Clinical Exome Sequencing of Five Year Old Girl with Hepatosplenomegaly, Cholestasis, and Hypercholesterolemia

Background: Progressive familial intrahepatic cholestasis type 3 is an autosomal recessive condition characterised by hepatocellular phospholipid export deficiency, impaired secretion, caused by mutations in the ABCB4 gene. Lack of phospholipids produces unstable micelles with toxic effect on the bile ducts, leading to cholestasis.

Objective: 5 year old girl referred for pediatric checkup and further genetic examination due to hepatosplenomegaly, cholestasis presented as elevated GGT and hypercholesterolemia. First symptom was anemia, at 7 months of age. She was hospitalized for elevated hepatic transaminases, and hypercholesterolemia. Thorough evaluation in finding the etiology was done. Major metabolic diseases, extrahepatic biliary obstruction and infectious pathology were all excluded. Later patient manifested cholestasis with liver and spleen enlargement, telangiectasia, poor weight gain, pruritus and signs of rickets. Treatment was started with ursodeoxycholic acid . At first glycogen storage disease type 6 was suspected; later dismissed by Sanger sequencing of the PYGL gene. Parents refused liver biopsy, thus clinical exome sequencing was recommended.

Methods: Clinical exome sequencing of 4811 clinically relevant genes was performed on a NextSeq Illumina instrument. Upon quality control, DNA sequences were mapped to hg19, and a total number of 7790 high-confidence genetic variants were called.

Results: Two candidate pathogenic variants c.2165G>C; p.Gly722Ala; and c.833G>T; p.Arg278Met in ABCB4 were identified. Genetic variant c.2165G>C has been reported in the Clinvar database, while to the best of our knowledge, c.833G>T is not reported and was discovered for the very first time. Both meet several pathogenicity criteria. Pathogenic mutations in ABCB4 are associated with PFIC type 3 ( PFIC3; OMIM: 171060)

Conclusion: We conclude that patients who present with cholestasis, in their differential diagnosis should be considered for PFIC, even though cholestasis is not the dominant sign. Here we show that compound heterozygosity of one novel and one known ABCB4 mutation could lead to PFIC3.