ClinVar Genomic variation as it relates to human health
NM_005431.2(XRCC2):c.643C>T (p.Arg215Ter)
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.
Likely pathogenic(3); Uncertain significance(4)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_005431.2(XRCC2):c.643C>T (p.Arg215Ter)
Variation ID: 30063 Accession: VCV000030063.21
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q36.1 7: 152648842 (GRCh38) [ NCBI UCSC ] 7: 152345927 (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 Oct 11, 2015 May 1, 2024 Mar 14, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_005431.2:c.643C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005422.1:p.Arg215Ter nonsense NC_000007.14:g.152648842G>A NC_000007.13:g.152345927G>A NG_027988.2:g.32324C>T LRG_323:g.32324C>T LRG_323t1:c.643C>T LRG_323p1:p.Arg215Ter - Protein change
- R215*
- Other names
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- Canonical SPDI
- NC_000007.14:152648841: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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Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
- 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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XRCC2 | - | - |
GRCh38 GRCh37 |
687 | 790 |
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
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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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Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Mar 14, 2024 | RCV000022966.10 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
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Jan 30, 2024 | RCV000210083.13 | |
Uncertain significance (3) |
criteria provided, multiple submitters, no conflicts
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Aug 17, 2023 | RCV000236424.7 | |
Likely pathogenic (1) |
criteria provided, single submitter
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- | RCV001261591.1 |
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
(Nov 20, 2015)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: yes
Allele origin:
germline
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University of Washington Department of Laboratory Medicine, University of Washington
Accession: SCV000266232.1
First in ClinVar: Mar 20, 2016 Last updated: Mar 20, 2016 |
Number of individuals with the variant: 1
Clinical Features:
breast cancer (present)
Age: 60-69 years
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Uncertain significance
(Jun 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000292822.11
First in ClinVar: Jul 24, 2016 Last updated: Jul 24, 2016 |
Comment:
This variant is denoted XRCC2 c.643C>T at the cDNA level and p.Arg215Ter (R215X) at the protein level. The substitution creates a nonsense variant, which changes … (more)
This variant is denoted XRCC2 c.643C>T at the cDNA level and p.Arg215Ter (R215X) at the protein level. The substitution creates a nonsense variant, which changes an Arginine to a premature stop codon (CGA>TGA) in the last exon of the gene. XRCC2 Arg215Ter was detected in the apparent homozygous state in a child undergoing whole exome sequencing, the offspring of consanguineous parents, who had features suggestive of Fanconi Anemia (Shamseldin 2012). This variant has also been observed in at least two individuals with a personal history or breast cancer (Shirts 2016, Lolas Hamameh 2017). However, this variant was also identified in 1/951 individuals with atherosclerosis, with no significant personal or family history of cancer (Johnston 2015). This variant results in the loss of the last 66 amino acids of the protein for which the clinical significance is unknown. This variant was observed at an allele frequency of 0.007% (5/66,720) in individuals of European non-Finnish ancestry in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016).The lost region is not within any known functional domain (O'Regan 2001). Based on the currently available information, we consider XRCC2 Arg215Ter to be a variant of uncertain significance. (less)
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Short stature, microcephaly, and endocrine dysfunction
Affected status: yes
Allele origin:
germline
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Pathology and Clinical Laboratory Medicine, King Fahad Medical City
Accession: SCV001438863.1
First in ClinVar: Oct 25, 2020 Last updated: Oct 25, 2020 |
Number of individuals with the variant: 2
Ethnicity/Population group: Arab
Geographic origin: Middle East
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Likely pathogenic
(Mar 14, 2024)
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criteria provided, single submitter
Method: research
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Fanconi anemia complementation group U
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004801236.2
First in ClinVar: Mar 16, 2024 Last updated: Apr 06, 2024 |
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Likely pathogenic
(Jan 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV001187421.5
First in ClinVar: Mar 16, 2020 Last updated: May 01, 2024 |
Comment:
The p.R215* variant (also known as c.643C>T), located in coding exon 3 of the XRCC2 gene, results from a C to T substitution at nucleotide … (more)
The p.R215* variant (also known as c.643C>T), located in coding exon 3 of the XRCC2 gene, results from a C to T substitution at nucleotide position 643. This changes the amino acid from an arginine to a stop codon within coding exon 3. This alteration occurs at the 3' terminus of theXRCC2 gene and is not expected to trigger nonsense-mediated mRNA decay. However, premature stop codons are typically deleterious in nature and a significant portion of the protein is affected (Ambry internal data). This alteration was detected in a homozygous state in an individual diagnosed with Fanconi anemia who had consanguineous parents (Shamseldin HE et al. J. Med. Genet. 2012 Mar;49:184-6). Functional analyses have shown that p.R215* creates an unstable protein, with increased sensitivity to DNA crosslinking agents similar to other known pathogenic mutations causing Fanconi anemia; reintroduction of wild-type XRCC2 protein in complementation studies restored normal cellular phenotype, providing further evidence for the pathogenicity of p.R215* (Park JY et al. J. Med. Genet. 2016 Oct;53:672-680). Further studies showed that the p.R215* alteration results in less than 50% rescue in two out of three different homologous recombination assays compared to wild-type (Hilbers FS et al. Hum. Mutat. 2016 09;37:914-25). This alteration has also been reported in one breast cancer proband from a cohort of Palestinian breast cancer patients (Lolas Hamameh S et al. Int. J. Cancer. 2017 Aug;141:750-756). In addition, this alteration was reported in a breast cancer proband from a cohort of 192 Spanish families with histories suggestive of hereditary breast and ovarian cancer without a BRCA mutation (Bonache S et al. J. Cancer Res. Clin. Oncol., 2018 Dec;144:2495-2513). While this alteration has been shown to be associated with Fanconi Anemia and lead to impaired protein function, its association with breast cancer remains unclear. Based on the majority of available evidence to date, this variant is likely to be pathogenic. (less)
