ClinVar Miner

Submissions for variant NM_002878.3(RAD51D):c.38C>T (p.Thr13Ile) (rs1064795830)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000486273 SCV000572010 uncertain significance not provided 2017-06-12 criteria provided, single submitter clinical testing This variant is denoted RAD51D c.38C>T at the cDNA level, p.Thr13Ile (T13I) at the protein level, and results in the change of a Threonine to an Isoleucine (ACC>ATC). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. RAD51D Thr13Ile was not observed in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016). Since Threonine and Isoleucine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. RAD51D Thr13Ile occurs at a position where amino acids with properties similar to Threonine are tolerated across species and is located in the ssDNA and XRCC2 binding domains (Miller 2004, Kim 2011). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether RAD51D Thr13Ile is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Invitae RCV000546552 SCV000651743 uncertain significance Breast-ovarian cancer, familial 4 2019-10-31 criteria provided, single submitter clinical testing This sequence change replaces threonine with isoleucine at codon 13 of the RAD51D protein (p.Thr13Ile). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with RAD51D-related conditions. ClinVar contains an entry for this variant (Variation ID: 422517). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). 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.
Color RCV000773179 SCV000906740 uncertain significance Hereditary cancer-predisposing syndrome 2018-12-19 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000546552 SCV001160332 uncertain significance Breast-ovarian cancer, familial 4 2019-02-23 criteria provided, single submitter clinical testing The RAD51D c.38C>T; p.Thr13Ile variant (rs1064795830) is reported as uncertain in the ClinVar database (Variation ID: 422517). This variant is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. The threonine at codon 13 is moderately conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant may be deleterious. However, given the lack of clinical and functional data, the significance of this variant is uncertain at this time.
Ambry Genetics RCV000773179 SCV001182997 uncertain significance Hereditary cancer-predisposing syndrome 2020-02-12 criteria provided, single submitter clinical testing The p.T13I variant (also known as c.38C>T), located in coding exon 1 of the RAD51D gene, results from a C to T substitution at nucleotide position 38. The threonine at codon 13 is replaced by isoleucine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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