This sequence change replaces glutamic acid with alanine at codon 33 of the BRCA1 protein (p.Glu33Ala). The glutamic acid residue is highly conserved and there is a moderate physicochemical difference between glutamic acid and alanine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in the literature in an individual affected with breast and/or ovarian cancer (PMID: 15131401). ClinVar contains an entry for this variant (Variation ID: 234092). One experimental study performed in yeast cells has shown that this missense change had a detrimental effect on protein function for cell survival in vitro (PMID: 21922593). In summary, this variant is a rare missense change with a deleterious effect on protein function in vitro. While it is absent from the population and reported in affected individuals, the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
ClinVar Genomic variation as it relates to human health
NM_007294.4(BRCA1):c.98A>C (p.Glu33Ala)
Germline
Classification
Help
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.
(4)
Help
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.
Uncertain significance
4
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_007294.4(BRCA1):c.98A>C (p.Glu33Ala)
Variation ID: 234092 Accession: VCV000234092.14
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 17q21.31 17: 43115762 (GRCh38) [ NCBI UCSC ] 17: 41267779 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 May 29, 2016 May 1, 2024 Dec 18, 2023 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- E33A
- Other names
- -
- Canonical SPDI
- NC_000017.11:43115761:T:G
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
functionally_normal; Sequence Ontology [ SO:0002219]The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.98A>C, a MISSENSE variant, produced a function score of -0.36, corresponding to a functional classification of FUNCTIONAL. SGE function score ranges for classification are as follows: ‘functional’, score > -0.748; ‘intermediate’, -0.748 > score > -1.328; ‘non-functional’, score < -1.328. The median synonymous SNV scored 0.0 and the median nonsense SNV scored -2.12. [submitted by Brotman Baty Institute, University of Washington]
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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.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- 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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| BRCA1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
13041 | 14847 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Mar 26, 2022 | RCV000214380.5 | |
| Uncertain significance (1) |
criteria provided, single submitter
|
Jan 12, 2017 | RCV000544483.8 | |
| Uncertain significance (2) |
criteria provided, single submitter
|
Dec 18, 2023 | RCV001076972.5 |
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. |
|
|---|---|---|---|---|---|
|
Uncertain significance
(Jan 12, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary breast ovarian cancer syndrome
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000636088.4
First in ClinVar: Dec 26, 2017 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces glutamic acid with alanine at codon 33 of the BRCA1 protein (p.Glu33Ala). The glutamic acid residue is highly conserved and there … (more)
This sequence change replaces glutamic acid with alanine at codon 33 of the BRCA1 protein (p.Glu33Ala). The glutamic acid residue is highly conserved and there is a moderate physicochemical difference between glutamic acid and alanine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in the literature in an individual affected with breast and/or ovarian cancer (PMID: 15131401). ClinVar contains an entry for this variant (Variation ID: 234092). One experimental study performed in yeast cells has shown that this missense change had a detrimental effect on protein function for cell survival in vitro (PMID: 21922593). In summary, this variant is a rare missense change with a deleterious effect on protein function in vitro. While it is absent from the population and reported in affected individuals, the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
|
|
|
Uncertain significance
(Mar 26, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV000278593.5
First in ClinVar: May 29, 2016 Last updated: May 01, 2024 |
Comment:
The p.E33A variant (also known as c.98A>C), located in coding exon 2 of the BRCA1 gene, results from an A to C substitution at nucleotide … (more)
The p.E33A variant (also known as c.98A>C), located in coding exon 2 of the BRCA1 gene, results from an A to C substitution at nucleotide position 98. The glutamic acid at codon 33 is replaced by alanine, an amino acid with dissimilar properties. This alteration has been identified in several breast cancer families (Muller D et al. Fam. Cancer, 2004;3:15-20; Martelotto LG et al. Genome Biol., 2014 Oct;15:484). This alteration was partially functional in a yeast-based assay but showed wild-type like function in multiple other assays (Millot GA et al. Hum. Mutat., 2011 Dec;32:1470-80; Starita LM et al. Am. J. Hum. Genet., 2018 10;103:498-508; Findlay GM et al. Nature, 2018 10;562:217-222; Starita LM et al. Genetics, 2015 Jun;200:413-22). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
|
|
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Uncertain Significance
(Dec 18, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Breast-ovarian cancer, familial, susceptibility to, 1
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
All of Us Research Program, National Institutes of Health
Accession: SCV004842736.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
|
Comment:
This missense variant replaces glutamic acid with alanine at codon 33 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact … (more)
