Screening for rare variants in the PNPLA3 gene in obese liver biopsy patients.
BACKGROUND
Previous research has clearly implicated the PNPLA3 gene in the etiology of nonalcoholic fatty liver disease as a polymorphism in the gene was found to be robustly associated to the disease. However, data on the involvement of rare PNPLA3 variants in the development of nonalcoholic fatty liver disease (NAFLD) is currently limited. Therefore, we performed an extensive mutation analysis study on a cohort of obese liver biopsy patients to determine PNPLA3 variation and its correlation with fatty liver disease.


METHODS
We screened the entire coding region of the PNPLA3 gene in DNA samples of 393 obese liver biopsy patients with varying degrees of fatty liver disease. Mutation analysis was performed by high-resolution melting curve analysis in combination with direct sequencing.


RESULTS
We identified several common polymorphisms as well as one rare synonymous variant (c.867G>A rs139896256), one rare intronic variant (c.979+13C>T) and 3 nonsynonymous coding variants (p.A76T, p.A104V and p.T200M) in the PNPLA3 gene. In silico analysis indicated that the p.A104V variant will probably have no functional effect, whereas for the p.A76T and p.T200M variant a possible pathogenic effect is suggested.


CONCLUSIONS
Overall, we showed that novel variants in PNPLA3 are very rare in our liver biopsy cohort, thereby indicating that their impact on the etiology of NAFLD is probably limited. Nevertheless, for the three rare coding variants that were identified in patients with advanced liver disease, further functional characterization will be essential to verify their potential disease causality.
Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
Doreen
D
Zegers
Department of Endocrinology, Diabetology and Metabolic Diseases, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
An
A
Verrijken
Department of Gastroenterology and Hepatology, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
Sven
S
Francque
Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
Fenna
F
de Freitas
Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
Sigri
S
Beckers
Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
Evi
E
Aerts
Department of Abdominal Surgery, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
Martin
M
Ruppert
Department of Abdominal Surgery, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
Guy
G
Hubens
Department of Gastroenterology and Hepatology, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
Peter
P
Michielsen
Department of Medical Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium. Electronic address: wim.vanhul@uantwerpen.be.
Wim
W
Van Hul
Department of Endocrinology, Diabetology and Metabolic Diseases, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Antwerp, Belgium.
Luc F
LF
Van Gaal
D000328:Adult; D001706:Biopsy; D004252:DNA Mutational Analysis; D005260:Female; D006801:Humans; D008049:Lipase / Q000235:genetics*; D008099:Liver / Q000473:pathology*; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D065626:Non-alcoholic Fatty Liver Disease / Q000235:genetics*; D009765:Obesity / Q000150:complications*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D000217:Acyltransferases; D054512:Phospholipases A2, Calcium-Independent
D008049:Lipase; D008565:Membrane Proteins; C533682:PNPLA3 protein, human; D000217:Acyltransferases; D054512:Phospholipases A2, Calcium-Independent