ClinVar Genomic variation as it relates to human health

In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 28135145, 26315354, 26787654, 27498913, 25186627, 29522266, 28873162)

The p.G224E variant (also known as c.671G>A), located in coding exon 6 of the NBN gene, results from a G to A substitution at nucleotide position 671. The glycine at codon 224 is replaced by glutamic acid, an amino acid with similar properties. This variant has been identified in individuals with various cancer types as well as healthy controls, including individuals positive for pathogenic mutations in other genes concordant with clinical histories (Ramus SJ et al. J. Natl. Cancer Inst. 2015 Nov;107Young EL et al. J. Med. Genet., 2016 06;53:366-76; Yurgelun MB et al. J. Clin. Oncol., 2017 Apr;35:1086-1095; Tung N et al. Cancer, 2015 Jan;121:25-33; Weitzel JN et al. Cancer, 2019 08;125:2829-2836; Hauke J et al. Cancer Med, 2018 04;7:1349-1358; Ferrer-Avargues R et al. Cancer Commun (Lond), 2021 03;41:218-228). 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.

Variant summary: NBN c.671G>A (p.Gly224Glu) results in a non-conservative amino acid change located in the Nibrin, second BRCT domain (IPR032429) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 250560 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in NBN causing Nijmegen Breakage Syndrome (4.4e-05 vs 0.0025), allowing no conclusion about variant significance. c.671G>A has been reported in the literature as a VUS in settings of multigene cancer panel testing in individuals affected with a variety of cancers such as colorectal, breast and other tumors (example, Tung_2015, Yurgelun_2017, Ferrer-Avargues_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Nijmegen Breakage Syndrome and/or associated tumors. At-least one co-occurrence with another pathogenic variant has been reported (Ferrer-Avargues_2021, MSH2 c.942+2T>A), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

DNA sequence analysis of the NBN gene demonstrated a sequence change, c.671G>A, in exon 6 that results in an amino acid change, p.Gly224Glu. This sequence change has been described in the gnomAD database with frequency of 0.012% in the non-Finnish European subpopulation (dbSNP rs199845467). The p.Gly224Glu change affects a moderately conserved amino acid residue located in a domain of the NBN protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Gly224Glu substitution. This variant has been reported in individuals with cancer as well as in healthy controls (PMID: 28135145, 27498913, 26315354, 24894818). Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Gly224Glu change remains unknown at this time.

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 224 of the NBN protein (p.Gly224Glu). This variant is present in population databases (rs199845467, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer, colorectal cancer and sarcoma (PMID: 27498913, 28135145). ClinVar contains an entry for this variant (Variation ID: 141380). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

The NBN c.671G>A variant is predicted to result in the amino acid substitution p.Gly224Glu. This variant has been reported in individuals with colorectal cancer (Yurgelun et al. 2017. PubMed ID: 28135145) and sarcoma ( Ballinger et al. 2016. PubMed ID: 27498913), as well as in healthy controls (Damiola et al. 2014. PubMed ID: 24894818; Ramus et al. 2015. PubMed ID: 26315354). This variant is reported in 0.012% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/8-90983432-C-T) and is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/141380/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

The frequency of this variant in the general population, 0.00012 (15/128658 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer and in healthy controls (PMID: 31206626 (2019), 29522266 (2018), 28135145 (2017), 26787654 (2016), 26315354 (2015), 25186627 (2015)), as well as in breast cancer cases and control individuals in a large scale breast cancer association study (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/NBN)). It was also reported in an affected individual with Lynch Syndrome with a pathogenic MSH2 variant (PMID: 33630411 (2021)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.