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Novel PRKAG2 variant presenting as liver cirrhosis: report of a family with 2 cases and review of literature
BMC Medical Genomics volume 14, Article number: 33 (2021)
Mutations in the PRKAG2 gene encoding the 5′ Adenosine Monophosphate-Activated Protein Kinase (AMPK), specifically in its γ2 regulatory subunit, lead to Glycogen storage disease of heart, fetal congenital disorder (PRKAG2 syndrome). These mutations are rare, and their functional roles have not been fully elucidated. PRKAG2 syndrome is autosomal dominant disorder inherited with full penetrance. It is characterized by the accumulation of glycogen in the heart tissue, which is clinically manifested as hypertrophic cardiomyopathy. There is little knowledge about the characteristics of this disease. This study reports a genetic defect in an Iranian family with liver problems using targeted-gene sequencing.
A 4-year-old girl presented with short stature, hepatomegaly, and liver cirrhosis. As there was no specific diagnosis made based on the laboratory data and liver biopsy results, targeted-gene sequencing (TGS) was performed to detect the molecular basis of the disease. It was confirmed that this patient carried a novel heterozygous variant in the PRKAG2 gene. The echocardiography was a normal.
A novel heterozygous variant c.592A > T (p.Met198Leu) expands the mutational spectrum of the PRKAG2 gene in this family. Also, liver damage in patients with PRKAG2 syndrome has never been reported, which deserves further discussion.
Glycogen storage disease of heart, lethal congenital (PRKAG2 syndrome) is a disorder of glycogen metabolism, essentially heart-specific . It has autosomal dominant inheritance with complete penetrance . The disease is caused by mutations in the PRKAG2 gene, which encodes the non-catalytic subunit γ2 activated by the protein kinase AMP. The gene of PRKAG2 has 22 exons located in the 7q36.1 region. The prevalence of this disorder is rare, which is reported as 0.23–1% in patients with fatal infantile cardiomyopathy . To the best of our knowledge, less than 200 patients with genetically confirmed PRKAG2 syndrome have been reported so far . Clinical presentation of patients often represents during late adolescence and rare manifestations during childhood were described [5,6,7]. Mutation in the PRKAG2 gene is identified mainly by cardiac symptoms. To date, other symptoms such as skeletal muscle involvement, and sometimes-enlarged kidneys were reported; however, the exact spectrum of signs are not fully elucidated yet [2, 3]. In rare, sporadic cases, heart failure and respiratory compromise have been reported, which leads to death within a few weeks or months after birth [8,9,10].
In this study, we investigated the affected case in an Iranian family with a novel heterozygous PRKAG2 mutation who presented with liver problems.
A 4-year-old Iranian girl was referred to our center for genetic analysis presented with a history of mild hepatomegaly and short stature. She is the second child of a non-consanguineous family. She was delivered following a normal vaginal delivery after term pregnancy with a birth weight of 2.50 kg, and height of 46 cm. No hypoglycemia was noted in the perinatal period and the postnatal transition.
At the age of one, she was admitted because of hepatomegaly, diarrhea, and developmental delay. Biochemical tests revealed alanine aminotransferase (ALT) 13 IU/L, and aspartate aminotransferase (AST) 63 IU/L. Triglyceride was normal (66 mg/dl) with a normal cholesterol level (136 mg/dl), but a high level of LDH (1024 U/L). Peripheral blood smear showed hypochromic microcytic anemia (hemoglobin of 10.8 g/dl and a hematocrit of 34.6%, the mean corpuscular volume of 60.40 fl, and low mean corpuscular hemoglobin 18.81 pg) and normal platelet count (221,000/µL). Hence, blood gas analysis and electrolyte levels were normal, but a low level of CPK (18 U/L), was documented as shown in Table 1.
Urine amino acid analysis by chromatography presented a weak band in cysteine and moderate bond in arginine. Lung fluid showed inflammatory cells mostly PMNs admixed with respiratory columnar cells and squamous cells in the proteinaceous background. No fungal elements were identified. Histology of the liver tissue revealed cirrhosis. According to clinical presentation and liver biopsy, storage disease was suggested by the local pediatrician without genetic analysis, so treatment with frequent feeds and cornstarch was initiated.
At the age of 3, Targeted gene sequencing (TGS) with a custom-targeted Ion AmpliSeq™ panel was performed. The panel included 7219 amplicons covering 450 genes associated with Inborn Metabolic Diseases consisting of glycogen storage disorders genes with hepatic involvement. Sanger sequencing validated identified the variants, using an ABI Prism 3500 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Analyses were done using an Ion Torrent 540 chip (Life Technologies, Guilford, CT, South San Francisco, CA). The human GRCh37/hg 19 was used as the reference. Polyphen2, SIFT, and Mutation Taster were used for in silico analysis, GERP and Phastcons scores were used to evaluate the conservation of the variants. The population frequency of each variation was evaluated, using data from the gnomAD database. ACMG guidelines were used for variant interpretation . The sequence variants were described according to the Human Genome Variation Society Nomenclature . The sequence variant RefSeq NM_001040633.1 was used. Interestingly, a novel heterozygous variant c.592A > T (p.Met198Leu) was detected, in the exon 1 of the PRKAG2 gene, by TGS and suggested PRKAG2 syndrome. Further functional tests are needed.
On admission, the patient’s echocardiogram revealed normal heart function with very mild MR, and TR. Tandem mass spectrometry (MS/MS) analysis using urine revealed normal results for Glc4.
