ClinVar Genomic variation as it relates to human health
NM_001079866.2(BCS1L):c.167G>A (p.Arg56Gln)
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.167G>A (p.Arg56Gln)
Variation ID: 2573519 Accession: VCV002573519.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q35 2: 218661154 (GRCh38) [ NCBI UCSC ] 2: 219525877 (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 29, 2023 Jul 29, 2023 Jun 27, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001079866.2:c.167G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073335.1:p.Arg56Gln missense NM_001257342.2:c.167G>A NP_001244271.1:p.Arg56Gln missense NM_001257343.2:c.167G>A NP_001244272.1:p.Arg56Gln missense NM_001257344.2:c.167G>A NP_001244273.1:p.Arg56Gln missense NM_001318836.2:c.-40-252G>A intron variant NM_001320717.2:c.167G>A NP_001307646.1:p.Arg56Gln missense NM_001371443.1:c.167G>A NP_001358372.1:p.Arg56Gln missense NM_001371444.1:c.167G>A NP_001358373.1:p.Arg56Gln missense NM_001371446.1:c.167G>A NP_001358375.1:p.Arg56Gln missense NM_001371447.1:c.167G>A NP_001358376.1:p.Arg56Gln missense NM_001371448.1:c.167G>A NP_001358377.1:p.Arg56Gln missense NM_001371449.1:c.167G>A NP_001358378.1:p.Arg56Gln missense NM_001371450.1:c.167G>A NP_001358379.1:p.Arg56Gln missense NM_001371451.1:c.-40-252G>A intron variant NM_001371452.1:c.-41-605G>A intron variant NM_001371453.1:c.-310G>A 5 prime UTR NM_001371454.1:c.-310G>A 5 prime UTR NM_001371455.1:c.-310G>A 5 prime UTR NM_001371456.1:c.-310G>A 5 prime UTR NM_001374085.1:c.167G>A NP_001361014.1:p.Arg56Gln missense NM_001374086.1:c.-310G>A 5 prime UTR NM_004328.5:c.167G>A NP_004319.1:p.Arg56Gln missense NR_163955.1:n.1179G>A non-coding transcript variant NC_000002.12:g.218661154G>A NC_000002.11:g.219525877G>A NG_008018.1:g.6499G>A NG_033099.1:g.3387C>T NG_033099.2:g.3469C>T LRG_539:g.6499G>A LRG_539t1:c.167G>A LRG_539p1:p.Arg56Gln LRG_539t2:c.167G>A LRG_539p2:p.Arg56Gln - Protein change
- R56Q
- Other names
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- Canonical SPDI
- NC_000002.12:218661153:G:A
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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
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
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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
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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 |
491 | 529 |
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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Uncertain significance (1) |
criteria provided, single submitter
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Jun 27, 2023 | RCV003317855.1 |
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
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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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Uncertain significance
(Jun 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004020961.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
Comment:
Variant summary: BCS1L c.167G>A (p.Arg56Gln) results in a conservative amino acid change located in the BCS1, N-terminal domain (IPR014851) of the encoded protein sequence. Three … (more)
Variant summary: BCS1L c.167G>A (p.Arg56Gln) results in a conservative amino acid change located in the BCS1, N-terminal domain (IPR014851) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251472 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.167G>A has been reported in the literature in at least one compound heterozygous individual affected with Fanconi syndrome with evidence of mitochondrial respiratory chain complex III deficiency (example: Kanako_2021). To our knowledge, no variant specific experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 34650211). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. (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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BCS1L mutations produce Fanconi syndrome with developmental disability. | Kanako KI | Journal of human genetics | 2022 | PMID: 34650211 |
Text-mined citations for this variant ...
HelpRecord last updated Jul 29, 2023
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.