ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.152T>C (p.Leu51Pro)
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.
Uncertain significance(1); Benign(2); Likely benign(2)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370658.1(BTD):c.152T>C (p.Leu51Pro)
Variation ID: 38482 Accession: VCV000038482.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15635591 (GRCh38) [ NCBI UCSC ] 3: 15677098 (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 Apr 4, 2013 Feb 20, 2024 Jan 11, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.152T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Leu51Pro missense NM_000060.4:c.212T>C NP_000051.1:p.Leu71Pro missense NM_001281723.4:c.152T>C NP_001268652.2:p.Leu51Pro missense NM_001281724.3:c.152T>C NP_001268653.2:p.Leu51Pro missense NM_001281725.3:c.152T>C NP_001268654.1:p.Leu51Pro missense NM_001281726.3:c.152T>C NP_001268655.2:p.Leu51Pro missense NM_001323582.2:c.152T>C NP_001310511.1:p.Leu51Pro missense NM_001370752.1:c.152T>C NP_001357681.1:p.Leu51Pro missense NM_001370753.1:c.152T>C NP_001357682.1:p.Leu51Pro missense NM_001407364.1:c.152T>C NP_001394293.1:p.Leu51Pro missense NM_001407365.1:c.152T>C NP_001394294.1:p.Leu51Pro missense NM_001407366.1:c.152T>C NP_001394295.1:p.Leu51Pro missense NM_001407367.1:c.152T>C NP_001394296.1:p.Leu51Pro missense NM_001407368.1:c.152T>C NP_001394297.1:p.Leu51Pro missense NM_001407369.1:c.152T>C NP_001394298.1:p.Leu51Pro missense NM_001407370.1:c.152T>C NP_001394299.1:p.Leu51Pro missense NM_001407371.1:c.152T>C NP_001394300.1:p.Leu51Pro missense NM_001407372.1:c.152T>C NP_001394301.1:p.Leu51Pro missense NM_001407373.1:c.152T>C NP_001394302.1:p.Leu51Pro missense NM_001407374.1:c.152T>C NP_001394303.1:p.Leu51Pro missense NM_001407375.1:c.152T>C NP_001394304.1:p.Leu51Pro missense NM_001407376.1:c.152T>C NP_001394305.1:p.Leu51Pro missense NM_001407377.1:c.152T>C NP_001394306.1:p.Leu51Pro missense NM_001407378.1:c.152T>C NP_001394307.1:p.Leu51Pro missense NM_001407379.1:c.152T>C NP_001394308.1:p.Leu51Pro missense NM_001407380.1:c.152T>C NP_001394309.1:p.Leu51Pro missense NM_001407381.1:c.152T>C NP_001394310.1:p.Leu51Pro missense NM_001407382.1:c.152T>C NP_001394311.1:p.Leu51Pro missense NM_001407383.1:c.152T>C NP_001394312.1:p.Leu51Pro missense NM_001407384.1:c.152T>C NP_001394313.1:p.Leu51Pro missense NM_001407386.1:c.152T>C NP_001394315.1:p.Leu51Pro missense NM_001407388.1:c.152T>C NP_001394317.1:p.Leu51Pro missense NM_001407390.1:c.152T>C NP_001394319.1:p.Leu51Pro missense NM_001407392.1:c.152T>C NP_001394321.1:p.Leu51Pro missense NM_001407394.1:c.152T>C NP_001394323.1:p.Leu51Pro missense NM_001407395.1:c.152T>C NP_001394324.1:p.Leu51Pro missense NM_001407396.1:c.152T>C NP_001394325.1:p.Leu51Pro missense NM_001407397.1:c.152T>C NP_001394326.1:p.Leu51Pro missense NM_001407398.1:c.152T>C NP_001394327.1:p.Leu51Pro missense NM_001407399.1:c.152T>C NP_001394328.1:p.Leu51Pro missense NM_001407400.1:c.152T>C NP_001394329.1:p.Leu51Pro missense NM_001407401.1:c.152T>C NP_001394330.1:p.Leu51Pro missense NC_000003.12:g.15635591T>C NC_000003.11:g.15677098T>C NG_008019.2:g.39240T>C - Protein change
- L51P
- Other names
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L71P
- Canonical SPDI
- NC_000003.12:15635590:T:C
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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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0.00180 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00154
1000 Genomes Project 30x 0.00156
Exome Aggregation Consortium (ExAC) 0.00159
1000 Genomes Project 0.00180
- 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
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. |
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BTD | - | - |
GRCh38 GRCh37 |
669 | 755 |
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. |
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Benign/Likely benign (4) |
criteria provided, multiple submitters, no conflicts
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Jan 11, 2024 | RCV000021900.15 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
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Nov 9, 2016 | RCV000427971.8 |
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
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. |
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Uncertain significance
(Nov 12, 2015)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: no
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000593787.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
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Likely benign
(Nov 09, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000521147.4
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
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Likely benign
(Apr 20, 2018)
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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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Counsyl
Accession: SCV000800810.1
First in ClinVar: May 30, 2018 Last updated: May 30, 2018 |
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Benign
(-)
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criteria provided, single submitter
Method: research
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Biotinidase deficiency
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001435233.1
First in ClinVar: Oct 02, 2020 Last updated: Oct 02, 2020 |
Comment:
The heterozygous p.Leu71Pro variant in BTD has been identified in the compound heterozygous state, in trans with a frameshift variant and in cis with a … (more)
The heterozygous p.Leu71Pro variant in BTD has been identified in the compound heterozygous state, in trans with a frameshift variant and in cis with a rare missense variant, in an individual from Hungary with biotinidase deficiency (PMID: 14707518). This variant has also been identified in >1% of South Asian chromosomes and 8 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive biotinidase deficiency. (less)
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Benign
(Jan 11, 2024)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000754950.5
First in ClinVar: Apr 04, 2013 Last updated: Feb 20, 2024 |
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Benign
(Jan 14, 2020)
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no assertion criteria provided
Method: clinical testing
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Biotinidase deficiency
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV002081544.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
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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 |
Mutations causing biotinidase deficiency in children ascertained by newborn screening in Western Hungary. | Milánkovics I | Molecular genetics and metabolism | 2007 | PMID: 17185019 |
Biotinidase deficiency: novel mutations and their biochemical and clinical correlates. | Wolf B | Human mutation | 2005 | PMID: 15776412 |
Neonatal screening for biotinidase deficiency in Hungary: clinical, biochemical and molecular studies. | László A | Journal of inherited metabolic disease | 2003 | PMID: 14707518 |
Text-mined citations for rs397514333 ...
HelpRecord last updated Oct 08, 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.