ClinVar

Description

The NBN p.Lys219Asnfs*16 variant was identified in 50 of 30494 proband chromosomes (frequency: 0.002) from individuals or families with pancreatic ductal adenocarcinoma, medulloblastoma, prostate cancer, breast cancer, ovarian cancer, non-Hodgkin lymphoma, or colorectal cancer and was present in 20 of 6450 control chromosomes (frequency: 0.003) from healthy individuals (Borecka 2016, Ciara 2010, Cybulski 2004, Domagala 2015, Kraus 2017, Lhota 2016, Steffen 2004, Susswein 2015, Tung 2015). This variant is a Slavic founder mutation with carrier frequency among newborns in the range of 1/154 in the Czech Republic to 1/190 in Poland (Steffen 2004). The variant was also identified in dbSNP (ID: rs587776650 as "With Pathogenic allele"), ClinVar (classified as pathogenic by Invitae, GeneDx, Ambry Genetics and twelve other submitters), and LOVD 3.0 (4x). The variant was identified in control databases in 55 of 276598 chromosomes at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 50 of 126360 chromosomes (freq: 0.0004), Other in 1 of 6436 chromosomes (freq: 0.0002), Finnish in 2 of 25738 chromosomes (freq: 0.00008), and Latino in 2 of 34324 chromosomes (freq: 0.00006); it was not observed in the African, Ashkenazi Jewish, East Asian, or South Asian populations. Functional studies have reported that the variant leads to two truncated fragments, p26 and p70 nibrin, and the translation of a short N-terminal protein with FHA/BRCT domains, therefore maintaining some function of the full-length NBS1 protein (Dzikiewicz-Krawczyk 2008, Cilli 2014). The variant has been associated with an increased risk of breast cancer and medulloblastoma, and a significant increase in overall cancer risks (Zhang 2013, Ciara 2010, Gao 2013, Borecka 2016). The c.657_661del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 219 and leads to a premature stop codon at position 234. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the NBN gene are an established mechanism of disease in NBN-associated cancer and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.