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NM_001079866.2(BCS1L):c.-50+405A>G

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(1); Likely pathogenic(1); Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3
First in ClinVar:
Aug 5, 2018
Most recent Submission:
Mar 22, 2021
Last evaluated:
May 28, 2019
Accession:
VCV000553134.4
Variation ID:
553134
Description:
single nucleotide variant
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NM_001079866.2(BCS1L):c.-50+405A>G

Allele ID
541892
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q35
Genomic location
2: 218660148 (GRCh38) GRCh38 UCSC
2: 219524871 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001079866.2:c.-50+405A>G MANE Select
NM_001257342.2:c.-68A>G 5 prime UTR
NM_001257343.2:c.-120A>G 5 prime UTR
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:218660147:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
dbSNP: rs898301590
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Apr 10, 2018 RCV001334241.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 28, 2019 RCV000668517.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BCS1L - - GRCh38
GRCh37
294 323

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Jul 28, 2017)
criteria provided, single submitter
Method: clinical testing
GRACILE syndrome
Affected status: unknown
Allele origin: unknown
Counsyl
Accession: SCV000793135.1
First in ClinVar: Aug 05, 2018
Last updated: Aug 05, 2018
Publications:
PubMed (2)
PubMed: 1938948828496993
Likely pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
GRACILE syndrome
Affected status: unknown
Allele origin: unknown
Mendelics
Accession: SCV001136212.1
First in ClinVar: Jan 09, 2020
Last updated: Jan 09, 2020
Pathogenic
(Apr 10, 2018)
criteria provided, single submitter
Method: clinical testing
Mitochondrial complex III deficiency nuclear type 1
Affected status: yes
Allele origin: paternal
Baylor Genetics
Accession: SCV001527033.1
First in ClinVar: Mar 22, 2021
Last updated: Mar 22, 2021
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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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 this variant

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Title Author Journal Year Link
Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic. Bick D Journal of pediatric genetics 2017 PMID: 28496993
Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency. Gil-Borlado MC Mitochondrion 2009 PMID: 19389488

Text-mined citations for rs898301590...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 25, 2022