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Two Novel Variants of Undetermined Significance in the ABCC2 Gene Were Identified in a Patient with Dubin-Johnson Syndrome

  • Ranran Shi1,#,
  • Ning Geng1,#,
  • Zhenzhen Zhao2,
  • Yong Zhou3 and
  • Yongning Xin1,* 
 Author information
Gene Expression   2023;22(3):258-261

doi: 10.14218/GE.2022.00019

Dubin-Johnson syndrome (DJS), also known as chronic idiopathic jaundice, black liver-jaundice syndrome, etc. most often develops in adolescents or young adults, and is more common in males, with clinical manifestations of asymptomatic long-term mild-moderate jaundice. The disease belongs to hereditary non-hemolytic jaundice. It is an autosomal recessive genetic disease caused by variants in the ATP-binding cassette subfamily C member (ABCC2) gene. It is characterized by intermittent, predominantly conjugated hyperbilirubinemia and liver pigmentation. Routine ABCC2 gene variant analysis can help in the diagnosis of DJS. In the present study, we reported a patient with Dubin-Johnson syndrome who underwent jaundice-related gene sequencing and identified two novel unknown and significant variants: c.2439+5G>A(p.?) and c.2345_2347del (p.Tyr782_Leu783delinsPhe) of the ABCC2 gene.

A 27-year-old male patient presented to the hospital with "elevated bilirubin detected 11 years ago". It was established that the patient had elevated bilirubin 11 years ago and complained of total bilirubin up to "100 µmol/L", with the deepening of urine color, mild yellow sclera, no white clay-like stool, no loss of appetite, fatigue, skin itching and other discomforts at that time, no special treatment during the period, and the bilirubin was elevated in several check-ups. Three days ago, the liver function test was performed in our hospital: total bilirubin 73.21 µmol/L, direct bilirubin 53.43 µmol/L, indirect bilirubin 19.78 µmol/L, total serum bile acids 28.50 µmol/L. The patient had a previous history of "peripheral facial nerve palsy and facial muscle spasm (left)", no other past medical history, no history of infectious disease, and no history of drug allergy. Personal history: The patient was born in Boyang County, Jiangxi Province, with no history of contact with epidemic areas or epidemic water, no history of eating raw fish or raw meat, no history of tobacco or alcohol addiction, no history of industrial dust or toxic exposure, etc. The patient is married and has a son, and his wife and child are in good health. Family history: The patient’s parents were healthy and denied any history of infectious diseases and tumors in the family. The patient was not aware of his family’s genetic history and the authors were unable to make a family genetic map of the patient.

Physical examination: stable vital signs, no yellowing of the skin, mild yellowing of the sclera, no signs of chronic liver disease. There were no obvious positive signs on the abdominal examination. No edema in both lower limbs. The results of relevant ancillary tests were summarized in Table 1. Imaging examinations: CT scan of the whole abdomen showed no significant abnormalities. Ultrasound suggested fatty liver. A liver puncture biopsy showed a large number of pigment granule deposits (Fig. 1).

Table 1

Laboratory results of this patient

Stool Routine and Occult BloodOB
Routine coagulation testsPT10.9S
Multi-tumor markersGlycoantigen CA-502.46 IU/ml
Glycoantigen CA-1994.98 U/ml
Thyroid function testsFT36.28 pmol/L
FT413.12 pmol/L
TSH1.78u IU/ml
Copper Blue ProteinCopper Blue Protein
Hepatitis B five testsHBsAg
Direct anti-human globulin (Coombs) testDirect anti-human globulin (Coombs) test
ANA antibody spectrumAll items
ANCAAll items
Autoimmune liver disease antibodiesAll items
Liver FunctionTBIL77.90 µmol/L
DBIL43.20 µmol/L
IBIL34.70 µmol/L
TBA28.50 µmol/L
Alb43.67 g/L
transferrin saturation30.82%
ferritin264.8 µg/L
Urine RoutineUrine bilirubin++
Blood routineMCV90.20 fl
HCV serologyHepatitis C virus core antigen
Results of a liver puncture biopsy.
Fig. 1  Results of a liver puncture biopsy.

(a) Liver biopsy specimen of the patient Visually, the liver tissue is darker than normal liver tissue; (b) Hematoxylin and eosin staining (original magnification ×10) shows large deposits of pigment particles (red arrows); (c) Immunohistochemistry of the liver tissue also shows large deposits of pigment particles (red arrows).

Further diagnostic work-up: The patient was subsequently sequenced for jaundice-related genes, and two new variants of unknown significance were identified: namely c.2439+5G>A(p.?) and c.2345_2347del(p.Tyr782_Leu783delinsPhe) of the ABCC2 gene (Fig. 2).

Gene sequencing results of this patient.
Fig. 2  Gene sequencing results of this patient.

(a) c.2439+5G>A(p.?); (b) c.2345_2347del(p.Tyr782_Leu783delinsPhe).

Treatment was given to protect liver function. After treatment, the patient’s blood biochemical parameters improved and reached the following values: liver function tests: total protein 63.27 g/L, globulin 19.60 g/L, total bilirubin 62.90 µmo1/L, direct bilirubin 34.80 µmol/L, indirect bilirubin 28.10 µmol/g, total serum bile acids 23.10 µmol/L. In order to observe the patient’s long-term prognosis, we recommend that the patient be followed up in the hepatology clinic within 2 weeks after discharge. But the patient did not follow the doctor’s orders again for a post-discharge follow-up visit. Therefore, we are currently missing information that could be attained from the patient’s follow-up visit.

