MED12-related Hardikar syndrome- Two additional cases and novel phenotypic features including cholangiocarcinoma

Hardikar syndrome (HS) is an ultra-rare multiple congenital malformation syndrome in females. Cardinal features include cleft lip and/or cleft palate, biliary anomalies, liver disease, intestinal malrotation, pigmentary retinopathy, coarctation of the aorta, hydronephrosis, and ectopic ureters. The molecular basis of Hardikar syndrome was only recently described as nonsense or frameshift pathogenic variants in MED12. MED12 (mediator complex subunit 12) (OMIM* 300188) is a component of Mediator which is a multiprotein complex that can function in transcriptional activation or repression. Only 10 patients affected with HS have been previously described in the literature, of which gene-disease association was confirmed in 7 cases. Here, we report novel phenotypic features in 2 additional patients with MED12-related HS. Patient 1 (P1) is a 20-year-old adopted female who was born at 34 weeks gestation. She was born with multiple congenital abnormalities involving craniofacial, cardiovascular, gastrointestinal, and genitourinary systems. She had cleft lip and palate that was repaired early in life along with pharyngeal flap closure for velopharyngeal insufficiency at 6 years of age. Her cardiovascular phenotype includes coarctation of the aorta and patent ductus arteriosus that required stenting and ligation. She has dysmorphic facial features, chorioretinal lesions, C2/C3 retrolisthesis and scoliosis. Genitourinary malformations included ureteral stenosis, obstructive uropathy, partial bladder agenesis which eventually led to ESRD and kidney transplantation at 4 years of age. She received growth hormone (GH) supplementation for GH deficiency associated short stature. She had intestinal malrotation that required Ladd’s procedure. She recently presented with right upper quadrant pain, fatigue, poor appetite, and weight loss. A liver ultrasound identified multiple hypoechoic lesions throughout the liver, the largest measuring up to 5.3 cm which was confirmed on MRI. The liver function panel had been normal. She had an elevated Cancer Antigen 19-9 at 12,774 (ref: 0- 37 U/mL) and normal AFP and CEA levels. Targeted liver biopsy of the larger lesion in the right hepatic lobe revealed an adenocarcinoma, most likely consistent with an intrahepatic cholangiocarcinoma. The origin of the cancer was presumed to be from a previously unidentified choledochal cyst. The lesion was deemed unresectable, and she was considered not to be a candidate for a liver transplant. Palliative chemotherapy was offered. Recent proband-only exome sequencing revealed a mosaic (31.58%) pathogenic variant MED12: c.4018 C>T p.Q1340X (NM_005120.2). Follow-up X-inactivation studies on blood were highly skewed with ratio of 94:6. Brain magnetic resonance angiography following diagnosis of Hardikar syndrome identified a stable 3 mm left vertebral artery aneurysm and 2 mm right distal posterior cerebral artery and a 3.82 x 3.49 mm left [V4] segment vertebral artery aneurysm. Patient 2 (P2) is a 13-month-old female who was born at 39w3d gestation via C-section to a 29-year-old G1P1 mother. Diagnoses of cleft lip with palate, bilateral urinary tract dilation, and right upper quadrant cyst were made prenatally. Postnatally, she was noted to have dysmorphic facial features including overfolded helix, microtia, and bilateral preauricular pits. Postnatal renal ultrasound showed bilateral severe hydronephrosis with marked bilateral hydroureter, mild dysplasia with parenchymal thinning, and small right renal cyst. MRI of the abdomen was significant for cystic structure at the porta hepatis suggestive for an enlarged and irregular gallbladder, as well as additional cystic foci adjacent to the porta hepatis and common bile duct which likely represent choledochal cysts. Her ophthalmology evaluation was suggestive of subretinal/choroidal depigmented area in clusters with questionable early cataracts. Trio exome sequencing was recommended which identified a de novo heterozygous pathogenic variant in MED12: c.2224C>T (p.Gln742X; NM_005120.2). Follow-up X-inactivation analysis on blood showed highly skewed inactivation with a ratio of 100:0. As described in the patients with loss-of-function variants in MED12, both of our patients had cleft lip and palate, along with biliary system anomalies. To our knowledge, this is the second time individuals with Hardikar syndrome associated with nonsense or frameshift variants in MED12 have been described.