ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.950del (p.Val317fs)
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.950del (p.Val317fs)
Variation ID: 1453530 Accession: VCV001453530.7
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15644866 (GRCh38) [ NCBI UCSC ] 3: 15686373 (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 Mar 28, 2022 Feb 14, 2024 Mar 12, 2021 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.950del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Val317fs frameshift NM_000060.4:c.1010delT NP_000051.1:p.Val337Glyfs frameshift NM_001281723.4:c.950delT NP_001268652.2:p.Val317Glyfs frameshift NM_001281724.3:c.950del NP_001268653.2:p.Val317fs frameshift NM_001281725.3:c.950delT NP_001268654.1:p.Val317Glyfs frameshift NM_001323582.2:c.950delT NP_001310511.1:p.Val317Glyfs frameshift NM_001370752.1:c.950del NP_001357681.1:p.Val317fs frameshift NM_001370753.1:c.399+2809del intron variant NM_001407364.1:c.950delT NP_001394293.1:p.Val317Glyfs frameshift NM_001407365.1:c.950delT NP_001394294.1:p.Val317Glyfs frameshift NM_001407366.1:c.950delT NP_001394295.1:p.Val317Glyfs frameshift NM_001407367.1:c.950delT NP_001394296.1:p.Val317Glyfs frameshift NM_001407368.1:c.950delT NP_001394297.1:p.Val317Glyfs frameshift NM_001407369.1:c.950delT NP_001394298.1:p.Val317Glyfs frameshift NM_001407370.1:c.950delT NP_001394299.1:p.Val317Glyfs frameshift NM_001407371.1:c.950delT NP_001394300.1:p.Val317Glyfs frameshift NM_001407372.1:c.950delT NP_001394301.1:p.Val317Glyfs frameshift NM_001407373.1:c.950delT NP_001394302.1:p.Val317Glyfs frameshift NM_001407374.1:c.950delT NP_001394303.1:p.Val317Glyfs frameshift NM_001407375.1:c.950delT NP_001394304.1:p.Val317Glyfs frameshift NM_001407376.1:c.950delT NP_001394305.1:p.Val317Glyfs frameshift NM_001407377.1:c.950delT NP_001394306.1:p.Val317Glyfs frameshift NM_001407378.1:c.950delT NP_001394307.1:p.Val317Glyfs frameshift NM_001407379.1:c.950delT NP_001394308.1:p.Val317Glyfs frameshift NC_000003.12:g.15644866del NC_000003.11:g.15686373del NG_008019.2:g.48515del NG_008019.3:g.48516del - Protein change
- V317fs
- Other names
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- Canonical SPDI
- NC_000003.12:15644865:T:
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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
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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 |
645 | 705 |
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
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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 (1) |
criteria provided, single submitter
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Mar 12, 2021 | RCV002002455.6 |
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 12, 2021)
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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: SCV002237004.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Val337Glyfs*26) in the BTD gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Val337Glyfs*26) in the BTD gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 207 amino acid(s) of the BTD protein. 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.Thr351Lysfs*12) have been determined to be pathogenic (PMID: 12359137, 15776412, 20083419). 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 profound biotinidase deficiency (PMID: 22698809). This variant is not present in population databases (ExAC no frequency). (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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Increased incidence of profound biotinidase deficiency among Hispanic newborns in California. | Cowan TM | Molecular genetics and metabolism | 2012 | PMID: 22698809 |
The identification of novel mutations in the biotinidase gene using denaturing high pressure liquid chromatography (dHPLC). | Iqbal F | Molecular genetics and metabolism | 2010 | PMID: 20083419 |
Biotinidase deficiency: novel mutations and their biochemical and clinical correlates. | Wolf B | Human mutation | 2005 | PMID: 15776412 |
Seventeen novel mutations that cause profound biotinidase deficiency. | Wolf B | Molecular genetics and metabolism | 2002 | PMID: 12359137 |
Text-mined citations for rs2125503248 ...
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.