ClinVar Miner

Submissions for variant NM_015450.3(POT1):c.1617A>T (p.Gln539His)

gnomAD frequency: 0.00001  dbSNP: rs973319258
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV001012431 SCV001172878 uncertain significance Hereditary cancer-predisposing syndrome 2019-11-18 criteria provided, single submitter clinical testing The p.Q539H variant (also known as c.1617A>T), located in coding exon 13 of the POT1 gene, results from an A to T substitution at nucleotide position 1617. The glutamine at codon 539 is replaced by histidine, an amino acid with highly similar properties. This amino acid position is 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.
Invitae RCV001037854 SCV001201286 uncertain significance Tumor predisposition syndrome 3 2023-10-11 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 539 of the POT1 protein (p.Gln539His). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with POT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 819671). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POT1 protein function. 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.
GeneDx RCV002267065 SCV002549339 uncertain significance not provided 2023-08-04 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in an individual with melanoma (Wong et al., 2019); This variant is associated with the following publications: (PMID: 28393830, 30664638)

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