rs1554194690
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_183050.4(BCKDHB):βc.811_824delβ(p.Asp271CysfsTer25) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,762 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (β β ). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes π: 6.8e-7 ( 0 hom. )
Consequence
BCKDHB
NM_183050.4 frameshift
NM_183050.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.44
Genes affected
BCKDHB (HGNC:987): (branched chain keto acid dehydrogenase E1 subunit beta) This gene encodes the E1 beta subunit of branched-chain keto acid dehydrogenase, which is a multienzyme complex associated with the inner membrane of mitochondria. This enzyme complex functions in the catabolism of branched-chain amino acids. Mutations in this gene have been associated with maple syrup urine disease (MSUD), type 1B, a disease characterized by a maple syrup odor to the urine in addition to mental and physical retardation and feeding problems. Alternative splicing at this locus results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 6-80200998-GAGTGATGTTACTCT-G is Pathogenic according to our data. Variant chr6-80200998-GAGTGATGTTACTCT-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 557213.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCKDHB | NM_183050.4 | c.811_824del | p.Asp271CysfsTer25 | frameshift_variant | 7/10 | ENST00000320393.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDHB | ENST00000320393.9 | c.811_824del | p.Asp271CysfsTer25 | frameshift_variant | 7/10 | 1 | NM_183050.4 | P1 | |
BCKDHB | ENST00000356489.9 | c.811_824del | p.Asp271CysfsTer25 | frameshift_variant | 7/11 | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460762Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 726746
GnomAD4 exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
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32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Maple syrup urine disease Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 19, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 557213). This variant is also known as c.808_821del, p.Ser270_Leu274del. This premature translational stop signal has been observed in individual(s) with maple syrup urine disease (PMID: 17922217). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp271Cysfs*25) in the BCKDHB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BCKDHB are known to be pathogenic (PMID: 16786533, 22593002). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at