ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.941_942del (p.Ile314fs)
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.941_942del (p.Ile314fs)
Variation ID: 553614 Accession: VCV000553614.8
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 3p25.1 3: 15644857-15644858 (GRCh38) [ NCBI UCSC ] 3: 15686364-15686365 (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 Aug 5, 2018 Feb 28, 2024 Mar 22, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370658.1:c.941_942del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Ile314fs frameshift NM_000060.4:c.1001_1002del NM_000060.4:c.1001_1002delTT NP_000051.1:p.Ile334Serfs frameshift NM_001281723.4:c.941_942delTT NP_001268652.2:p.Ile314Serfs frameshift NM_001281724.3:c.941_942del NP_001268653.2:p.Ile314fs frameshift NM_001281725.3:c.941_942delTT NP_001268654.1:p.Ile314Serfs frameshift NM_001323582.2:c.941_942delTT NP_001310511.1:p.Ile314Serfs frameshift NM_001370752.1:c.941_942del NP_001357681.1:p.Ile314fs frameshift NM_001370753.1:c.399+2800_399+2801del intron variant NM_001407364.1:c.941_942delTT NP_001394293.1:p.Ile314Serfs frameshift NM_001407365.1:c.941_942delTT NP_001394294.1:p.Ile314Serfs frameshift NM_001407366.1:c.941_942delTT NP_001394295.1:p.Ile314Serfs frameshift NM_001407367.1:c.941_942delTT NP_001394296.1:p.Ile314Serfs frameshift NM_001407368.1:c.941_942delTT NP_001394297.1:p.Ile314Serfs frameshift NM_001407369.1:c.941_942delTT NP_001394298.1:p.Ile314Serfs frameshift NM_001407370.1:c.941_942delTT NP_001394299.1:p.Ile314Serfs frameshift NM_001407371.1:c.941_942delTT NP_001394300.1:p.Ile314Serfs frameshift NM_001407372.1:c.941_942delTT NP_001394301.1:p.Ile314Serfs frameshift NM_001407373.1:c.941_942delTT NP_001394302.1:p.Ile314Serfs frameshift NM_001407374.1:c.941_942delTT NP_001394303.1:p.Ile314Serfs frameshift NM_001407375.1:c.941_942delTT NP_001394304.1:p.Ile314Serfs frameshift NM_001407376.1:c.941_942delTT NP_001394305.1:p.Ile314Serfs frameshift NM_001407377.1:c.941_942delTT NP_001394306.1:p.Ile314Serfs frameshift NM_001407378.1:c.941_942delTT NP_001394307.1:p.Ile314Serfs frameshift NM_001407379.1:c.941_942delTT NP_001394308.1:p.Ile314Serfs frameshift NC_000003.12:g.15644857_15644858del NC_000003.11:g.15686364_15686365del NG_008019.2:g.48506_48507del NG_008019.3:g.48507_48508del - Protein change
- I314fs
- Other names
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- Canonical SPDI
- NC_000003.12:15644856:TT:
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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.
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
- 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
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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 |
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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
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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/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Mar 22, 2022 | RCV000669098.7 |
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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Likely pathogenic
(Aug 31, 2017)
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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: SCV000793803.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
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Likely pathogenic
(Mar 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Biotinidase deficiency
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002318765.1
First in ClinVar: Apr 02, 2022 Last updated: Apr 02, 2022 |
Comment:
Frameshift: predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated … (more)
Frameshift: predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region. This variant has been reported as pathogenic (ClinVar ID: VCV000553614). The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0000119). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Focal-onset seizure (present) , Seizure (present)
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Likely pathogenic
(Dec 05, 2021)
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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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Baylor Genetics
Accession: SCV004211492.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Nov 14, 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: SCV002214270.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 28, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the BTD protein in which other variant(s) (p.Leu498Phefs*13) have … (more)
For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the BTD protein in which other variant(s) (p.Leu498Phefs*13) have been determined to be pathogenic (PMID: 17382128, 19728141, 29359854). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 553614). This variant has not been reported in the literature in individuals affected with BTD-related conditions. This variant is present in population databases (rs749162799, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Ile334Serfs*19) in the BTD gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 210 amino acid(s) of the BTD protein. (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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Clinical features, BTD gene mutations, and their functional studies of eight symptomatic patients with biotinidase deficiency from Southern China. | Liu Z | American journal of medical genetics. Part A | 2018 | PMID: 29359854 |
Diagnosis, treatment, follow-up and gene mutation analysis in four Chinese children with biotinidase deficiency. | Ye J | Journal of inherited metabolic disease | 2009 | PMID: 19728141 |
Hearing loss in biotinidase deficiency: genotype-phenotype correlation. | Sivri HS | The Journal of pediatrics | 2007 | PMID: 17382128 |
Text-mined citations for rs749162799 ...
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.