14. SMAD4 p.I500V Gene ImpactΒΆ

The next tab we will investigate is the Gene Impact tab. In this tab the first dropdown is Gene and Transcript, which provides the user with relevant information including the Gene Name, NCBI description as well as the ability to change the transcript. By clicking on the blue transcript icon, you can then change the default transcript by selecting a different transcripts if available, which will be stored throughout the evaluation as well as if you see this gene in a future sample. The default transcript selected is based on clinical relevance and other heuristics, that are outlined in this blog: https://blog.goldenhelix.com/whats-in-a-name-the-intricacies-of-identifying-variants/. For this gene there is only one transcript, so click Close.

Gene Transcript

Figure 14-1: Opening the Gene Transcript tab.

The next dropdown to investigate is the Gene Region and Mutation Profile, which provides previous counts of variants in ClinVar as well as those present in your internal catalog. For this interface you can change the settings to look at Missense mutations that occur within the same Exon that have been classified as Pathogenic. You can see that there are 3 variants located within 6 amino acid positions of the SMAD4 p.I500V variant and the region contains no benign variants. With this evidence, we can apply PM1 to the evaluation by selecting Hot Spot and No benigns.

Gene Region
Gene Region

Figure 14-2: Applying PM1 in the Gene Region and Mutation Profile.

To determine the missense mutation rate for the SMAD4 gene, we can then focus on the next drop down, Missense as Mechanism of Disease. For this gene, the Z-score produced by the Exome Aggregation Consortium (EXAC) is high, 4.18, which indicates that there is a low rate of bening missense variants in this gene and that there are other missense variants that provide a common mechanism for disease. Together, this provides the first supporting evidence criteria, PP2.

Z-score

Figure 14-3: Z-score from EXAC.

Moving on to the Computational Evidence section, we can see the conservation and functional prediction algorithms such as: SIFT, PolyPhen2, PhyloP and GERP++. These algorithms indicate that the variant is predicted to be damaging (SIFT and PolyPhen) and occur in a conserved region (PhyloP and GERP), which applies PP3. PP3 states that multiple lines of computational evidence support a deleterious effect on the gene or gene product. Answering All Deleterious brings our current classification for the SMAD4 p.I500V to a Likely Pathogenic classification. This completes the Gene Impact tab, so we will move on to the Studies tab.

Z-score

Figure 14-4: ACMG supporting criteria PP3.