ClinVar Genomic variation as it relates to human health

DNA sequence analysis of the POT1 gene demonstrated a sequence change, c.670G>A, in exon 9 that results in an amino acid change, p.Asp224Asn. This sequence change has been described in the gnomAD database with a frequency of 0.016% in the non-Finnish European subpopulation (dbSNP rs202187871). This variant has been observed to segregate with melanoma in one family and with Hodgkin lymphoma in another family (PMID: 24686846, 29693246). Functional studies demonstrated that this sequence change affects protein function, leading to telomere lengthening and fragility (PMID: 29693246). The p.Asp224Asn change affects a highly conserved amino acid residue located in a domain of the POT1 protein that is not known to be functional. The p.Asp224Asn substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to insufficient evidences, the clinical significance of the p.Asp224Asn change remains unknown at this time.

The p.D224N variant (also known as c.670G>A), located in coding exon 5 of the POT1 gene, results from a G to A substitution at nucleotide position 670. The aspartic acid at codon 224 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in multiple melanoma-prone families (Shi J et al. Nat. Genet., 2014 May;46:482-6; Artomov M et al. J. Natl. Cancer Inst., 2017 12;109) and in three siblings and a mother all affected with Hodgkin's lymphoma (McMaster ML et al. Br. J. Haematol., 2018 05;181:372-377). A recent study also identified this variant in a family affected by multiple cancer types, including cutaneous melanoma and hematopoietic syndromes- chronic myeloid leukemia (CML), Hodgkin's lymphoma, follicular lymphoma, and lentigo myeloid leukemia (LMM) (Nathan V. Br J Haematol. 2021 01;192(2):e57-e60). In a functional study, this alteration demonstrated deficient telomere binding in vitro and increased telomere length and fragility compared to wildtype cells (McMaster ML et al. Br. J. Haematol. 2018 05;181:372-377). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Observed in individuals with melanoma, chronic lymphocytic leukemia, and glioblastoma (PMID: 29522175, 34193977, 29625052, 36876055); Co-segregates with melanoma and/or hematologic malignancies in multiple families, but was also present in unaffected individuals (PMID: 29693246, 33216348, 24686846, 35977101); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31919090, 32155570, 24784786, 25431349, 24686849, 27528712, 27365461, 26403419, 24686846, 25244922, 29693246, 29522175, 30556179, 32033110, 32987645, 32191290, 29625052, Szmyd2021, 34193977, 33216348, 36656928, 36539277, 28393830, 34218205, 36876055, 35977101, 36451132, 37183325, 37167549)

POT1: PM1, PP1, PS3:Supporting

The frequency of this variant in the general population, 0.00016 (20/128806 chromosomes in European (Non-Finnish) subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals/families with melanoma or lymphoma and in their unaffected family members (PMIDs: 24686846 (2014), 27365461 (2016), 29522175 (2017), and 29693246 (2018)). This variant has also been detected in at least one individual with glioblastoma, one individual with lymphocytic leukemia and in individuals with lung adenocarcinoma (PMIDs: 29625052 (2018) and 31919090 (2020)). Functional studies have shown that this variant results in impaired telomeric binding in vitro and increased telomere length and fragility while the telomerase activity remains comparable to wild type and no significant increase in telomere dysfunction-induced damage foci is detected (PMID: 29693246 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 224 of the POT1 protein (p.Asp224Asn). This variant is present in population databases (rs202187871, gnomAD 0.01%). This missense change has been observed in individual(s) with cutaneous melanoma, glioblastoma multiforme, and/or Hodgkin lymphoma and other hematologic malignancies (PMID: 24686846, 29625052, 29693246, 33216348). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 139527). 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 with a negative predictive value of 80%. Experimental studies have shown that this missense change affects POT1 function (PMID: 29693246). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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.