What is hot – or not??? – Looking at Hotspots and Coldspots of Pathogenicity in the STXBP1 Gene

In today genomic medicine era, it remains challenging to understand the functional consequence of a gene variant’s contribution towards disease. Guilt by association is one of the criteria upon which a new variant is judged. We can look at healthy populations data and compare it to established Pathogenic and Likely Pathogenic variants.  This helps us understand if a new variant may have a propensity to cause disease. The thought is that if a new variant is occurring at a region previously established as causing pathogenicity, then the new variant may be pathogenic too (ACMG guideline: PM1 “moderate” assessment criteria).

Is my variant guilty of pathogenicity because of its proximity to a pathogenicity hotspot?

In the image above, we see that there are hotspots (red) and coldspots (blue) for pathogenicity in STXBP1.  The hotspot values were generated from the known Pathogenic and Likely-Pathogenic listed in ClinVar.  The coldspot values (highMAF) come from variants seen in healthy populations. In yellow we have Variants of Uncertain Significance (VUS). Intensity of the peak is a measure of both how many times different variations are seen at an amino acid position and if their nearest neighbors have the same assignment. This plot suggest there are spots in STXBP1 that can tolerate sequence diversity (blue bars) and spots where a hit leads to pathogenic behavior (red bars).  Further, the VUS are landing in both red bar and blue bar regions. Perhaps we can consider VUS to be either pathogenic or benign by this association? Yet, there is a critical assumption that leads to a question: How legitimate is it that every variant in healthy populations (“highMAF”) is ASSUMED to be benign?

2,504 healthy population genomes – Calculating the rare variants in each person

To dig into the validity (or invalidity) of this assumption, we can look to a large population study and ask how many times do we see variation and what are their types. The 1000 Genomes Project Consortium shows an average person has about 4,500,000 million variations. Of these, about 100,000 are somewhat rare because they are seen in less than 1/200 persons (<0.005 MAF). The even more rare “singletons” of the study occur at a frequency of 1 per 2504 persons. This restriction gives us about 10,000 more rare variations to think about per each person. Yet, to get even more rare and be able to ask the question how many variants per person meet the 1 per 200,000 USA definition for Rare Disease frequency, the study size would need to be 100x bigger. Nevertheless, we have interesting data reported in the 1000 Genomes study on healthy population variants that are also seen as pathogenic in Human Gene Mutation Database (HGMD) and ClinVar datasets. Filtering the observed path in healthy population as frequency per individual, every person can expect to harbor 20-25 variants of established pathogenicity.

A larger study by Karczewski et al. 2019 is approaching the scale need for assessing Rare Disease.  A dataset of 141,456 human genomes (125,748 exomes and 15,708 genomes) was harvested from the wildtype controls used in various disease studies. The exomes observe variation mostly in the coding sequence of a gene, while the genomes record variant information across the gene (coding + upstream/downstream/introns). The result is a deeper measure of the frequency of missense variation that approaches the 1 in 200,000 genomes needed for Rare Disease designation.  Currently the National Organization for Rare Disease (NORD) list 1258 disease in their database. STXBP1 cross references to two of these (Dravet and West Syndromes).  Both of these syndromes each have a support group, which are two of the 283 total family foundation groups that are listed in the NORD member list.

Yet the situation for Rare Disease is larger.  In the NIH’s Genetics and Rare Disease (GARD), there are 6264 unique genetic diseases listed. This suggest there are thousands of genes for which we can expect to have gene variant issues leading to disease. ClinVar currently list 7046 is the number of “Genes with variants specific to one protein-coding gene.”  Basically it appears that a third of your 20,000 protein coding genes could take a hit that increases your risk or likeliness of coming down with genetic disease symptoms. 

The GARD lists an intriguing statistics that 20-25 Americans are living with Rare Disease.  The USA’s current population is 327.2 Million, so roughly 1 in 15 individuals world wide are probably living with rare disease. Assuming monogenic cause, then at least 51 million pathogenic might residing in the human population.  Add polygenic burden and the number may be a multiple (100, 150, 200, 250….??) for variants associated with disease currently being experienced today. Guilt by association to hotspots and coldspots might provide some answer, but functional studies are the more definitive proof, and +50 million is a lot of animal models to build!!

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