ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.56_59dup (p.Gly21fs)
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.56_59dup (p.Gly21fs)
Variation ID: 1075658 Accession: VCV001075658.6
- Type and length
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Duplication, 4 bp
- Location
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Cytogenetic: 3p25.1 3: 15635494-15635495 (GRCh38) [ NCBI UCSC ] 3: 15677001-15677002 (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 Sep 21, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.56_59dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Gly21fs frameshift NM_000060.4:c.116_119dup NP_000051.1:p.Gly41Profs frameshift NM_001281723.4:c.56_59dup NP_001268652.2:p.Gly21Profs frameshift NM_001281724.3:c.56_59dup NP_001268653.2:p.Gly21fs frameshift NM_001281725.3:c.56_59dup NP_001268654.1:p.Gly21Profs frameshift NM_001281726.3:c.56_59dup NP_001268655.2:p.Gly21Profs frameshift NM_001323582.2:c.56_59dup NP_001310511.1:p.Gly21Profs frameshift NM_001370752.1:c.56_59dup NP_001357681.1:p.Gly21fs frameshift NM_001370753.1:c.56_59dup NP_001357682.1:p.Gly21fs frameshift NM_001407364.1:c.56_59dup NP_001394293.1:p.Gly21Profs frameshift NM_001407365.1:c.56_59dup NP_001394294.1:p.Gly21Profs frameshift NM_001407366.1:c.56_59dup NP_001394295.1:p.Gly21Profs frameshift NM_001407367.1:c.56_59dup NP_001394296.1:p.Gly21Profs frameshift NM_001407368.1:c.56_59dup NP_001394297.1:p.Gly21Profs frameshift NM_001407369.1:c.56_59dup NP_001394298.1:p.Gly21Profs frameshift NM_001407370.1:c.56_59dup NP_001394299.1:p.Gly21Profs frameshift NM_001407371.1:c.56_59dup NP_001394300.1:p.Gly21Profs frameshift NM_001407372.1:c.56_59dup NP_001394301.1:p.Gly21Profs frameshift NM_001407373.1:c.56_59dup NP_001394302.1:p.Gly21Profs frameshift NM_001407374.1:c.56_59dup NP_001394303.1:p.Gly21Profs frameshift NM_001407375.1:c.56_59dup NP_001394304.1:p.Gly21Profs frameshift NM_001407376.1:c.56_59dup NP_001394305.1:p.Gly21Profs frameshift NM_001407377.1:c.56_59dup NP_001394306.1:p.Gly21Profs frameshift NM_001407378.1:c.56_59dup NP_001394307.1:p.Gly21Profs frameshift NM_001407379.1:c.56_59dup NP_001394308.1:p.Gly21Profs frameshift NM_001407380.1:c.56_59dup NP_001394309.1:p.Gly21Profs frameshift NM_001407381.1:c.56_59dup NP_001394310.1:p.Gly21Profs frameshift NM_001407382.1:c.56_59dup NP_001394311.1:p.Gly21Profs frameshift NM_001407383.1:c.56_59dup NP_001394312.1:p.Gly21Profs frameshift NM_001407384.1:c.56_59dup NP_001394313.1:p.Gly21Profs frameshift NM_001407386.1:c.56_59dup NP_001394315.1:p.Gly21Profs frameshift NM_001407388.1:c.56_59dup NP_001394317.1:p.Gly21Profs frameshift NM_001407390.1:c.56_59dup NP_001394319.1:p.Gly21Profs frameshift NM_001407392.1:c.56_59dup NP_001394321.1:p.Gly21Profs frameshift NM_001407394.1:c.56_59dup NP_001394323.1:p.Gly21Profs frameshift NM_001407395.1:c.56_59dup NP_001394324.1:p.Gly21Profs frameshift NM_001407396.1:c.56_59dup NP_001394325.1:p.Gly21Profs frameshift NM_001407397.1:c.56_59dup NP_001394326.1:p.Gly21Profs frameshift NM_001407398.1:c.56_59dup NP_001394327.1:p.Gly21Profs frameshift NM_001407399.1:c.56_59dup NP_001394328.1:p.Gly21Profs frameshift NM_001407400.1:c.56_59dup NP_001394329.1:p.Gly21Profs frameshift NM_001407401.1:c.56_59dup NP_001394330.1:p.Gly21Profs frameshift NC_000003.12:g.15635495_15635498dup NC_000003.11:g.15677002_15677005dup NG_008019.2:g.39144_39147dup - Protein change
- G21fs
- Other names
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- Canonical SPDI
- NC_000003.12:15635494:CCCT:CCCTCCCT
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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 |
- | 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
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 (1) |
criteria provided, single submitter
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Sep 21, 2023 | RCV001389326.5 |
Submissions - Germline
Classification
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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
(Sep 21, 2023)
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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: SCV001590651.4
First in ClinVar: May 10, 2021 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1075658). This variant has not been … (more)
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1075658). This variant has not been reported in the literature in individuals affected with BTD-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly41Profs*12) in the BTD gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BTD are known to be pathogenic (PMID: 20083419). (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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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 |
Text-mined citations for rs2125453296 ...
HelpRecord last updated Feb 28, 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.