DJS presents with chronic jaundice and hyperbilirubinemia in the form of conjugated hyperbilirubinemia and is a rare autosomal recessive liver disease without the features of chronic liver disease.1 DJS is caused by variants in the ABCC2 gene, which provides instructions for the production of a transporter protein called multidrug resistance protein 2 (MRP2), which is involved in the material export of cells and plays an important role in the secretion of bound bilirubin from hepatocytes into the biliary system. Variants in the ABCC2 gene result in the under-expression of tubular MRP2, which affects bound bilirubin into the biliary system that in turn leads to the accumulation of conjugated bilirubin in the hepatocytes, as well as elevated levels of conjugated bilirubin in the blood.2 DJS has traditionally been considered a benign disease that does not require treatment. However, recent studies have shown that variants in the genes responsible for hyperbilirubinemia, as well as minor genetic variants, may lead to increased sensitivity of the liver to drug toxicity.3 After the diagnosis of DJS is important to exclude other diseases that may cause liver damage such as biliary obstructive disease, acute or chronic liver injury, intrahepatic cholestasis, and portal shunt.3 DJS needs to be differentiated from Rotor syndrome, breast milk jaundice, Gilbert-Meulengracht syndrome, hemolysis and other blood disorders, as well as Crigler-Najjar syndrome in addition to other diseases.4

In our case, the patient was diagnosed with DJS by combining the medical history, clinical manifestations, and ancillary tests. With the development of sequencing technologies, genetic and epigenetic studies of complex diseases are becoming more common. ABCC2 variants found in DJS patients include gene deletions, missense variants, nonsense variants, and splice site variants.5 Such variants now include the c.2439+5G>A(p.?) of the ABCC2 gene found in this patient. The variant is a minor variant in the intron region. Although there is no inclusion in the following; literature in the HGMD database; the thousand genomes (1000g2015aug_ALL) database, ESP6500siv2_ALL or dbSNP147 database, bioinformatics software predicts that the variant significantly affects mRNA splicing. According to previous studies, many sequence variants are single nucleotide changes in introns or exons that do not result in amino acid changes and therefore may have no functional impact.6 The clinical significance of c.2439+5G>A(p.?) is not yet clear. Furthermore, the c.2345_2347del(p.Tyr782_Leu783delinsPhe) of the ABCC2 gene is a minor deletion insertion variant (expected to result in a deletion at amino acids 782 to 783 of the encoded protein and the Phe was inserted into the position), which was not previously reported in the HGMD database, the thousand genomes (1000g2015aug_ALL) database, the ESP6500siv2_ALL or the dbSNP147 databases. The clinical significance of c.2345_2347del (p.Tyr782_Leu783delinsPhe) cannot yet be clarified. Based on previous research results, the authors hypothesized that such small deletion insertion variants may result in apical localization of ABCC2 proteins that are either not functionally active or cause a lack of maturation and impaired sorting of ABCC2 proteins.6

Lina Wu et al. found at least one nonsynonymous variant in the ABCC2 gene in all Chinese DJS patients.7 The variants that have been identified are all heterozygous, with only two cases having complex heterozygous variants, suggesting the involvement of other clinically relevant ABCC2 variants. Two novel pure heterozygous variants have been identified abroad, c.1013_1014delTG and 974C->G, located in the eighth exon of the ABCC2 gene, but relatively few genetic analyses of DJS cases have been performed in China.6,810 In the present report, the variants in the patient were confirmed by gene sequencing to be c.2439+5G>A(p.?) and c.2345_2347del (p.Tyr782_Leu783delinsPhe) that belonged to heterozygous variants and were identified as variants of undetermined significance. DJS cases carrying c.2345_2347del(p.Tyr782_Leu783delinsPhe) and c.2439+5G>A(p.?) of the ABCC2 gene, as well as other variants of undetermined significance may be associated with additional ABCC2 variants in hereditary or metabolic liver disease. Reporting novel variants of the ABCC2 gene variant in DJS could help reduce the rate of under- and misdiagnosis of the disease. Evaluation of rare, potentially ABCC2 variants could contribute to genetic studies of DJS.



ATP-binding cassette subfamily C member


Dubin-Johnson syndrome


multidrug resistance protein 2



None to declare.

Ethical statement

This case report was performed in accordance with the Declaration of Helsinki, and was approved by the Institutional Research Human or Animal Ethics Committee of Qingdao Municipal Hospital, and was based on the principles of the Declaration of Helsinki and its appendices. Written informed consent for publication was obtained from the patient for this case report.


This study was supported by a grant from the National Natural Science Foundation of China (No. 32171277).

Conflict of interest

The authors have no conflict of interests related to this publication.

Authors’ contributions

Treating the patient (RRS, NG and YNX); drafting the manuscript (RRS and NG); assisting in writing the manuscript (ZZZ); supervising and editing the manuscript (YNX). All authors have read and agreed to the final manuscript.


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Two Novel Variants of Undetermined Significance in the ABCC2 Gene Were Identified in a Patient with Dubin-Johnson Syndrome

Ranran Shi, Ning Geng, Zhenzhen Zhao, Yong Zhou, Yongning Xin
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