ClinVar Genomic variation as it relates to human health

This sequence change affects a donor splice site in intron 3 of the TSC2 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 TSC2 are known to be pathogenic (PMID: 10205261, 17304050). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 834629). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 c.225+2T>C intronic variant results from a T to C substitution two nucleotide after coding exon 2 of the TSC2 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and may result in the creation or strengthening of a novel splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay. The exact functional effect of the altered amino acid sequence is unknown. Additionally, +2T>C alterations are capable of generating wild-type transcripts in some genomic contexts and should be interpreted with caution (Lin JH et al. Hum Mutat. 2019 10;40:1856-1873). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Identified in an individual with epilepsy in the published literature, however, further clinical details were not provided (PMID: 34926809); Identified as a secondary finding in an individual undergoing whole exome sequencing (PMID: 32794656); Targeted RNA studies in blood from a patient without TSC2-related features previously tested at GeneDx suggest altered RNA splicing at low levels; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 18466115, 32794656, 34926809)

The c.225+2T>C variant in the TSC2 gene has not been previously reported in association with disease and was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant alters the canonical donor splice site in intron 3, which is predicted to result in abnormal gene splicing. Notably, a different nucleotide change at this position (c.225+2T>A) has been previously reported de novo in an individual with features of tuberous sclerosis complex (Nellist et al., 2015), suggesting the c.225+2T>C variant may similarly be associated with tuberous sclerosis complex. Heterozygous loss of function is an established mechanism of disease for the TSC2 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.225+2T>C variant as likely pathogenic for tuberous sclerosis complex in an autosomal dominant manner based on the information above. [ACMG evidence codes used: PVS1_Strong; PM2]