16.3: Using web-based bioinformatic tools- gnomAD

When studying a disease that appears to have a genetic component, it is common to identify the causative allele(s) of the gene involved. In the case of recessive alleles, such studies often involve pedigree analyses of families. Once a disease-associated allele is identified, it can be informative to determine whether that allele is found in individuals who do not display the disease trait. For dominant alleles, the presence of an allele without the disease phenotype indicates genetic background effects that influence the disease allele’s penetrance and expressivity.

The accumulating library of exomic sequence data includes (July 2024) more than "730,947 exome sequences and 76,215 whole-genome sequences from unrelated individuals" from around the globe and continues to increase and become more diverse - more non-European people analyzed over time. This data library can be searched using gnomAD.^[561] The user (you), inputs a gene’s official name, as listed in OMIM or GenBank; gnomAD then displays sequence data from unrelated individuals. This allows for the identification of alleles and mutations present in a range of human populations. Let us try using the gene associated with sickle cell anemia, the HBB gene (hemoglobin, beta, OMIM: 141900). Mutations (disease-associated alleles) in HBB have been implicated in a number of human diseases. The allele associated with the sickle cell phenotype involves a missense mutation from GLU to VAL, known as GLU7VAL (↓). We discover that within the gnomAD database of “normal”, that is disease-free individuals, this allele occurs with a frequency of ~0.0044 (with a single homozygous individual identified)(→). The heterozygotic individuals would not be expected to display any overt phenotype under most conditions, while the homozygous individual would be expected to have sickle cell disease. The vast majority of the people with the HBB Glu7Val allele are of African descent, as is the one homozygous individual. When this was originally written (June 2019) there was only one other homozygous individual within the library (Glu122Gln). 71 out of 85 of the people carrying this allele are of African descent, as is the homozygous individual.

Data from gnomAD enables us to make informed guesses as to the impact of various genetic differences on the activity of a gene product.^[562] If, for example, a dominant allele has been linked to a disease and yet that allele is detected in the gnomAD database, we might suggest either that that allele is not the cause of the disease, or that the effects of the allele are influenced by variations in other genes, leading to reduced penetrance and/or expressivity. If an allele is present in a heterozygous condition, but not a homozygous one, we can tentatively assume that negative selection is acting on the allele. If, on the other hand, alleles are present at different frequencies in different populations, that may be evidence for the action of positive selection dependent on environmental factors. The frequency of alleles in different populations can reflects the effects of founder effects, bottlenecks, and genetic drift. Take for example three other HBB alleles, p.Gly70Ser, p.Glu122Gln, and p.Gln40Ter (Ter=stop)(↓). We see that the Gly70Ser and Glu40Ter alleles are present primarily in non-Finnish Europeans, while the Glu122Gln allele is found in South Asians. It is not clear exactly what the effects of such missense mutations will be on the functions of the polypeptide – it could change folding, change interactions with other polypeptides and molecules, add or remove sites of post-translational modification, or change catalytic activities, if the polypeptide has such an activity. It is likely that the Glu40Ter mutation will produce a short, likely non-functional 39 amino acid polypeptide, compared to the 147 amino acid long wild type polypeptide. It is unlikely that the truncated protein is functional, but if it accumulates it could interfere with the function or molecular interactions of the full length wild type polypeptide.

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