4(ACADS):c.319C>T (p.Arg107Cys)

Allele ID
18865
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.31
Genomic location
12: 120737094 (GRCh38) GRCh38 UCSC
12: 121174897 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.121174897C>T
NC_000012.12:g.120737094C>T
NM_001302554.2:c.319C>T NP_001289483.1:p.Arg107Cys missense
... more HGVS
Protein change
R107C
Other names
p.R107C:CGT>TGT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00097
Exome Aggregation Consortium (ExAC) 0.00106
Trans-Omics for Precision Medicine (TOPMed) 0.00049
The Genome Aggregation Database (gnomAD) 0.00019
Links
ClinGen: CA312209
UniProtKB: P16219#VAR_000312
OMIM: 606885.0002
dbSNP: rs61732144
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Aug 7, 2017 RCV000185680.4
Conflicting interpretations of pathogenicity 9 criteria provided, conflicting interpretations Apr 27, 2019 RCV000004030.14
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ACADS - - GRCh38
GRCh37
145 162

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Feb 02, 2015)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
(Autosomal recessive inheritance)
Allele origin: germline
Knight Diagnostic Laboratories,Oregon Health and Sciences University
Accession: SCV000223916.1
Submitted: (May 29, 2015)
Evidence details
Pathogenic
(Mar 11, 2016)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: unknown
Counsyl
Accession: SCV000485196.1
Submitted: (Nov 23, 2016)
Evidence details
Pathogenic
(Aug 07, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000238601.11
Submitted: (Nov 28, 2017)
Evidence details
Comment:
This mutation is denoted c.319 C>T at the cDNA level or p.Arg107Cys (R107C) at the protein level. And resulting in the replacement of an Arginine ... (more)
Pathogenic
(Nov 03, 2017)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: germline
Invitae
Accession: SCV000632503.2
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change replaces arginine with cysteine at codon 107 of the ACADS protein (p.Arg107Cys). The arginine residue is highly conserved and there is a ... (more)
Pathogenic
(Jan 06, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000228753.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893276.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Jan 18, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000376674.3
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (5)
Comment:
The ACADS c.319C>T (p.Arg107Cys) missense variant has been reported in at least three studies in which it is found in a total of 11 patients ... (more)
Pathogenic
(Dec 29, 2015)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine
Accession: SCV000711743.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (4)
Comment:
The p.Arg107Cys variant (NM_000017.2 c.319C>T) in ACADS has been reported in at least 11 individuals with clinical features of Acyl-CoA-dehydrogenase deficiency . Three of these ... (more)
Uncertain significance
(Apr 27, 2019)
criteria provided, single submitter
Method: clinical testing
Deficiency of butyryl-CoA dehydrogenase
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000930208.1
Submitted: (Apr 29, 2019)
Evidence details
Pathogenic
(Feb 01, 2008)
no assertion criteria provided
Method: literature only
SCAD DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000024196.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)
Naito, E., Indo, Y., Tanaka, K.  (more...)
Pathogenic
(Aug 07, 2014)
no assertion criteria provided
Method: literature only
Deficiency of butyryl-CoA dehydrogenase
Allele origin: germline
GeneReviews
Accession: SCV000188412.2
Submitted: (Aug 13, 2014)
Evidence details
Publications
PubMed (1)

Citations for this variant

Title Author Journal Year Link
Short-Chain Acyl-CoA Dehydrogenase Deficiency Wolfe L - 2018 PMID: 21938826
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Proteomic investigation of cultivated fibroblasts from patients with mitochondrial short-chain acyl-CoA dehydrogenase deficiency. Edhager AV Molecular genetics and metabolism 2014 PMID: 24485985
Follow-up of patients with short-chain acyl-CoA dehydrogenase and isobutyryl-CoA dehydrogenase deficiencies identified through newborn screening: one center's experience. Pena L Genetics in medicine : official journal of the American College of Medical Genetics 2012 PMID: 22241096
Vulnerability to oxidative stress in vitro in pathophysiology of mitochondrial short-chain acyl-CoA dehydrogenase deficiency: response to antioxidants. Zolkipli Z PloS one 2011 PMID: 21483766
Toxic response caused by a misfolding variant of the mitochondrial protein short-chain acyl-CoA dehydrogenase. Schmidt SP Journal of inherited metabolic disease 2011 PMID: 21170680
Short-chain acyl-CoA dehydrogenase (SCAD) deficiency: an examination of the medical and neurodevelopmental characteristics of 14 cases identified through newborn screening or clinical symptoms. Waisbren SE Molecular genetics and metabolism 2008 PMID: 18676165
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
Short-chain acyl-CoA dehydrogenase gene mutation (c.319C>T) presents with clinical heterogeneity and is candidate founder mutation in individuals of Ashkenazi Jewish origin. Tein I Molecular genetics and metabolism 2008 PMID: 18054510
Identification of two variant short chain acyl-coenzyme A dehydrogenase alleles, each containing a different point mutation in a patient with short chain acyl-coenzyme A dehydrogenase deficiency. Naito E The Journal of clinical investigation 1990 PMID: 1692038
Short chain acyl-coenzyme A dehydrogenase (SCAD) deficiency. Immunochemical demonstration of molecular heterogeneity due to variant SCAD with differing stability. Naito E The Journal of clinical investigation 1989 PMID: 2808706
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ACADS - - - -
Naito, E., Indo, Y., Tanaka, K. Short chain acyl-CoA dehydrogenase (SCAD) deficiency: demonstration of molecular heterogeneity and identification of point mutations. (Abstract) Am. J. Hum. Genet. 45 (suppl.): A208, 1989. - - - -

Record last updated Oct 27, 2019