De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females



Hardikar syndrome (MIM 612726) is a rare multiple congenital anomaly syndrome characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, but with preserved cognition. Only four patients have been reported previously, and none had a molecular diagnosis. Our objective was to identify the genetic basis of Hardikar syndrome (HS) and expand the phenotypic spectrum of this disorder.


We performed exome sequencing on two previously reported and five unpublished female patients with a clinical diagnosis of HS. X-chromosome inactivation (XCI) studies were also performed.


We report clinical features of HS with previously undescribed phenotypes, including a fatal unprovoked intracranial hemorrhage at age 21. We additionally report the discovery of de novo pathogenic nonsense and frameshift variants in MED12 in these seven individuals and evidence of extremely skewed XCI in all patients with informative testing.


Pathogenic missense variants in the X-chromosome gene MED12 have previously been associated with Opitz–Kaveggia syndrome, Lujan syndrome, Ohdo syndrome, and nonsyndromic intellectual disability, primarily in males. We propose a fifth, female-specific phenotype for MED12, and suggest that nonsense and frameshift loss-of-function MED12 variants in females cause HS. This expands the MED12-associated phenotype in females beyond intellectual disability.

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Fig. 1: Photos of Hardikar syndrome patients.
Fig. 2: Schematic representation of the MED12 gene (not to scale).

Data availability

All variants have been deposited into ClinVar, VCV000432691, VCV000280361, VCV000620451, VCV000520705.


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We thank all the patients and families who participated in this study. There are no funders to acknowledge.

Author information




Conceptualization: E.B., D.L., H.H.; Data curation: D.L; Formal Analysis: D.L; Investigation: R.L., D.C., M.V., N.D.L., E.R.V, T.W., S.P., J.J., S.V., E.Z., A.H., P.C., A.G., T.S., T.B., D.P.; Resources: H.H.; Visualization: A.S, D.L; Writing – original draft: A.S.,K.S., D.L; Writing – review & editing: E.B., H.H.

Corresponding author

Correspondence to Elizabeth Bhoj MD PhD.

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The authors declare no competing interests.

Ethics Declaration

All individuals’ families from the different institutions agreed to participate in this study and signed appropriate consent forms. The Institutional Review Board of the Children’s Hospital of Philadelphia approved this study. Permission for clinical photographs was given separately.

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Li, D., Strong, A., Shen, K.M. et al. De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females. Genet Med (2020).

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