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Uncertain significance
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Fanconi anemia complementation group U
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001137560.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Uncertain significance
(Aug 17, 2023)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000950846.4
First in ClinVar: Aug 14, 2019 Last updated: Feb 14, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies have shown that this premature translational stop signal affects XRCC2 function (PMID: 27233470). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 30063). This premature translational stop signal has been observed in individual(s) with breast cancer, male infertility, and has been observed to be homozygous in an individual with Fanconi anemia (PMID: 22232082, 26046366, 26845104, 28486781, 30306255). This variant is present in population databases (rs143153871, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Arg215*) in the XRCC2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 66 amino acid(s) of the XRCC2 protein. (less)
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Uncertain significance
(Dec 09, 2016)
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no assertion criteria provided
Method: literature only
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FANCONI ANEMIA, COMPLEMENTATION GROUP U (1 patient)
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000044257.6
First in ClinVar: Apr 04, 2013 Last updated: Oct 11, 2015 |
Comment on evidence:
In a 2.5-year-old boy, born of consanguineous Saudi Arabian parents, with an atypical form of Fanconi anemia, complementation group U (FANCU; 617247), Shamseldin et al. … (more)
In a 2.5-year-old boy, born of consanguineous Saudi Arabian parents, with an atypical form of Fanconi anemia, complementation group U (FANCU; 617247), Shamseldin et al. (2012) identified a homozygous c.643C-T transition (c.643C-T, NM_005431) in the XRCC2 gene, resulting in an arg215-to-ter (R215X) substitution predicted to remove the C terminus and abolish XRCC2 activity. The mutation was found by whole-exome sequencing followed by autozygome filtering. Chromosome testing in patient fibroblasts showed a marked increase in the frequency of dsDNA breaks in response to damage, indicating a defect in homologous recombination repair. Complementation studies were not performed. Shamseldin et al. (2012) noted the phenotypic similarities to Xrcc2-null mice (Deans et al., 2000). Park et al. (2016) performed detailed studies on cells derived from the patient reported by Shamseldin et al. (2012). The mutant protein was not found by Western blot analysis, indicating that it is unstable, but likely not subject to nonsense-mediated mRNA decay since the mutation occurs in the last exon. Expression of wildtype XRCC2 corrected all 3 abnormal cellular phenotypes that were apparent in patient cells: cellular sensitivity to DNA interstrand crosslinking agents, chromosome instability, and accumulation of cells at the G2/M stage of the cell cycle. Patient cells showed normal levels of monoubiquitinated FANCD2 (613984), a central step in the FA pathway, and decreased assembly of RAD51 (179617) foci, suggesting that XRCC2 acts downstream of this event. Patient cells showed defective assembly of the components of the BCDX2 complex, particularly RAD51C (602774). Patient cells also showed increased sensitivity to ionizing radiation, consistent with a defect in proteins that act downstream in the FA pathway. (less)
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Pathogenic
(Mar 08, 2017)
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no assertion criteria provided
Method: curation
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not provided
Affected status: yes
Allele origin:
germline
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Leiden Open Variation Database
Accession: SCV001364736.1
First in ClinVar: Jun 27, 2020 Last updated: Jun 27, 2020 |
Comment:
Curator: Arleen D. Auerbach. Submitter to LOVD: Johan den Dunnen.
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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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Pathogenic Variants in Cancer Predisposition Genes and Prostate Cancer Risk in Men of African Ancestry. | Matejcic M | JCO precision oncology | 2020 | PMID: 32832836 |
Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings. | Bonache S | Journal of cancer research and clinical oncology | 2018 | PMID: 30306255 |
Genomic analysis of inherited breast cancer among Palestinian women: Genetic heterogeneity and a founder mutation in TP53. | Lolas Hamameh S | International journal of cancer | 2017 | PMID: 28486781 |
Functional Analysis of Missense Variants in the Putative Breast Cancer Susceptibility Gene XRCC2. | Hilbers FS | Human mutation | 2016 | PMID: 27233470 |
Complementation of hypersensitivity to DNA interstrand crosslinking agents demonstrates that XRCC2 is a Fanconi anaemia gene. | Park JY | Journal of medical genetics | 2016 | PMID: 27208205 |
Improving performance of multigene panels for genomic analysis of cancer predisposition. | Shirts BH | Genetics in medicine : official journal of the American College of Medical Genetics | 2016 | PMID: 26845104 |
Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. | Johnston JJ | American journal of human genetics | 2015 | PMID: 26046366 |
Exome sequencing reveals a novel Fanconi group defined by XRCC2 mutation. | Shamseldin HE | Journal of medical genetics | 2012 | PMID: 22232082 |
Xrcc2 is required for genetic stability, embryonic neurogenesis and viability in mice. | Deans B | The EMBO journal | 2000 | PMID: 11118202 |
Text-mined citations for rs143153871 ...
HelpRecord last updated Sep 29, 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.