ClinVar Genomic variation as it relates to human health

The c.994-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 9 in the TP53 gene. This alteration occurs at the 3' terminus of the TP53 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 35 amino acids of the protein. The exact functional effect of this alteration is unknown; however, the impacted region is critical for protein function (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Two other alterations impacting the same acceptor site (c.994-1G>C and c.994-1G>A) have been shown to have an impact on splicing and have been reported in individuals with Li-Fraumeni syndrome (Verselis SJ, et al. Oncogene. 2000 Aug; 19(37):4230-5; Hwang SJ et al. Am J Hum Genet. 2003 Apr;72(4):975-83). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The splice acceptor c.994-2A>G variant has been reported previously in heterozygous state in patients affected with Li-Fraumeni syndrome (Bachinski, E. et. al., 2005).The variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant mutates a splice-acceptor sequence, potentially resulting in exon skipping and the production of abnormal proteins. This variant has been reported to the ClinVar database as Likely Pathogenic. The nucleotide change in TP53 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

This sequence change affects an acceptor splice site in intron 9 of the TP53 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with clinical features of Li-Fraumeni syndrome (PMID: 10980596, 12610779, 20522432, 26014290, 26911350). ClinVar contains an entry for this variant (Variation ID: 487000). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.