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

Abstract

BACKGROUND:

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.

METHODS:

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.

RESULTS:

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.

CONCLUSION:

Collectively, 1.79% of individuals in our studied population were estimated carriers of rare variants that are potentially associated with NAFLD.

• Authors: Supichaya Boonvisut, Ken Yoshida, Kazuhiro Nakayama, Kazuhisa Watanabe, Hiroshi Miyashita, Sadahiko Iwamoto
• Journal: Lipids in health and disease (Lipids Health Dis) Vol. 16 Issue 1 Pg. 183 (Sep 26 2017) ISSN: 1476-511X [Electronic] England
• PMID: 28950858 (Publication Type: Journal Article)

Chemical References

• Carrier Proteins
• Membrane Proteins
• TM6SF2 protein, human
• microsomal triglyceride transfer protein
• Lipase
• adiponutrin, human

Topics

• Alleles
• Asian People
• Base Sequence
• Carrier Proteins (genetics)
• Exons
• Gene Expression
• Gene Frequency
• Genetic Association Studies
• Genetic Predisposition to Disease
• High-Throughput Nucleotide Sequencing
• Humans
• Lipase (genetics)
• Male
• Membrane Proteins (genetics)
• Non-alcoholic Fatty Liver Disease (diagnosis, ethnology, genetics, pathology)
• Odds Ratio
• Polymorphism, Single Nucleotide
• Risk Factors
• Sequence Deletion