ClinVar Genomic variation as it relates to human health
NM_001079866.2(BCS1L):c.217del (p.Arg73fs)
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_001079866.2(BCS1L):c.217del (p.Arg73fs)
Variation ID: 2004262 Accession: VCV002004262.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2q35 2: 218661202 (GRCh38) [ NCBI UCSC ] 2: 219525925 (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 Feb 8, 2023 Feb 20, 2024 Jun 10, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001079866.2:c.217del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073335.1:p.Arg73fs frameshift NM_001257342.2:c.217del NP_001244271.1:p.Arg73fs frameshift NM_001257343.2:c.217del NP_001244272.1:p.Arg73fs frameshift NM_001257344.2:c.217del NP_001244273.1:p.Arg73fs frameshift NM_001318836.2:c.-40-202del intron variant NM_001320717.2:c.217del NP_001307646.1:p.Arg73fs frameshift NM_001371443.1:c.217del NP_001358372.1:p.Arg73fs frameshift NM_001371444.1:c.217del NP_001358373.1:p.Arg73fs frameshift NM_001371446.1:c.217del NP_001358375.1:p.Arg73fs frameshift NM_001371447.1:c.217del NP_001358376.1:p.Arg73fs frameshift NM_001371448.1:c.217del NP_001358377.1:p.Arg73fs frameshift NM_001371449.1:c.217del NP_001358378.1:p.Arg73fs frameshift NM_001371450.1:c.217del NP_001358379.1:p.Arg73fs frameshift NM_001371451.1:c.-40-202del intron variant NM_001371452.1:c.-41-555del intron variant NM_001371453.1:c.-260del 5 prime UTR NM_001371454.1:c.-260del 5 prime UTR NM_001371455.1:c.-260del 5 prime UTR NM_001371456.1:c.-260del 5 prime UTR NM_001374085.1:c.217del NP_001361014.1:p.Arg73fs frameshift NM_001374086.1:c.-260del 5 prime UTR NM_004328.5:c.217del NP_004319.1:p.Arg73fs frameshift NR_163955.1:n.1229del non-coding transcript variant NC_000002.12:g.218661204del NC_000002.11:g.219525927del NG_008018.1:g.6549del NG_033099.1:g.3339del NG_033099.2:g.3421del LRG_539:g.6549del LRG_539t1:c.217del LRG_539p1:p.Arg73Valfs LRG_539t2:c.217del LRG_539p2:p.Arg73Valfs - Protein change
- R73fs
- Other names
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- Canonical SPDI
- NC_000002.12:218661201:CCC:CC
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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
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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
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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BCS1L | - | - |
GRCh38 GRCh37 |
484 | 519 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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 (1) |
criteria provided, single submitter
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Jun 10, 2022 | RCV002815977.2 |
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
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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
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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
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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
(Jun 10, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003210715.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg73Valfs*43) in the BCS1L gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg73Valfs*43) in the BCS1L gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BCS1L are known to be pathogenic (PMID: 12215968, 17314340, 19162478, 19508421, 22277166, 25895478). This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with BCS1L-related conditions. (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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Exome sequencing reveals novel BCS1L mutations in siblings with hearing loss and hypotrichosis. | Zhang J | Gene | 2015 | PMID: 25895478 |
BCS1L gene mutation presenting with GRACILE-like syndrome and complex III deficiency. | Lynn AM | Annals of clinical biochemistry | 2012 | PMID: 22277166 |
Clinical and biochemical spectrum of mitochondrial complex III deficiency caused by mutations in the BCS1L gene. | Ramos-Arroyo MA | Clinical genetics | 2009 | PMID: 19508421 |
Infantile mitochondrial encephalomyopathy with unusual phenotype caused by a novel BCS1L mutation in an isolated complex III-deficient patient. | Blázquez A | Neuromuscular disorders : NMD | 2009 | PMID: 19162478 |
Missense mutations in the BCS1L gene as a cause of the Björnstad syndrome. | Hinson JT | The New England journal of medicine | 2007 | PMID: 17314340 |
GRACILE syndrome, a lethal metabolic disorder with iron overload, is caused by a point mutation in BCS1L. | Visapää I | American journal of human genetics | 2002 | PMID: 12215968 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 20, 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.