rs397514395
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001370658.1(BTD):c.873delT(p.Ser291ArgfsTer23) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001370658.1 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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BTD | NM_001370658.1 | c.873delT | p.Ser291ArgfsTer23 | frameshift_variant | Exon 4 of 4 | ENST00000643237.3 | NP_001357587.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251388Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135860
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727248
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
Biotinidase deficiency Pathogenic:7
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This sequence change creates a premature translational stop signal (p.Ser311Argfs*23) in the BTD gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 233 amino acid(s) of the BTD protein. This variant is present in population databases (rs397514395, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with biotinidase deficiency (PMID: 9396567, 10400129, 12359137, 17185019, 22698809, 25174816, 27657684). ClinVar contains an entry for this variant (Variation ID: 25052). For these reasons, this variant has been classified as Pathogenic. -
The BTD c.873del; Ser291ArgfsTer23 variant (rs397514395; ClinVar Variation ID: 25052), also known as c.933delT; p.Ser311fs in traditional nomenclature, is reported in the literature in the compound heterozygous state in multiple individuals affected with profound or partial biotinidase deficiency (Borsatto 2014, Milankovics 2007, Pomponio 1997, Wolf 2002, Wolf 2017). This variant is found on only three chromosomes in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. This variant causes a frameshift by deleting a single nucleotide in the last exon of the BTD gene. While this is not expected to lead to nonsense-mediated decay, this is predicted to result in a truncated protein lacking the last 233 amino acids of the BTD protein. Based on available information, this variant is considered to be pathogenic. References: Borsatto T et al. Biotinidase deficiency: clinical and genetic studies of 38 Brazilian patients. BMC Med Genet. 2014;15:96. PMID: 25174816. Milankovics I et al. Mutations causing biotinidase deficiency in children ascertained by newborn screening in Western Hungary. Mol Genet Metab. 2007;90(3):345-348. PMID: 17185019. Pomponio RJ et al. Mutations in the human biotinidase gene that cause profound biotinidase deficiency in symptomatic children: molecular, biochemical, and clinical analysis. Pediatr Res. 1997;42(6):840-848. PMID: 9396567 Wolf B et al. Seventeen novel mutations that cause profound biotinidase deficiency. Mol Genet Metab. 2002;77(1-2):108-111. PMID: 12359137. Wolf B. Successful outcomes of older adolescents and adults with profound biotinidase deficiency identified by newborn screening. Genet Med. 2017;19(4):396-402. PMID: 27657684. -
not provided Pathogenic:3
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Frameshift variant predicted to result in abnormal protein length as the last 233 amino acids are replaced with 22 different amino acids, and other similar variants have been reported; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20549359, 9396567, 10400129, 27657684, 35195902, 38299772, 38523675) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at