Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD

• Published in: Lipids in health and disease Vol. 16; no. 1; p. 183
• Main Authors: Boonvisut, Supichaya, Yoshida, Ken, Nakayama, Kazuhiro, Watanabe, Kazuhisa, Miyashita, Hiroshi, Iwamoto, Sadahiko
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 26.09.2017; BioMed Central; BMC
• Subjects: Alcohol; Alcoholic beverages; Alleles; Analysis; Asian Continental Ancestry Group; Association study; Base Sequence; Cardiovascular diseases; Carrier Proteins - genetics; Exons; Fatty liver; Gene deletion; Gene Expression; Gene Frequency; Genes; Genetic aspects; Genetic Association Studies; Genetic factors; Genetic Predisposition to Disease; Hepatocytes; Hepatology; Heritability; High-Throughput Nucleotide Sequencing; Humans; Lipase - genetics; Lipids; Liver diseases; Male; Males; Membrane Proteins - genetics; Metabolism; Minority & ethnic groups; Mutation; Non-alcoholic fatty liver disease; Non-alcoholic Fatty Liver Disease - diagnosis; Non-alcoholic Fatty Liver Disease - ethnology; Non-alcoholic Fatty Liver Disease - genetics; Non-alcoholic Fatty Liver Disease - pathology; Odds Ratio; Polymorphism, Single Nucleotide; Population studies; Proteins; Rare variants; Re-sequencing; Risk Factors; Rodents; Sequence Deletion; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Splicing; Studies; Japan; Association study; Re-sequencing; Non-alcoholic fatty liver disease; Rare variants
• ISSN: 1476-511X; 1476-511X
• DOI: 10.1186/s12944-017-0570-y

Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake. NAFLD is influenced by genetic factors, and the heritability has been estimated at 0.35 to 0.6 by twin studies. We explored rare variants in known NAFLD-associated genes to investigate whether these rare variants are involved in the susceptibility to NAFLD. The target genes for re-sequencing were PNPLA3, TM6SF2, and MTTP. All exons of these three genes were amplified from a discovery panel of 950 Japanese males, and the identified rare variants were further tested for genetic association in 3014 individuals from the Japanese general population and for in vitro functional evaluation. Target re-sequencing analysis using next-generation sequencing identified 29 rare variants in 65 Japanese males (6.84%), 12 of which were newly identified base substitutions. A splicing mutation in TM6SF2 that resulted in deletion of 31 amino acids was identified in an NAFLD case. Among eight genotyped rare single-nucleotide polymorphisms (SNPs; minor allele frequency < 0.02), rs143392071 (Tyr220Cys, PNPLA3) significantly increased (odds ratio = 3.52, P = 0.008) and rs756998920 (Val42Ile, MTTP) significantly decreased (odds ratio = 0.03, P = 0.019) the NAFLD risk. Functional assays showed that these two SNPs disrupted protein functions and supported the genetic association. Collectively, 1.79% of individuals in our studied population were estimated carriers of rare variants that are potentially associated with NAFLD.