This missense variant replaces glutamic acid with alanine at codon 33 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact BRCA1 function in a homology-directed repair, a BARD1 binding, a ubiquitin ligase and a haploid cell proliferation assay (PMID: 25823446, 30209399, 30219179). This variant has been reported in a suspected hereditary breast cancer family (PMID: 15131401). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. (less)
Number of individuals with the variant: 1
|
|
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not provided
(-)
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no classification provided
Method: in vitro
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Breast-ovarian cancer, familial 1
Affected status: not applicable
Allele origin:
not applicable
|
Brotman Baty Institute, University of Washington
Accession: SCV001242826.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020 |
Method: saturation genome editing in haploid cells
Result:
FUNCTIONAL:-0.362577558915998
|
Comment:
Comment:
The p.E33A variant (also known as c.98A>C), located in coding exon 2 of the BRCA1 gene, results from an A to C substitution at nucleotide position 98. The glutamic acid at codon 33 is replaced by alanine, an amino acid with dissimilar properties. This alteration has been identified in several breast cancer families (Muller D et al. Fam. Cancer, 2004;3:15-20; Martelotto LG et al. Genome Biol., 2014 Oct;15:484). This alteration was partially functional in a yeast-based assay but showed wild-type like function in multiple other assays (Millot GA et al. Hum. Mutat., 2011 Dec;32:1470-80; Starita LM et al. Am. J. Hum. Genet., 2018 10;103:498-508; Findlay GM et al. Nature, 2018 10;562:217-222; Starita LM et al. Genetics, 2015 Jun;200:413-22). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Comment:
This missense variant replaces glutamic acid with alanine at codon 33 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact BRCA1 function in a homology-directed repair, a BARD1 binding, a ubiquitin ligase and a haploid cell proliferation assay (PMID: 25823446, 30209399, 30219179). This variant has been reported in a suspected hereditary breast cancer family (PMID: 15131401). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Germline Functional Evidence
| Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|---|---|---|---|---|
|
functionally_normal
|
Method citation(s):
|
|
Brotman Baty Institute, University of Washington
Accession: SCV001242826.1
|
Comment:
The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.98A>C, a MISSENSE variant, produced a function score of -0.36, corresponding to a functional classification of FUNCTIONAL. … (more)
The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.98A>C, a MISSENSE variant, produced a function score of -0.36, corresponding to a functional classification of FUNCTIONAL. SGE function score ranges for classification are as follows: ‘functional’, score > -0.748; ‘intermediate’, -0.748 > score > -1.328; ‘non-functional’, score < -1.328. The median synonymous SNV scored 0.0 and the median nonsense SNV scored -2.12. (less)
|
Comment:
This sequence change replaces glutamic acid with alanine at codon 33 of the BRCA1 protein (p.Glu33Ala). The glutamic acid residue is highly conserved and there is a moderate physicochemical difference between glutamic acid and alanine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in the literature in an individual affected with breast and/or ovarian cancer (PMID: 15131401). ClinVar contains an entry for this variant (Variation ID: 234092). One experimental study performed in yeast cells has shown that this missense change had a detrimental effect on protein function for cell survival in vitro (PMID: 21922593). In summary, this variant is a rare missense change with a deleterious effect on protein function in vitro. While it is absent from the population and reported in affected individuals, the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Comment:
The p.E33A variant (also known as c.98A>C), located in coding exon 2 of the BRCA1 gene, results from an A to C substitution at nucleotide position 98. The glutamic acid at codon 33 is replaced by alanine, an amino acid with dissimilar properties. This alteration has been identified in several breast cancer families (Muller D et al. Fam. Cancer, 2004;3:15-20; Martelotto LG et al. Genome Biol., 2014 Oct;15:484). This alteration was partially functional in a yeast-based assay but showed wild-type like function in multiple other assays (Millot GA et al. Hum. Mutat., 2011 Dec;32:1470-80; Starita LM et al. Am. J. Hum. Genet., 2018 10;103:498-508; Findlay GM et al. Nature, 2018 10;562:217-222; Starita LM et al. Genetics, 2015 Jun;200:413-22). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Comment:
This missense variant replaces glutamic acid with alanine at codon 33 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact BRCA1 function in a homology-directed repair, a BARD1 binding, a ubiquitin ligase and a haploid cell proliferation assay (PMID: 25823446, 30209399, 30219179). This variant has been reported in a suspected hereditary breast cancer family (PMID: 15131401). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. | Starita LM | American journal of human genetics | 2018 | PMID: 30219179 |
| Accurate classification of BRCA1 variants with saturation genome editing. | Findlay GM | Nature | 2018 | PMID: 30209399 |
| Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. | Starita LM | Genetics | 2015 | PMID: 25823446 |
| Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations. | Martelotto LG | Genome biology | 2014 | PMID: 25348012 |
| Assessment of human Nter and Cter BRCA1 mutations using growth and localization assays in yeast. | Millot GA | Human mutation | 2011 | PMID: 21922593 |
| BRCA1 testing in breast and/or ovarian cancer families from northeastern France identifies two common mutations with a founder effect. | Muller D | Familial cancer | 2004 | PMID: 15131401 |
| https://sge.gs.washington.edu/BRCA1/ | - | - | - | - |
Text-mined citations for rs876660844 ...
HelpThese 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 Oct 08, 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.