Expanding the Phenotypic Spectrum of HIVEP2-Related Intellectual Disability: Description of Two Portuguese Patients and Review of the Literature

Abstract

Introduction

Pathogenic variants in HIVEP2 have been associated with a neurodevelopmental disorder mainly characterized by intellectual disability, severe language impairment, and motor developmental delay. Since its first description in 2016, only 15 patients have been described in the literature.

Methods

Here, we report 2 additional unrelated Portuguese children presenting intellectual disability and motor delay in whom de novo nonsense pathogenic variants in HIVEP2 have been identified by next-generation sequencing analysis.

Results

In patient 1, the variant c.2827C>T, p.(Arg943*) was detected, whereas patient 2 carried the variant c.6667C>T, p.(Arg2223*). Interestingly, patient 1 presented with a rapid growth of the occipitofrontal diameter in the first months of life due to external hydrocephalus, a feature that, as far as we know, has never been reported in patients with HIVEP2 pathogenic variants.

Conclusion

This report expands the phenotypic spectrum of this rare syndrome and provides deeper insights by comparing the clinical features of our patients with previously reported affected individuals.

Introduction

In recent years, pathogenic variants in HIVEP2 (human immunodeficiency virus type I enhancer binding protein 2) have been described in patients with intellectual disability, developmental delay, behavioral abnormalities, and unspecific dysmorphic features in a condition denominated “Mental Retardation, Autosomal Dominant 43” (MRD43; OMIM #616977). However, the number of patients reported thus far is still too small to fully characterize the molecular and phenotypic spectrum of this syndrome.

HIVEP2, located in chromosome 6, is a member of the ZAS gene family and encodes a large protein with 2 separate zinc-finger domains that bind to specific DNA sequences, including the kappa B-motif, acting as a transcription factor. It regulates the transcription of several genes involved in multiple pathways, such as immune response [Takagi et al., 2001; Kimura et al., 2005], adipogenesis [Jin et al., 2006], bone remodeling [Saita et al., 2007], and, importantly, brain development [Dörflinger et al., 1999; Fukuda et al., 2002]. Hivep2 knock-out mice exhibited behavioral abnormalities, hyperactivity, cognitive impairment, and mild chronic inflammation of the brain, demonstrating its functional relevance [Takagi et al., 2006; Takao et al., 2013].

Here, we report the molecular and clinical characterization of 2 unrelated Portuguese individuals with de novo variants in HIVEP2. Both patients presented with intellectual disability and delayed motor and language development, overlapping the clinical features of previously described patients and further supporting the significance of HIVEP2 in neurodevelopment.

Materials and Methods

DNA was obtained from peripheral blood of the patients and their parents. Clinical exome sequencing analysis was performed in both patients. In the patients' parents, analysis of clinically relevant HIVEP2 variants was performed by Sanger sequencing. Pathogenicity of identified variants was classified according to the guidelines of the American College of Medical Genetics and Genomics [Richards et al., 2015]. The nomenclature of variants was based on HIVEP2 transcript NM_006734.3.

Case Presentation

Patient 1

Patient 1 is a 10-year-old boy born by caesarean section at 39 weeks of gestation from nonconsanguineous healthy parents. At birth, he had a weight of 4,000 g (85th–97th percentile), length of 52 cm (85th percentile), and occipitofrontal circumference of 36 cm (85th–97th percentile). Apgar scores were 9 and 10 at the 1st and 5th minute, respectively. He presented a rapidly increasing head circumference, reaching >97th percentile at the 9th month of age. By that time, transfontanellar ultrasonography revealed enlarged pericerebral spaces suggesting external hydrocephalus, further confirmed by magnetic resonance imaging (MRI) performed at 10 months. Frontal bossing was remarkable. The MRI also showed a thin corpus callosum and mild cerebral atrophy, as well as enlarged cerebrospinal fluid spaces predominantly in the frontotemporal region and ventriculomegaly involving frontal horns.

He has downslanting palpebral fissures but no additional dysmorphic features.

The patient presented delayed psychomotor development, global hypotonia, poor cephalic control at 7 months, and first walked with no support when 4 years old with wide-based gait. By the age of 6, he was still not toilet trained. At present, he remains nonverbal. Formal developmental evaluation at 5 years revealed severe impairment, assessed by the Griffiths Mental Development Scale (0–2 years), with language as the most compromised area. He has been attending a school with special education and receives physical, speech/language, and occupational therapies. Ophthalmologic evaluation detected alternating esotropia with pseudoparalysis of lateral rectus submitted to corrective surgery, and hypermetropic astigmatism requiring refractive correction. Additional medical concerns included sialorrhea managed with botulinum toxin, gastroesophageal reflux (worse for liquids), food allergy to kiwi and strawberry, and cryptorchidism submitted to orchidopexy. At his last clinical evaluation at 11.5 years of age, his weight was 51 kg, height 155 cm (85th–97th percentile), and body mass index 21.3 (85th–97th percentile).

