Variant summary: BTD c.70_71delAC (p.Thr24ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251430 control chromosomes. To our knowledge, no occurrence of c.70_71delAC in individuals affected with Biotinidase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic.
ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.70_71del (p.Thr24fs)
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.
(1)
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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
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370658.1(BTD):c.70_71del (p.Thr24fs)
Variation ID: 3251587 Accession: VCV003251587.1
- Type and length
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Microsatellite, 2 bp
- Location
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Cytogenetic: 3p25.1 3: 15635506-15635507 (GRCh38) [ NCBI UCSC ] 3: 15677013-15677014 (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 Jul 15, 2024 Jul 15, 2024 Apr 2, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001370658.1:c.70_71del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Thr24fs frameshift NM_001370658.1:c.70_71delAC MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
frameshift NM_001281723.4:c.70_71del NP_001268652.2:p.Thr24fs frameshift NM_001281724.3:c.70_71del NP_001268653.2:p.Thr24fs frameshift NM_001281725.3:c.70_71del NP_001268654.1:p.Thr24fs frameshift NM_001281726.3:c.70_71del NP_001268655.2:p.Thr24fs frameshift NM_001323582.2:c.70_71del NP_001310511.1:p.Thr24fs frameshift NM_001370752.1:c.70_71del NP_001357681.1:p.Thr24fs frameshift NM_001370753.1:c.70_71del NP_001357682.1:p.Thr24fs frameshift NM_001407364.1:c.70_71del NP_001394293.1:p.Thr24fs frameshift NM_001407365.1:c.70_71del NP_001394294.1:p.Thr24fs frameshift NM_001407366.1:c.70_71del NP_001394295.1:p.Thr24fs frameshift NM_001407367.1:c.70_71del NP_001394296.1:p.Thr24fs frameshift NM_001407368.1:c.70_71del NP_001394297.1:p.Thr24fs frameshift NM_001407369.1:c.70_71del NP_001394298.1:p.Thr24fs frameshift NM_001407370.1:c.70_71del NP_001394299.1:p.Thr24fs frameshift NM_001407371.1:c.70_71del NP_001394300.1:p.Thr24fs frameshift NM_001407372.1:c.70_71del NP_001394301.1:p.Thr24fs frameshift NM_001407373.1:c.70_71del NP_001394302.1:p.Thr24fs frameshift NM_001407374.1:c.70_71del NP_001394303.1:p.Thr24fs frameshift NM_001407375.1:c.70_71del NP_001394304.1:p.Thr24fs frameshift NM_001407376.1:c.70_71del NP_001394305.1:p.Thr24fs frameshift NM_001407377.1:c.70_71del NP_001394306.1:p.Thr24fs frameshift NM_001407378.1:c.70_71del NP_001394307.1:p.Thr24fs frameshift NM_001407379.1:c.70_71del NP_001394308.1:p.Thr24fs frameshift NM_001407380.1:c.70_71del NP_001394309.1:p.Thr24fs frameshift NM_001407381.1:c.70_71del NP_001394310.1:p.Thr24fs frameshift NM_001407382.1:c.70_71del NP_001394311.1:p.Thr24fs frameshift NM_001407383.1:c.70_71del NP_001394312.1:p.Thr24fs frameshift NM_001407384.1:c.70_71del NP_001394313.1:p.Thr24fs frameshift NM_001407386.1:c.70_71del NP_001394315.1:p.Thr24fs frameshift NM_001407388.1:c.70_71del NP_001394317.1:p.Thr24fs frameshift NM_001407390.1:c.70_71del NP_001394319.1:p.Thr24fs frameshift NM_001407392.1:c.70_71del NP_001394321.1:p.Thr24fs frameshift NM_001407394.1:c.70_71del NP_001394323.1:p.Thr24fs frameshift NM_001407395.1:c.70_71del NP_001394324.1:p.Thr24fs frameshift NM_001407396.1:c.70_71del NP_001394325.1:p.Thr24fs frameshift NM_001407397.1:c.70_71del NP_001394326.1:p.Thr24fs frameshift NM_001407398.1:c.70_71del NP_001394327.1:p.Thr24fs frameshift NM_001407399.1:c.70_71del NP_001394328.1:p.Thr24fs frameshift NM_001407400.1:c.70_71del NP_001394329.1:p.Thr24fs frameshift NM_001407401.1:c.70_71del NP_001394330.1:p.Thr24fs frameshift NC_000003.12:g.15635507AC[1] NC_000003.11:g.15677014AC[1] NG_008019.2:g.39156AC[1] NG_008019.3:g.39157AC[1] - Protein change
- T24fs
- Other names
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- Canonical SPDI
- NC_000003.12:15635505:CACAC:CAC
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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
Help
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
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. |
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| 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 (1) |
criteria provided, single submitter
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Apr 2, 2024 | RCV004587993.1 |
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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Pathogenic
(Apr 02, 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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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV005075841.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
Comment:
Variant summary: BTD c.70_71delAC (p.Thr24ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: BTD c.70_71delAC (p.Thr24ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251430 control chromosomes. To our knowledge, no occurrence of c.70_71delAC in individuals affected with Biotinidase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic. (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:
Variant summary: BTD c.70_71delAC (p.Thr24ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251430 control chromosomes. To our knowledge, no occurrence of c.70_71delAC in individuals affected with Biotinidase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Jul 23, 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.