Abstract Homozygosity for pathogenic variants in the leptin gene leads to congenital leptin deficiency causing early-onset extreme obesity. This monogenic form of obesity has mainly been detected in patients from consanguineous families. Prevalence estimates for the general population using the Exome Aggregation Consortium (ExAC) database reported a low frequency of leptin mutations. One in approximately 15 million individuals will be homozygous for a deleterious leptin variant. With the present study, we aimed to extend these findings utilizing the augmented Genome Aggregation Database (gnomAD) v2.1.1 including more than 140,000 samples. In total, 68 non-synonymous and 7 loss-of-function (LoF) leptin variants were deposited in gnomAD. By predicting functional implications with the help of in silico tools, like SIFT, PolyPhen2 and MutationTaster2021, the prevalence of hetero- and homozygosity for putatively pathological variants (n = 32; pathogenic prediction by at least two tools) in the leptin gene were calculated. Across all populations, the estimated prevalence for heterozygosity for functionally relevant variants was approximately 1:2,100 and 1:17,860,000 for homozygosity. This prevalence deviated between the individual populations. Accordingly, people from South Asia were at greater risk to carry a possibly damaging leptin variant than individuals of other ancestries. Generally, this study emphasises the scarcity of deleterious leptin variants in the general population with varying prevalence for distinct study groups.

Prevalence Estimates of Putatively Pathogenic Leptin Variants in the gnomAD Database