Past medical family history of the patient revealed that proband had a sibling (boy) who expired at the age of 15 years old with pulmonary and liver symptoms. Figure 1 presents the pedigree of the family with 2 affected children. The proband's brother had a heterozygous variant c.1897C > A (p.Leu633Ile) which was detected in the exon 14 of the CFTR gene by WES. Their parents were also examined for this mutation. The father of the family carried a heterozygous mutation too, but he was always healthy with no pulmonary symptoms. The proband's brother also had a liver biopsy, which revealed cirrhosis with no known underlying cause. He had undergone liver transplantation at the age of 6. At the age of 14, his echocardiogram showed mild MR, TR, and severe pulmonary hypertension. Finally, the proband's brother died at age 15 before mutation analysis for the PRKAG2 gene. Proband was normal for mutation on the CFTR gene by WES (Fig. 1).
Discussion and conclusions
The present study of an Iranian family identifies, for the first time, a novel missense variant of the PRKAG2 gene (c.592A > T, p.Met198Leu), which was identified by TGS. It has been reported to cause glycogen storage disease of the heart, fetal congenital disorder (PRKAG2 syndrome), and atypical involvement of the liver.
The γ2-regulatory subunit of AMP-activated protein kinase (AMPK) is an enzyme that regulated the amount of ATP, which is essential for metabolic activity. It is encoded by the PRKAG2 gene . Mutations in this protein kinase are related to a wide variety of manifestations, including glycogen accumulation, Wolff–Parkinson–White syndrome, and conduction disorder [2, 3, 5]. However, conduction disorder is not always available in PRKAG2 syndrome, and it may appear in the future [13, 14]. Electrocardiographic abnormalities are usually in PRKAG2 syndrome, but we did not find it in our proband. According to reports, the mechanism of impaired glucose metabolism and increased glycogen storage in cells caused by PRKAG2 mutations is still unclear .
To date, about 21 mutations have been demonstrated to be associated with PRKAG2 syndrome . Most of these mutations are missenses, and the most abundant ones are p.R302Q  and p.N488I . Hence, the clinical manifestations were different in the families carrying the mutations in the PRKAG2 gene. Even in the same family, the affected patients did not present the same manifestations with similar mutations. Cardiac conduction disorder is the main feature of affected members, as reported previously. To find and carefully evaluate all reported mutations and unusual effects on the presentation of PRKG2, we did a literature search until October 2020. Sporadic cases were reported to have enlarged and dysmorphic kidneys and chronic kidney disorder, as presented in Table 2 [2, 4]. In this study, we presented a family with two children both having liver cirrhosis and pulmonary symptoms with no cardiac problem. Further research and more cases are needed to determine the clinical correlation between the presence of a detected novel mutation and the adverse outcomes of a patient with PRKAG2 syndrome. The integration of biochemical, transcriptional, and functional datasets using human induced pluripotent stem cells (iPScs), micro-tissues, and mouse models allowed us to analyze how mutations produce the phenotypes observed in PRKAG2 mutations.
Our case shows that molecular analysis (especially using TGS) is an important method to diagnose GSD subtypes. Early genetic diagnosis of TGS has many benefits, including time- and cost-effectiveness, correct treatment, accurate recurrence risk recommendations, and screening of the patients where appropriate . Unfortunately, we do not have the genetic analysis of parents and expired brother to determine whether the expired brother had the same mutation or not.
In conclusion, we are reporting a novel variant of PRKAG2 that is associated with PRKAG2 syndrome in an Iranian family. Molecular screening for PRKAG2 mutations may be considered in patients who have liver problems. The case highlights the advantage of targeted sequencing in diagnosing a patient with PRKAG2 syndrome, which may present unusual manifestation.
Availability of data and materials
The data that support the findings of this study are available from Gazi University of Medical Sciences but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of Gazi University of Medical Sciences. The datasets generated and/or analyzed during the current study are available in the Genbank repository (GRCh37/hg19, https://www.ncbi.nlm.nih.gov/genome/guide/human/) for PRKAG2: NM_001040633.1 and CFTR: NM_ 000492.4 (https://www.ncbi.nlm.nih.gov/nuccore).
AMP-activated protein kinase
Hematoxylin and Eosin
Induced pluripotent stem cells
Left anterior descending artery
Left ventricular hypertrophy
Progressive familial intrahepatic cholestasis
Protein kinase AMP-activated non-catalytic subunit gamma 2
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The authors are grateful to the patient and her family for their participation. We thank Dr. SH. Rajaei for his contribution to the echocardiography analysis.
The fees of sequencing and data analysis were funded by the Transplant Research Center, affiliated with Shiraz University of Medical Sciences, Shiraz, Iran (Grant No. 1396-01-106-15748) and National Institute for Medical Research Development (Grant No. 976961). The funder had no role in the study design, data collection, analysis, decision to publish, or manuscript preparation.
Ethics approval and consent to participate
The patients’ parents or legal guardians provided a written informed consent form for participation in the study. Parents of the participant gave written informed consent. The ethics committee of Shiraz University of Medical Sciences approved this study (Approval #: IR.SUMS.REC.1396.S805).
Consent for publication
The parents signed the informed consent on behalf of the both patients (proband and her brother), authorizing their molecular studies and publication of this case report. Written consent is available for review by the editor-in-chief of this journal.
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Beyzaei, Z., Ezgu, F., Geramizadeh, B. et al. Novel PRKAG2 variant presenting as liver cirrhosis: report of a family with 2 cases and review of literature. BMC Med Genomics 14, 33 (2021). https://doi.org/10.1186/s12920-021-00879-1
- PRKAG2 syndrome
- Wolff–Parkinson–White syndrome
- Targeted gene sequencing