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    1. A 5-year-old south Asian female was incidentally found to have hepatomegaly on a trip to India, where she became acutely ill with fever, vomiting, and abdominal pain. Blood work done at that time demonstrated mildly elevated liver function tests (AST 48 U/L, ALT 80 U/L), and an abdominal ultrasound revealed hepatomegaly without biliary or splenic abnormalities. She was prescribed an antibiotic and her symptoms gradually resolved.A month after her return to the United States, her pediatrician noted persistent hepatomegaly and the new development of fever. She was referred to the emergency department because of suspicion of a tropical infectious disease. A repeat ultrasound demonstrated persistent hepatomegaly. Her transaminases (AST 133 U/L, ALT 112 U/L) remained elevated. The infectious workup was negative for cytomegalovirus, hepatitis A, Lyme disease, and malaria. She did have a positive Epstein-Barr virus IgM. Repeat blood work was obtained at follow-up infectious disease clinic visit where she was again found to have hepatomegaly (7 cm below the costal margin) and mildly abnormal transaminases. A computed tomography of the abdomen and pelvis (Figure 1) was performed that demonstrated hepatomegaly but had otherwise normal findings. Her fever resolved within 2 weeks. She was otherwise well and was not on any medications. There was no family history of liver disease. Her immunizations were up to date. Because of persistent hepatomegaly, she was referred to the liver clinic.Open in a separate windowFigure 1Computed tomography of abdomen and pelvis. The liver is enlarged, measuring up to 17 cm in width and craniocaudal dimension. The contour is smooth. The hepatic parenchyma is homogenous without a focal mass. There is no intrahepatic biliary dilatation. The portal and hepatic venous systems are patent and nondilated.In the liver clinic, she was noted to have an enlarged, firm liver, palpable 8 cm below the costal margin with no associated splenomegaly. Test results for autoimmune hepatitis, WD, and alpha-1-antitrypsin deficiency were negative. Nonfasting lipid levels were abnormal; repeat testing showed a fasting total cholesterol of 305 mg/dL and a triglyceride level of 142 mg/dL.On the basis of a clinical suspicion of a diagnosis of CESD, a liver biopsy was performed. It revealed diffuse, microvesicular steatosis in the hepatic parenchyma (Figure 2(a)). Portal tracts were expanded by foamy macrophages containing finely vacuolated material, which was periodic acid-Schiff positive and resistant to diastase digestion. Trichrome stain for collagen showed mild portal fibrosis with early delicate bridging fibrosis. Ultrastructurally, the cytoplasm had a moth-eaten appearance with the presence of lipid droplets and cholesterol crystals (Figure 2(b)). There was no evidence of hepatocellular necrosis, cholestasis, or bile duct proliferation.Open in a separate windowFigure 2(a) Liver biopsy, periodic acid-Schiff stain with diastase (magnification, ×40). Lipid demonstrated within the hepatocellular cytoplasm (arrows). (b) Electron micrograph (direct magnification, ×2500). The hepatocellular cytoplasm in places has a moth-eaten appearance with lipid droplets (arrows). Additionally, some foci show cholesterol crystals (∗) free in the hepatocellular cytoplasm.Liver tissue was sent to Dr. D. Wenger's Lysosomal Diseases Testing Laboratory at Thomas Jefferson University. She was found to have a low acid lipase activity of 7.2 (no units provided by Dr. D. Wenger's laboratory) in the liver. Follow-up testing through a commercial laboratory demonstrated low level of lysosomal acid lipase activity (0.008 nmol/punch/h) in blood. Lysosomal acid lipase gene sequence analysis was performed, which demonstrated that she was heterozygous for the following two mutations: c.57_60delTGAG and c.894G>A. Both parents underwent mutation analysis. The mother was confirmed to have the c.894G>A mutation while the father carried the c.57_60delTGAG mutation. The c.57_60delTGAG is a new mutation not previously described in the literature in patients with CESD.Go to:

      Case: Lin Patient-female, south Asian, 5 years old at diagnosis

      CasePresentingHPOs: HP:0001945, HP:0002013, HP:0002027, HP:0002240

      CasePresentingHPOsFreeText: Mildly elevated liver function tests (AST 48 U/L, ALT 80 U/L) upon initial visit, transaminases (AST 133 U/L, ALT 112 U/L) remained elevated after a month. Non-fasting lipid levels were abnormal; repeat testing showed a fasting total cholesterol of 305 mg/dL and a triglyceride level of 142 mg/dL. Diffuse, microvesicular steatosis in the hepatic parenchyma. Portal tracts were expanded by foamy macrophages containing finely vacuolated material, which was periodic acid-Schiff positive and resistant to diastase digestion. Trichrome stain for collagen showed mild portal fibrosis with early delicate bridging fibrosis. Ultrastructurally, the cytoplasm had a moth-eaten appearance with the presence of lipid droplets and cholesterol crystals. Low acid lipase activity of 7.2 (no units provided) in the liver, with follow up low level of lysosomal acid lipase activity (0.008 nmol/punch/h) in blood.

