For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370847). 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.Tyr36*) 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).
ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.47dup (p.Tyr16Ter)
Germline
Classification
Help
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.
(2)
Help
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.
Pathogenic/Likely pathogenic
2
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001370658.1(BTD):c.47dup (p.Tyr16Ter)
Variation ID: 370847 Accession: VCV000370847.6
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15635485-15635486 (GRCh38) [ NCBI UCSC ] 3: 15676992-15676993 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Jan 6, 2017 Feb 20, 2024 Jul 12, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001370658.1:c.47dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Tyr16Ter nonsense NM_000060.4:c.107dup NP_000051.1:p.Tyr36Terfs frameshift nonsense NM_001281723.4:c.47dup NP_001268652.2:p.Tyr16Terfs frameshift nonsense NM_001281724.3:c.47dup NP_001268653.2:p.Tyr16Ter nonsense NM_001281725.3:c.47dup NP_001268654.1:p.Tyr16Terfs frameshift nonsense NM_001281726.3:c.47dup NP_001268655.2:p.Tyr16Terfs frameshift nonsense NM_001323582.2:c.47dup NP_001310511.1:p.Tyr16Terfs frameshift nonsense NM_001370752.1:c.47dup NP_001357681.1:p.Tyr16Ter nonsense NM_001370753.1:c.47dup NP_001357682.1:p.Tyr16Ter nonsense NM_001407364.1:c.47dup NP_001394293.1:p.Tyr16Terfs frameshift nonsense NM_001407365.1:c.47dup NP_001394294.1:p.Tyr16Terfs frameshift nonsense NM_001407366.1:c.47dup NP_001394295.1:p.Tyr16Terfs frameshift nonsense NM_001407367.1:c.47dup NP_001394296.1:p.Tyr16Terfs frameshift nonsense NM_001407368.1:c.47dup NP_001394297.1:p.Tyr16Terfs frameshift nonsense NM_001407369.1:c.47dup NP_001394298.1:p.Tyr16Terfs frameshift nonsense NM_001407370.1:c.47dup NP_001394299.1:p.Tyr16Terfs frameshift nonsense NM_001407371.1:c.47dup NP_001394300.1:p.Tyr16Terfs frameshift nonsense NM_001407372.1:c.47dup NP_001394301.1:p.Tyr16Terfs frameshift nonsense NM_001407373.1:c.47dup NP_001394302.1:p.Tyr16Terfs frameshift nonsense NM_001407374.1:c.47dup NP_001394303.1:p.Tyr16Terfs frameshift nonsense NM_001407375.1:c.47dup NP_001394304.1:p.Tyr16Terfs frameshift nonsense NM_001407376.1:c.47dup NP_001394305.1:p.Tyr16Terfs frameshift nonsense NM_001407377.1:c.47dup NP_001394306.1:p.Tyr16Terfs frameshift nonsense NM_001407378.1:c.47dup NP_001394307.1:p.Tyr16Terfs frameshift nonsense NM_001407379.1:c.47dup NP_001394308.1:p.Tyr16Terfs frameshift nonsense NM_001407380.1:c.47dup NP_001394309.1:p.Tyr16Terfs frameshift nonsense NM_001407381.1:c.47dup NP_001394310.1:p.Tyr16Terfs frameshift nonsense NM_001407382.1:c.47dup NP_001394311.1:p.Tyr16Terfs frameshift nonsense NM_001407383.1:c.47dup NP_001394312.1:p.Tyr16Terfs frameshift nonsense NM_001407384.1:c.47dup NP_001394313.1:p.Tyr16Terfs frameshift nonsense NM_001407386.1:c.47dup NP_001394315.1:p.Tyr16Terfs frameshift nonsense NM_001407388.1:c.47dup NP_001394317.1:p.Tyr16Terfs frameshift nonsense NM_001407390.1:c.47dup NP_001394319.1:p.Tyr16Terfs frameshift nonsense NM_001407392.1:c.47dup NP_001394321.1:p.Tyr16Terfs frameshift nonsense NM_001407394.1:c.47dup NP_001394323.1:p.Tyr16Terfs frameshift nonsense NM_001407395.1:c.47dup NP_001394324.1:p.Tyr16Terfs frameshift nonsense NM_001407396.1:c.47dup NP_001394325.1:p.Tyr16Terfs frameshift nonsense NM_001407397.1:c.47dup NP_001394326.1:p.Tyr16Terfs frameshift nonsense NM_001407398.1:c.47dup NP_001394327.1:p.Tyr16Terfs frameshift nonsense NM_001407399.1:c.47dup NP_001394328.1:p.Tyr16Terfs frameshift nonsense NM_001407400.1:c.47dup NP_001394329.1:p.Tyr16Terfs frameshift nonsense NM_001407401.1:c.47dup NP_001394330.1:p.Tyr16Terfs frameshift nonsense NC_000003.12:g.15635486dup NC_000003.11:g.15676993dup NG_008019.2:g.39135dup - Protein change
- Y16*
- Other names
- -
- Canonical SPDI
- NC_000003.12:15635485:A:AA
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00000
- 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 | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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. |
|||
| BTD | - | - |
GRCh38 GRCh37 |
667 | 753 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Jul 12, 2022 | RCV000411926.6 |
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
Help
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
Help
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
Help
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. |
|
|---|---|---|---|---|---|
|
Likely pathogenic
(Apr 25, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Biotinidase deficiency
Affected status: unknown
Allele origin:
unknown
|
Counsyl
Accession: SCV000486263.2
First in ClinVar: Jan 06, 2017 Last updated: Dec 24, 2022 |
|
|
|
Pathogenic
(Jul 12, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Biotinidase deficiency
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003492174.2
First in ClinVar: Feb 07, 2023 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: 370847). 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: 370847). 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.Tyr36*) 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)
|
Comment:
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. |
Comment:
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370847). 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.Tyr36*) 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).
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| 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 rs1057516812 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Sep 29, 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.