ClinVar Genomic variation as it relates to human health
NM_001079866.2(BCS1L):c.1017T>C (p.Pro339=)
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.1017T>C (p.Pro339=)
Variation ID: 136505 Accession: VCV000136505.21
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q35 2: 218663143 (GRCh38) [ NCBI UCSC ] 2: 219527866 (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 Dec 6, 2016 Feb 20, 2024 Feb 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001079866.2:c.1017T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073335.1:p.Pro339= synonymous NM_001257342.2:c.1017T>C NP_001244271.1:p.Pro339= synonymous NM_001257343.2:c.1017T>C NP_001244272.1:p.Pro339= synonymous NM_001257344.2:c.1017T>C NP_001244273.1:p.Pro339= synonymous NM_001318836.2:c.657T>C NP_001305765.1:p.Pro219= synonymous NM_001320717.2:c.1017T>C NP_001307646.1:p.Pro339= synonymous NM_001371443.1:c.1017T>C NP_001358372.1:p.Pro339= synonymous NM_001371444.1:c.1017T>C NP_001358373.1:p.Pro339= synonymous NM_001371446.1:c.1017T>C NP_001358375.1:p.Pro339= synonymous NM_001371447.1:c.1017T>C NP_001358376.1:p.Pro339= synonymous NM_001371448.1:c.1017T>C NP_001358377.1:p.Pro339= synonymous NM_001371449.1:c.1017T>C NP_001358378.1:p.Pro339= synonymous NM_001371450.1:c.1017T>C NP_001358379.1:p.Pro339= synonymous NM_001371451.1:c.657T>C NP_001358380.1:p.Pro219= synonymous NM_001371452.1:c.516T>C NP_001358381.1:p.Pro172= synonymous NM_001371453.1:c.516T>C NP_001358382.1:p.Pro172= synonymous NM_001371454.1:c.516T>C NP_001358383.1:p.Pro172= synonymous NM_001371455.1:c.516T>C NP_001358384.1:p.Pro172= synonymous NM_001371456.1:c.516T>C NP_001358385.1:p.Pro172= synonymous NM_001374085.1:c.1017T>C NP_001361014.1:p.Pro339= synonymous NM_001374086.1:c.516T>C NP_001361015.1:p.Pro172= synonymous NM_004328.5:c.1017T>C NP_004319.1:p.Pro339= synonymous NR_163955.1:n.2024T>C non-coding transcript variant NC_000002.12:g.218663143T>C NC_000002.11:g.219527866T>C NG_008018.1:g.8488T>C NG_033099.1:g.1398A>G LRG_539:g.8488T>C LRG_539t1:c.1017T>C LRG_539p1:p.Pro339= - Protein change
- Other names
- p.P339P:CCT>CCC
- Canonical SPDI
- NC_000002.12:218663142:T:C
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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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0.18331 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD), exomes 0.07173
Exome Aggregation Consortium (ExAC) 0.07971
The Genome Aggregation Database (gnomAD) 0.15996
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.16577
Trans-Omics for Precision Medicine (TOPMed) 0.16836
1000 Genomes Project 0.18331
1000 Genomes Project 30x 0.18801
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
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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BCS1L | - | - |
GRCh38 GRCh37 |
484 | 520 |
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. |
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Benign (2) |
criteria provided, multiple submitters, no conflicts
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Mar 21, 2016 | RCV000123835.5 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Jun 10, 2021 | RCV000270977.7 | |
Benign (3) |
criteria provided, multiple submitters, no conflicts
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Jun 10, 2021 | RCV000323471.8 | |
Benign (1) |
criteria provided, single submitter
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Jan 13, 2018 | RCV000361877.5 | |
Benign (2) |
criteria provided, single submitter
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Feb 1, 2024 | RCV000677002.11 | |
Benign (1) |
criteria provided, single submitter
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Jun 10, 2021 | RCV001527150.2 |
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
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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Benign
(Oct 18, 2011)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000167178.12
First in ClinVar: Jun 23, 2014 Last updated: Apr 09, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
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Benign
(Mar 21, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000711833.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
p.Pro339Pro in exon 9 of BCS1L: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
p.Pro339Pro in exon 9 of BCS1L: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 50.45% (667/1322) of African chromosomes by the 1000 Genomes Project (Phase 3; dbSNP rs35843327). (less)
Number of individuals with the variant: 43
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Benign
(Jan 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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GRACILE syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000427452.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
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Benign
(Jan 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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Leigh syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000427453.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
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Benign
(Jan 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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Mitochondrial complex III deficiency nuclear type 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000427451.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
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Benign
(Jun 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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GRACILE syndrome
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001738081.1
First in ClinVar: Jun 24, 2021 Last updated: Jun 24, 2021 |
Sex: mixed
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Benign
(Jun 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Mitochondrial complex III deficiency nuclear type 1
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001738082.1
First in ClinVar: Jun 24, 2021 Last updated: Jun 24, 2021 |
Sex: mixed
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Benign
(Jun 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Pili torti-deafness syndrome
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001738080.1
First in ClinVar: Jun 24, 2021 Last updated: Jun 24, 2021 |
Sex: mixed
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Benign
(Feb 01, 2024)
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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: SCV001718504.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 20, 2024 |
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Benign
(Feb 22, 2016)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000802831.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
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Benign
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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GRACILE syndrome
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001455779.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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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
HelpThere 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 rs35843327 ...
HelpRecord last updated May 19, 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.