rs190867671
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_183050.4(BCKDHB):c.1149T>A(p.Tyr383Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. Y383Y) has been classified as Likely benign.
Frequency
Consequence
NM_183050.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCKDHB | NM_183050.4 | c.1149T>A | p.Tyr383Ter | stop_gained | 10/10 | ENST00000320393.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDHB | ENST00000320393.9 | c.1149T>A | p.Tyr383Ter | stop_gained | 10/10 | 1 | NM_183050.4 | P1 | |
BCKDHB | ENST00000356489.9 | c.1149T>A | p.Tyr383Ter | stop_gained | 10/11 | 1 | P1 | ||
BCKDHB | ENST00000491328.1 | n.204T>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Maple syrup urine disease Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 27, 2020 | Variant summary: BCKDHB c.1149T>A (p.Tyr383X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251330 control chromosomes. c.1149T>A has been reported in the literature as a homozygous variant in at-least one individual of Turkish ethnicity affected with classic Maple syrup urine disease (Nellis_2001) and has been subsequently cited by others (example, Henneke_2003). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity in patient fibroblasts (Henneke_2003). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Aug 10, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2020 | For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the BCKDHB protein. Other variant(s) that disrupt this region (p.Arg387*) have been determined to be pathogenic (PMID: 30228974, Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has been observed in individual(s) with maple syrup urine disease (PMID: 11112664, 14517957). ClinVar contains an entry for this variant (Variation ID: 553268). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr383*) in the BCKDHB gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 10 amino acid(s) of the BCKDHB protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at