Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
Infantile neuronal ceroid lipofuscinosis (INCL) is a progressive encephalopathy characterized by psychomotor deterioration, early visual loss, and an evanishing EEG. Mutations in the CLN1 gene encoding palmitoyl-protein thioesterase (ppt) have been reported in all Finnish INCL patients and in several non-Finnish North European patients. No cases have been contributed from the Mediterranean area thus far. We identified a single adenine insertion at nucleotide position 169 (A169i) in the CLN1 gene in a family in which the proband suffered from an INCL-like syndrome. The novel mutation was homozygous in blood from the proband, heterozygous in his healthy parents, and not found in control alleles. The mutation leads to an early stop codon resulting in an abnormal and truncated ppt protein. Our observations provide the first molecular characterization of an Italian INCL patient and expand the list of the known defects in INCL.