Two additional males with X‐linked, syndromic mental retardation carry de novo mutations in HNRNPH2

Abstract

To the Editor: This letter is intended to directly respond to and complement that submitted by Harmsen et al in which they describe a male with mental retardation, X-linked, syndromic, Bain-type (MRXSB) due to a de novo hemizygous mutation in HNRNPH2 (c.617G>A, p.Arg206Gln) previously identified in females by Bain et al and presumed to be embryonically lethal in males. We have identified two additional males with similar phenotypes carrying de novo mutations in HNRNPH2. Patient A is hemizygous for a second MRXSB mutation originally identified by Bain et al in three females within the nuclear localization sequence of HNRNPH2 (c.616C>T, p.Arg206Trp), serving as conclusive evidence that known MRXSB mutations are not embryonically lethal in males. Patient B is hemizygous for a private mutation in the second RNA recognition motif (RRM2) of HNRNPH2 (c.340C>T, p.Arg114Trp), suggesting that other mutations within this gene are capable of producing a range of similar phenotypes (Figure 1). Patient A is a 5-year-old male with global developmental delay. Development was normal until 3 months of age when his parents noted lack of head control and unusual posturing of his extremities. At age 2, a G-tube was placed and remains his primary nutrition source. MRI at age 3 raised the possibility of a remote, mild hypoxic brain injury, and electromyography showed signs of chronic myopathy. Peripheral nerve disease, Pompe disease, and spinal muscular atrophy were ruled out. At age 5, he required total support of his head and assistance keeping his mouth closed. He could not sit or crawl but could rotate while lying on his back. He was able to move his hands and fingers, but displayed extreme hypotonia in all extremities and trunk. He had no dysmorphic features. He was non-verbal but appeared to have some comprehension. He had a happy disposition and was social. He was thought to have a congenital myasthenic syndrome, a congenital myopathy, or a severe, early-onset mitochondrial disorder. Whole exome sequencing (WES) was performed on the patient and biological parents revealing a de novo, missense mutation, HNRNPH2(R206W), that has been previously associated with MRXSB. The variant was confirmed by Sanger sequencing. Phenotypic overlaps with heterozygous females include developmental delay with regression, tone abnormalities, brain abnormalities, and growth problems. Patient B is an 8-year-old male with global developmental delay, microcephaly, failure to thrive, intractable epilepsy, hypotonia, and cortical visual impairment. A vagal nerve stimulator was placed at age 2. At certain times in his life he would have over 10 generalized tonicclonic and dozens of myoclonic seizures daily. He was non-verbal and did not follow commands. There were frequent athetoid movements of the upper extremities. Dyskinetic movements of the face and tongue were observed. Feeding problems required placement of a G-tube. WES identified a private, de novo, missense mutation in HNRNPH2 (c.340C>T, p.Arg114Trp) that was confirmed by Sanger sequencing. The variant has a CADD PHRED of 22.4 and is considered likely pathogenic by the American College of Medical Genetics (ACMG) classification (rules: PS2, PM2). The mutation is predicted to affect protein function by SIFT (sift.bii.a-star.edu.sg) with a score of 0.00 (median sequence conservation = 3.07, sequences represented = 29), and MutationTaster (mutationtaster.org) predicts it is disease causing (accuracy = 0.9999, converted rank score = 0.5881). WES revealed five reference reads (7%) and 64 variant reads (93%) at the position, implying low level mosaicism for the reference allele. Phenotypic overlaps with MRXSB include developmental delay, seizures, tone abnormalities, and growth problems. A second variant with an ACMG classification of “uncertain significance” (rules: none meet criteria) was identified in patient B, inherited from his neurologically normal mother, in GRIA3 (c.419A>G, p.Q140R), encoding a glutamate receptor associated with mental retardation, X-linked 94. One male is hemizygous for the mutation, and one female is a carrier in gnomAD (accessed March 2019). The CADD PHRED is 26.3. The mutation is predicted to be tolerated by SIFT with a score of 0.16 (median sequence conservation = 3.15, sequences represented = 26), while MutationTaster predicts it to be disease causing (accuracy = 1, converted rank score = 0.8103). It is worth noting that missense variants within this gene that are associated with mental retardation are located between amino acid 450 and the C-terminus of the protein—not in the N-terminus where this mutation was found—and have been associated with macrocephaly, while HNRNPH2 has been associated with microcephaly. Furthermore, of ClinVar s 151 known pathogenic variants in GRIA3, only five Received: 2 April 2019 Revised: 21 May 2019 Accepted: 22 May 2019