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NM_001609.4(ACADSB):c.443C>T (p.Thr148Ile) AND Deficiency of 2-methylbutyryl-CoA dehydrogenase

Germline classification:
Conflicting interpretations of pathogenicity (8 submissions)
Last evaluated:
Oct 9, 2024
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000009780.29

Allele description

NM_001609.4(ACADSB):c.443C>T (p.Thr148Ile)

Gene:
ACADSB:acyl-CoA dehydrogenase short/branched chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q26.13
Genomic location:
Preferred name:
NM_001609.4(ACADSB):c.443C>T (p.Thr148Ile)
HGVS:
  • NC_000010.11:g.123040605C>T
  • NG_008003.1:g.36693C>T
  • NM_001330174.3:c.137C>T
  • NM_001609.4:c.443C>TMANE SELECT
  • NP_001317103.1:p.Thr46Ile
  • NP_001600.1:p.Thr148Ile
  • NP_001600.1:p.Thr148Ile
  • LRG_451t1:c.443C>T
  • LRG_451:g.36693C>T
  • LRG_451p1:p.Thr148Ile
  • NC_000010.10:g.124800121C>T
  • NM_001609.3:c.443C>T
Protein change:
T148I; THR148ILE
Links:
OMIM: 600301.0004; dbSNP: rs58639322
NCBI 1000 Genomes Browser:
rs58639322
Molecular consequence:
  • NM_001330174.3:c.137C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001609.4:c.443C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Deficiency of 2-methylbutyryl-CoA dehydrogenase (ACADSB)
Synonyms:
2-methylbutyryl-CoA dehydrogenase deficiency; SBCAD deficiency; 2-methylbutyric aciduria; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012392; MedGen: C1864912; Orphanet: 79157; OMIM: 610006; Human Phenotype Ontology: HP:0020147

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000030001OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2008)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000645153Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 10, 2024)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV000915461Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Apr 28, 2017)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001251416Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 9, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001527950Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001761004New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Likely pathogenic
(Jun 26, 2020)
inheritedclinical testing

Citation Link,

SCV002766172Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Nov 26, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV004810376Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Apr 4, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedunknown1not providednot provided1not providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Characterization of new ACADSB gene sequence mutations and clinical implications in patients with 2-methylbutyrylglycinuria identified by newborn screening.

Alfardan J, Mohsen AW, Copeland S, Ellison J, Keppen-Davis L, Rohrbach M, Powell BR, Gillis J, Matern D, Kant J, Vockley J.

Mol Genet Metab. 2010 Aug;100(4):333-8. doi: 10.1016/j.ymgme.2010.04.014. Epub 2010 May 23.

PubMed [citation]
PMID:
20547083
PMCID:
PMC2906669
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000030001.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 2 brothers, born of a consanguineous Arab couple from Lebanon, with 2-methylbutyryl-CoA dehydrogenase deficiency (610006), Sass et al. (2008) identified compound heterozygosity for mutations in the ACADSB gene: a 443C-T transition in exon 4, resulting in a thr148-to-ile (T148I) substitution, and a 1159G-A transition in exon 10, resulting in a glu387-to-lys (E387K; 600301.0005) substitution. One brother was diagnosed by newborn screening, and the other was diagnosed at age 3 years after his brother's diagnosis. Neither patient showed any clinical abnormalities, and both had normal development, but were lost to follow-up when the proband was 10 months old. The authors also identified homozygosity for the T148I mutation in 2 sibs from a consanguineous Turkish family. Both boys had normal development at age 6 and 7 years, respectively. In vitro studies of patient fibroblasts confirmed an impairment in isoleucine degradation.

In a child of European ancestry who was identified by newborn screening to have 2-methybutyryl-CoA dehydrogenase deficiency, Alfardan et al. (2010) identified compound heterozygosity for the T148I and E387K mutations. Alfardan et al. (2010) introduced the T148I mutation into an SBCAD expression vector and expressed it in E. coli. SBCAD protein was not detectable by Western blot analysis, and SBCAD enzyme activity was absent. Molecular modeling showed that the T148 residue resides in a hydrophilic pocket, where an Ile substitution might be disruptive.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000645153.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 148 of the ACADSB protein (p.Thr148Ile). This variant is present in population databases (rs58639322, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with SBCAD deficiency (PMID: 15615815, 17945527, 20547083, 30730842). ClinVar contains an entry for this variant (Variation ID: 9202). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ACADSB protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects ACADSB function (PMID: 20547083). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000915461.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The ACADSB c.443C>T (p.Thr148Ile) missense variant has been reported in at least three studies in which it is found in a total of six patients with acyl-CoA dehydrogenase, short/branched chain deficiency, including in three, of whom two are siblings, who carried the variant in a homozygous state, and three, of whom two are siblings, who carried the variant in a compound heterozygous state (Korman et al. 2005; Sass et al. 2008; Alfardan et al. 2010). The p.Thr148Ile variant was not detected in 92 control chromosomes and is reported at a frequency of 0.0023 in the South Asian population of the Exome Aggregation Consortium. In vitro expression in E. coli found that the p.Thr148Ile variant protein had almost undetectable activity compared to wild type (Alfardan et al. 2010). It should be noted that some individuals with this disorder may remain asymptomatic throughout life. Based on the evidence, the p.Thr148Ile variant is classified as pathogenic for acyl-CoA dehydrogenase, short/branched chain deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001251416.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001527950.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From New York Genome Center - CSER-NYCKidSeq, SCV001761004.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002766172.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Variant summary: ACADSB c.443C>T (p.Thr148Ile) results in a non-conservative amino acid change located in the Acyl-CoA dehydrogenase/oxidase, N-terminal domain (IPR013786) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00083 in 251424 control chromosomes (gnomAD). c.443C>T has been reported in the literature as a biallelic genotype in multiple individuals affected with Deficiency Of 2-Methylbutyryl Dehydrogenase (e.g. Korman_2005, Sass_2008, Porta_2019). These data indicate that the variant is very likely to be associated with disease. When the variant was expressed in E. coli, the variant had minimal protein yield and 2.8% normal activity (Alfardan_2010). Seven ClinVar submitters have assessed the variant since 2014: three classified the variant as uncertain significance, one as likely pathogenic, and three as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810376.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 18, 2024