ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.359G>A (p.Trp120Ter)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370658.1(BTD):c.359G>A (p.Trp120Ter)
Variation ID: 1069218 Accession: VCV001069218.9
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15642017 (GRCh38) [ NCBI UCSC ] 3: 15683524 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline May 10, 2021 Feb 20, 2024 Mar 9, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.359G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Trp120Ter nonsense NM_000060.4:c.419G>A NP_000051.1:p.Trp140Ter nonsense NM_001281723.4:c.359G>A NP_001268652.2:p.Trp120Ter nonsense NM_001281724.3:c.359G>A NP_001268653.2:p.Trp120Ter nonsense NM_001281725.3:c.359G>A NP_001268654.1:p.Trp120Ter nonsense NM_001281726.3:c.359G>A NP_001268655.2:p.Trp120Ter nonsense NM_001323582.2:c.359G>A NP_001310511.1:p.Trp120Ter nonsense NM_001370752.1:c.359G>A NP_001357681.1:p.Trp120Ter nonsense NM_001370753.1:c.359G>A NP_001357682.1:p.Trp120Ter nonsense NM_001407364.1:c.359G>A NP_001394293.1:p.Trp120Ter nonsense NM_001407365.1:c.359G>A NP_001394294.1:p.Trp120Ter nonsense NM_001407366.1:c.359G>A NP_001394295.1:p.Trp120Ter nonsense NM_001407367.1:c.359G>A NP_001394296.1:p.Trp120Ter nonsense NM_001407368.1:c.359G>A NP_001394297.1:p.Trp120Ter nonsense NM_001407369.1:c.359G>A NP_001394298.1:p.Trp120Ter nonsense NM_001407370.1:c.359G>A NP_001394299.1:p.Trp120Ter nonsense NM_001407371.1:c.359G>A NP_001394300.1:p.Trp120Ter nonsense NM_001407372.1:c.359G>A NP_001394301.1:p.Trp120Ter nonsense NM_001407373.1:c.359G>A NP_001394302.1:p.Trp120Ter nonsense NM_001407374.1:c.359G>A NP_001394303.1:p.Trp120Ter nonsense NM_001407375.1:c.359G>A NP_001394304.1:p.Trp120Ter nonsense NM_001407376.1:c.359G>A NP_001394305.1:p.Trp120Ter nonsense NM_001407377.1:c.359G>A NP_001394306.1:p.Trp120Ter nonsense NM_001407378.1:c.359G>A NP_001394307.1:p.Trp120Ter nonsense NM_001407379.1:c.359G>A NP_001394308.1:p.Trp120Ter nonsense NM_001407380.1:c.359G>A NP_001394309.1:p.Trp120Ter nonsense NM_001407381.1:c.422G>A NP_001394310.1:p.Trp141Ter nonsense NM_001407382.1:c.359G>A NP_001394311.1:p.Trp120Ter nonsense NM_001407383.1:c.359G>A NP_001394312.1:p.Trp120Ter nonsense NM_001407384.1:c.359G>A NP_001394313.1:p.Trp120Ter nonsense NM_001407386.1:c.359G>A NP_001394315.1:p.Trp120Ter nonsense NM_001407388.1:c.359G>A NP_001394317.1:p.Trp120Ter nonsense NM_001407390.1:c.359G>A NP_001394319.1:p.Trp120Ter nonsense NM_001407392.1:c.359G>A NP_001394321.1:p.Trp120Ter nonsense NM_001407394.1:c.359G>A NP_001394323.1:p.Trp120Ter nonsense NM_001407395.1:c.359G>A NP_001394324.1:p.Trp120Ter nonsense NM_001407396.1:c.359G>A NP_001394325.1:p.Trp120Ter nonsense NM_001407397.1:c.359G>A NP_001394326.1:p.Trp120Ter nonsense NM_001407398.1:c.359G>A NP_001394327.1:p.Trp120Ter nonsense NM_001407399.1:c.359G>A NP_001394328.1:p.Trp120Ter nonsense NM_001407400.1:c.359G>A NP_001394329.1:p.Trp120Ter nonsense NM_001407401.1:c.359G>A NP_001394330.1:p.Trp120Ter nonsense NC_000003.12:g.15642017G>A NC_000003.11:g.15683524G>A NG_008019.2:g.45666G>A - Protein change
- W120*, W140*, W141*
- Other names
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- Canonical SPDI
- NC_000003.12:15642016:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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BTD | - | - |
GRCh38 GRCh37 |
647 | 724 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 9, 2023 | RCV001381017.8 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Mar 09, 2023)
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criteria provided, single submitter
Method: clinical testing
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Biotinidase deficiency
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004211474.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Jan 02, 2020)
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criteria provided, single submitter
Method: clinical testing
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Biotinidase deficiency
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001579268.4
First in ClinVar: May 10, 2021 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the BTD protein. Other variant(s) that disrupt this region … (more)
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the BTD protein. Other variant(s) that disrupt this region (p.Leu498Phefs*13) have been determined to be pathogenic (PMID: 17382128, 29359854, 19728141). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has been observed in individuals with a positive newborn screening result for BTD-related disease (PMID: 29353266) This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the BTD gene (p.Trp140*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 404 amino acids of the BTD protein. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Clinical features, BTD gene mutations, and their functional studies of eight symptomatic patients with biotinidase deficiency from Southern China. | Liu Z | American journal of medical genetics. Part A | 2018 | PMID: 29359854 |
Twenty-seven mutations with three novel pathologenic variants causing biotinidase deficiency: a report of 203 patients from the southeastern part of Turkey. | Seker Yilmaz B | Journal of pediatric endocrinology & metabolism : JPEM | 2018 | PMID: 29353266 |
Diagnosis, treatment, follow-up and gene mutation analysis in four Chinese children with biotinidase deficiency. | Ye J | Journal of inherited metabolic disease | 2009 | PMID: 19728141 |
Hearing loss in biotinidase deficiency: genotype-phenotype correlation. | Sivri HS | The Journal of pediatrics | 2007 | PMID: 17382128 |
Text-mined citations for rs2125486425 ...
HelpRecord last updated Feb 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.