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NM_183050.4(BCKDHB):c.547C>T (p.Arg183Trp) AND not provided

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
Aug 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000082753.34

Allele description [Variation Report for NM_183050.4(BCKDHB):c.547C>T (p.Arg183Trp)]

NM_183050.4(BCKDHB):c.547C>T (p.Arg183Trp)

Gene:
BCKDHB:branched chain keto acid dehydrogenase E1 subunit beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q14.1
Genomic location:
Preferred name:
NM_183050.4(BCKDHB):c.547C>T (p.Arg183Trp)
HGVS:
  • NC_000006.12:g.80168944C>T
  • NG_009775.2:g.67318C>T
  • NM_000056.5:c.547C>T
  • NM_001318975.1:c.337C>T
  • NM_183050.4:c.547C>TMANE SELECT
  • NP_000047.1:p.Arg183Trp
  • NP_001305904.1:p.Arg113Trp
  • NP_898871.1:p.Arg183Trp
  • NP_898871.1:p.Arg183Trp
  • NC_000006.11:g.80878661C>T
  • NM_000056.5:c.547C>T
  • NM_183050.2:c.547C>T
  • NM_183050.3:c.547C>T
  • NR_134945.2:n.570C>T
Protein change:
R113W
Links:
dbSNP: rs149766077
NCBI 1000 Genomes Browser:
rs149766077
Molecular consequence:
  • NM_000056.5:c.547C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318975.1:c.337C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_183050.4:c.547C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134945.2:n.570C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
7

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000231229Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions)
Likely pathogenic
(Dec 17, 2015)
germlineclinical testing

Citation Link,

SCV000617632GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Likely pathogenic
(Sep 7, 2017)
germlineclinical testing

Citation Link,

SCV001747473CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely pathogenic
(Aug 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknown5not providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000231229.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided5not providednot providednot provided

From GeneDx, SCV000617632.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The R183W variant in the BCKDHB gene has previously been reported in association with classic maple syrup urine disease (MSUD) in an individual who was homozygous for R183W (Gorzelany et al., 2009).The R183W variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R183W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Another missense variant at this position (R183P) has also been reported in association with MSUD (Edelmann et al., 2001), supporting the functional importance of this region of the protein. In summary, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded

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

From CeGaT Center for Human Genetics Tuebingen, SCV001747473.20

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

BCKDHB: PM2, PM3, PM5, PP4:Moderate, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Nov 10, 2024