PMC6848451_01
Skin capillary malformations, facial feature, and heart and liver arteriovenous malformations of the patient. (A) Multiple flaky purplish red hemangiomas presented in the abdomen. (B) The characterized face of the patient shows a broad forehead, a small-pointed chin, and prominent ears. (C) The image of color Doppler b mode ultrasonography shows congenital heart disease: patent ductus arteriosus, patent foramen ovale, tricuspid, and mitral regurgitation. (D) The CT image shows enlarged portal vein draining directly into the inferior vena cava (red arrow). (E) Angiography shows enlarged left hepatic artery (red arrow).
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Multiple nevus flammeus protruded from her skin in the area of thorax, abdomen, and legs for more than 1 year (Figure 1A). Her face was characterized by a broad forehead, a small-pointed chin, and prominent ears (Figure 1B). When she was 10 months old, color Doppler (B-mode) ultrasonography revealed an enlarged right heart, patent ductus arteriosus (1.5 mm), severe tricuspid regurgitation, and pulmonary arterial hypertension (TR Vmax = 435 cm/s, SPAP = 76 mm Hg) (Figure 1C). The portal vein was dilated and directly connected to the inferior vena cava (Figure 1D), and then drained to the right atrium. The left hepatic artery (~2.6 mm, Vmax = 34 cm/s) was dilated (Figure 1E) and circuitous, and the right hepatic artery was small (1.8 mm). In addition, a de novo heterozygous missense variant in NOTCH2 [NM_024408.3:c.6125T > C, NP_077719.2:p.(Met2042Thr)] was identified only in the patient (Figure 2A, Table 1).
Sanger sequencing verified the two detected variants and homology modeling of the NOTCH2 variant. (A) Sanger sequencing of the trios confirmed the RASA1 and NOTCH2 variants. (B) NOTCH2 domain structure and the locations of pathogenic variants associated with Alagille syndrome and other diseases. The known pathogenic variants in ANK domain associated with Alagille syndrome were marked. Our reported p.Met2042Thr in this case is highlighted using red arrow. EGF Repeats, epidermal growth factor-like repeats; ANK, ankyrin repeats; LNR, Lin/Notch repeats; NRR, negative regulatory region, including the two heterodimeric portions (HDN and HDC) interact and LNRs; NLS, nuclear localization signal; PEST, proline/glutamic acid/serine/threonine rich domain; RAM, RBP-Jkappa-associated module. (C) In the WT ANK domain, Asp2040 formed two strong H-bonds with Met2042 and Asp2043. (D) In the mutant ANK domain, two normal H-bongs formed by Asp2040 were damaged, then Thr2042 formed two excrescent strong H-bonds with Asp2040 and Arg2044, respectively. Red represents O, blue represents N, and fluorescent green represents strong H-bond.
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In addition, a de novo heterozygous missense variant in NOTCH2 [NM_024408.3:c.6125T > C, NP_077719.2:p.(Met2042Thr)] was identified only in the patient (Figure 2A, Table 1). Her mother had a wild-type genotype (Figure 2A). It was located in the ANK domain of the Notch intracellular region (Figure 2B), which was highly conserved (GERP++_RS score = 5.84) and was classified as pathogenic according to the ACMG criteria. The variant was adjacent to the polypeptide binding region in the ANK domain (Figure 2B). Homology modeling and structural analysis of the p.(Met2042Thr) variation suggested that in the ANK domain of the wild-type NOTCH protein, the side chain of Asp2040 formed two strong H-bonds with the main chain amides of Met2042 and Asp2043 (Figure 2C). Thr2042 formed two excrescent strong H-bonds with Asp2040 and Arg2044, respectively (Figure 2D). Heterozygous variants in NOTCH2, with a high majority of missense variants, are known to cause Alagille syndrome. The patient had a broad forehead, a small-pointed chin and prominent ears.