ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.38G>T (p.Cys13Phe)
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.38G>T (p.Cys13Phe)
Variation ID: 801941 Accession: VCV000801941.26
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15635477 (GRCh38) [ NCBI UCSC ] 3: 15676984 (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 Jan 11, 2020 Apr 15, 2024 Sep 15, 2021 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.38G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Cys13Phe missense NM_000060.4:c.98G>T NP_000051.1:p.Cys33Phe missense NM_001281723.4:c.38G>T NP_001268652.2:p.Cys13Phe missense NM_001281724.3:c.38G>T NP_001268653.2:p.Cys13Phe missense NM_001281725.3:c.38G>T NP_001268654.1:p.Cys13Phe missense NM_001281726.3:c.38G>T NP_001268655.2:p.Cys13Phe missense NM_001323582.2:c.38G>T NP_001310511.1:p.Cys13Phe missense NM_001370752.1:c.38G>T NP_001357681.1:p.Cys13Phe missense NM_001370753.1:c.38G>T NP_001357682.1:p.Cys13Phe missense NM_001407364.1:c.38G>T NP_001394293.1:p.Cys13Phe missense NM_001407365.1:c.38G>T NP_001394294.1:p.Cys13Phe missense NM_001407366.1:c.38G>T NP_001394295.1:p.Cys13Phe missense NM_001407367.1:c.38G>T NP_001394296.1:p.Cys13Phe missense NM_001407368.1:c.38G>T NP_001394297.1:p.Cys13Phe missense NM_001407369.1:c.38G>T NP_001394298.1:p.Cys13Phe missense NM_001407370.1:c.38G>T NP_001394299.1:p.Cys13Phe missense NM_001407371.1:c.38G>T NP_001394300.1:p.Cys13Phe missense NM_001407372.1:c.38G>T NP_001394301.1:p.Cys13Phe missense NM_001407373.1:c.38G>T NP_001394302.1:p.Cys13Phe missense NM_001407374.1:c.38G>T NP_001394303.1:p.Cys13Phe missense NM_001407375.1:c.38G>T NP_001394304.1:p.Cys13Phe missense NM_001407376.1:c.38G>T NP_001394305.1:p.Cys13Phe missense NM_001407377.1:c.38G>T NP_001394306.1:p.Cys13Phe missense NM_001407378.1:c.38G>T NP_001394307.1:p.Cys13Phe missense NM_001407379.1:c.38G>T NP_001394308.1:p.Cys13Phe missense NM_001407380.1:c.38G>T NP_001394309.1:p.Cys13Phe missense NM_001407381.1:c.38G>T NP_001394310.1:p.Cys13Phe missense NM_001407382.1:c.38G>T NP_001394311.1:p.Cys13Phe missense NM_001407383.1:c.38G>T NP_001394312.1:p.Cys13Phe missense NM_001407384.1:c.38G>T NP_001394313.1:p.Cys13Phe missense NM_001407386.1:c.38G>T NP_001394315.1:p.Cys13Phe missense NM_001407388.1:c.38G>T NP_001394317.1:p.Cys13Phe missense NM_001407390.1:c.38G>T NP_001394319.1:p.Cys13Phe missense NM_001407392.1:c.38G>T NP_001394321.1:p.Cys13Phe missense NM_001407394.1:c.38G>T NP_001394323.1:p.Cys13Phe missense NM_001407395.1:c.38G>T NP_001394324.1:p.Cys13Phe missense NM_001407396.1:c.38G>T NP_001394325.1:p.Cys13Phe missense NM_001407397.1:c.38G>T NP_001394326.1:p.Cys13Phe missense NM_001407398.1:c.38G>T NP_001394327.1:p.Cys13Phe missense NM_001407399.1:c.38G>T NP_001394328.1:p.Cys13Phe missense NM_001407400.1:c.38G>T NP_001394329.1:p.Cys13Phe missense NM_001407401.1:c.38G>T NP_001394330.1:p.Cys13Phe missense NC_000003.12:g.15635477G>T NC_000003.11:g.15676984G>T NG_008019.2:g.39126G>T - Protein change
- C13F
- Other names
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- Canonical SPDI
- NC_000003.12:15635476:G: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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0.00020 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00012
1000 Genomes Project 30x 0.00016
Exome Aggregation Consortium (ExAC) 0.00016
Trans-Omics for Precision Medicine (TOPMed) 0.00016
1000 Genomes Project 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
- 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 |
645 | 705 |
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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Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Sep 15, 2021 | RCV000987126.4 | |
Uncertain significance (1) |
criteria provided, single submitter
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Dec 1, 2018 | RCV000998006.17 |
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
(May 28, 2019)
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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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Mendelics
Accession: SCV001136333.1
First in ClinVar: Jan 11, 2020 Last updated: Jan 11, 2020 |
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Uncertain significance
(Sep 15, 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: SCV003301955.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces cysteine with phenylalanine at codon 33 of the BTD protein (p.Cys33Phe). The cysteine residue is weakly conserved and there is a … (more)
This sequence change replaces cysteine with phenylalanine at codon 33 of the BTD protein (p.Cys33Phe). The cysteine residue is weakly conserved and there is a large physicochemical difference between cysteine and phenylalanine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This missense change has been observed in individual(s) with biotinidase deficiency (PMID: 26117549). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
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Uncertain significance
(Dec 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001153814.21
First in ClinVar: Feb 03, 2020 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 1
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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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Neurometabolic Disorders-Related Early Childhood Epilepsy: A Single-Center Experience in Saudi Arabia. | Mohamed S | Pediatrics and neonatology | 2015 | PMID: 26117549 |
Text-mined citations for rs141131444 ...
HelpRecord last updated Apr 15, 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.