      CaseNOTHPOs: HP:0032316, HP:0001744, HP:0001404, HP:0001396, HP:0001408

      CaseNOTHPOSFreeText:

      CasePreviousTesting: Abdominal ultrasound. Infection workup was negative for cytomegalovirus, hepatitis A, Lyme disease, and malaria. She did have a positive Epstein-Barr virus IgM. CT of the abdomen and pelvis revealed an enlarged liver measuring up to 17cm in width and craniocaudal dimension. Test results for autoimmune hepatitis, WD, and alpha-1-antitrypsin deficiency were negative. Liver biopsy.

      CaseGenotypingMethod: LAL gene sequence analysis was performed.

      Variant: c.57_60delTGAG and c.894G>A

      ClinVarID: or CAID: CA2573331826 and 203361

      gnomAD: This proband has a four-nucleotide deletion, c.57_60delTGAG, in exon 2 of the LIPA gene. This variant is predicted to result in a premature translation stop downstream of the deletion (p.Glu20GlyfsTer6). The variant is not present in gnomAD. This proband is scored default points.

      This proband has a synonymous variant, Gln298= on exon 8/10 in a cononical splice site, which causes an abnormal splicing that results in the in-frame skipping of exon 8. The variant is reported in 167/128942 European (non-Finnish) alleles at a frequency of 0.001295, with no homozygotes in gnomAD v2.1.1. This is the most frequent variant in CESD patients (present in 40-60% of patients reported in the literature), but it is not confirmed if this is due to a hotspot or a common ancestor. This proband is scored default points.

      AddCaseInfo: Confirmed in trans

      PreviouslyPublished: no

      VariantEvidence: Predicted evidence only for deletion variant.

      Expression analysis in patient fibroblasts found lysosomal acidic lipase (LAL) activity to be reduced to 6-12% of wild type (PMID: 22227072).

    1. 2.2.1. Patient #F061The patient was an Italian male, born from a consanguineous marriage, who was admitted to the hospital at 2 months of age for diarrhea and steatorrhea associated with abdominal distension, anemia (RBC 3.02 × 106/μL; Hb 7.7 g/dL), hepatosplenomegaly, increased liver enzymes (AST 86 IU/L—n.v. 10–40; ALT 38 IU/L—n.v. 5–35), hypoproteinemia (4.8 g/dL—n.v. 6.1–7.9) and failure to thrive. Peripheral blood smear showed the presence of vacuolated leukocytes; bone marrow biopsy showed vacuolization in histiocytes suggesting intralysosomal and cytoplasmic accumulation of lipids (foam cells). The adrenal glands were markedly enlarged and extensively seeded with calcific deposits. LAL activity in skin fibroblasts was 1.4 nmol/mg protein/min (n.v. 55.8 ± 15.6 nmol/mg protein/min). The clinical features and the severe LAL defect were consistent with the diagnosis of WD. The patient died of hepatic and adrenal failure at 6 months of age.

      Case: Patient #F061-male, Italy, 2 months old at onset, died at 6 months

      CasePresentingHPOs: HP:0002014, HP:0002570, HP:0003270, HP:0001903, HP:0001433, HP:0001508, HP:0008221

      CasePresentingHPOsFreeText: Anemia (RBC 3.02 × 106/μL; Hb 7.7 g/dL), increased liver enzymes (AST 86 IU/L—n.v. 10–40; ALT 38 IU/L—n.v. 5–35), hypoproteinemia (4.8 g/dL—n.v. 6.1–7.9). Presence of vacuolated leukocytes. Bone marrow biopsy showed vacuolization in histiocytes suggesting intralysosomal and cytoplasmic accumulation of lipids (foam cells). Adrenal glands seeded with calcific deposits. LAL activity in skin fibroblasts was 1.4 nmol/mg protein/min (n.v. 55.8 ± 15.6 nmol/mg protein/min). Hepatic and adrenal failure at 6 months of age. LAL activity is 2.5% of normal.

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting: peripheral blood smear, bone marrow biopsy

      CaseGenotypingMethod: LIPA gene exons and exon–intron boundaries were PCR amplified using sets of primers designed according to the LIPA genomic sequence. Putative mutations were confirmed by sequencing duplicate PCR products.

      Variant: c.229+1G>A homozygous

      ClinVarID: or CAID: CA211323057

      gnomAD: This proband is homozygous for a splice site variant, c.229+1G>A in intron 3, which is predicted to cause out-of-frame skipping of exon 3, generating a transcript with a PTC which would rapidly undergo degradation by NMD. The variant is not reported in gnomAD. This proband is scored reduced points due to alternative splicing.

      AddCaseInfo: consanguineous parents

      PreviouslyPublished: no

      VariantEvidence: predictive