Extensive etiologic investigation comprised (1) an array comparative genomic hybridization (array-CGH) which detected a duplication of the genomic region 14q13.1 (33,882,160–33,968,960), classified as of uncertain significance and not related to the phenotype; and (2) the molecular study of the PTEN gene (sequencing of exons and intron boundaries, and multiplex ligation-dependent probe amplification [MLPA] to exclude deletions or duplications) as well as of the most common pathogenic variants in the MED12 gene (sequencing of exons 21 and 22 to search for p.Arg961Trp and p.Asn1007Ser variants) causing Lujan-Fryns and FG type 1 (Opitz-Kaveggia) syndromes, all with negative results. In addition, MLPA for microdeletion syndromes was performed for chromosomal regions 15q11q13, 16p11, 22q13, and for several genes associated with X-linked mental retardation, also with normal results. Subsequently, clinical exome sequencing revealed the variant c.2827C>T, p.(Arg943*) in heterozygosity in exon 5 of HIVEP2, introducing a premature stop codon. Familial studies demonstrated that this variant was de novo, further reinforcing its pathogenic effect.

Patient 2

Patient 2 is a 11-year-old male born by caesarean section at 41 weeks of gestation with weight of 3,430 g (50th–85th percentile), length of 45.5 cm (<3rd percentile), and occipitofrontal circumference of 35 cm (50th–85th percentile). His Apgar scores were 9 and 10 at the 1st and 5th minute, respectively. His mother is healthy but his father was born with cleft palate and has cardiac arrhythmia. There was no history of consanguinity.

The patient presented intellectual disability manifested by delayed expressive language (first words at 2 years of age, sentences of 2–3 words at 3 years) with an intelligence quotient of 59 in a Wechsler Intelligence Scale for Children (WISC-III) test performed at 6 years of age. In addition, he was also diagnosed with an attention deficit and hyperactive disorder, managed with methylphenidate since he was 5 years, which improved his behavioral problems but had no significant impact on learning. At the motor level, he started to walk independently at 14 months but exhibited poor coordination. He had no specific dysmorphic features, and cerebral MRI was normal. Otorhinolaryngology evaluation detected adenoid hypertrophy and a type B tympanogram, managed with adenoidectomy and myringotomy when he was 2. Other medical issues include feeding difficulties since an early age, particularly for solid food, with no organic anomaly, constipation, and food-related iron deficiency anemia at 14 months of age. At his last clinical evaluation at 11.5 years of age, his weight was 44.4 kg, height 141 cm (15th–50th percentile), and body mass index 22.3 (97th percentile).

The patient went through extensive metabolic screening, array-CGH, and study of Fragile-X and KBG syndromes (sequencing of exons and intron boundaries of ANKRD11 gene), all with negative results. Clinical exome sequencing detected the likely pathogenic variant c.6667C>T, p.(Arg2223*) in heterozygosity in exon 10 of HIVEP2. The variant was found to be de novo.

Discussion

In this clinical report, we describe 2 patients with intellectual disability, as well as speech/language and motor delay of unknown etiology despite extensive molecular investigation. In both patients, the diagnosis was established through clinical exome sequencing which identified different de novo nonsense variants in HIVEP2. Patient 1 presented the variant c.2827C>T, p.(Arg943*) that has been previously reported by Srivastava et al. [2016] in a 4-year-old female patient with a quite similar clinical phenotype. In fact, both patients presented normal growth parameters, with moderate motor development problems, hypotonia, and delayed speech. Furthermore, cerebral MRI revealed a thin corpus callosum in the 2 individuals. A distinct feature of our patient was the macrocrania due to external hydrocephalus, a feature that has never been reported in other patients with HIVEP2 pathogenic variants. Recently, an additional female patient has been described carrying the c.2827C>T pathogenic variant, in a study concerning genetic ethiologies of corpus callosum abnormalities. Like the other 2 patients, this affected individual also presented global developmental delay and mildly thin body of the corpus callosum, in addition to a hypoplastic frontal lobe and a dilatation of the lateral ventricles [Miyamoto et al., 2021].

The likely pathogenic variant identified in patient 2, c.6667C>T, p.(Arg2223*), has been recently reported by Park et al. [2019] in a patient with a milder phenotype, not presenting behavioral problems, muscular hypotonia or other neurological alterations. As hypothesized, the c.6667C>T variant is in the last exon of the HIVEP2 gene producing a truncated protein that could potentially retain some residual function, leading to a less severe phenotype [Park et al., 2019]. In contrast, the patient reported herein has attention deficit and hyperactive disorder, highlighting the need for additional patients to derive genotype-phenotype correlations.

The first patients with deleterious variants in HIVEP2 have been described in 2016 [Srivastava et al., 2016], although HIVEP2 had already been implicated as a cause of intellectual disability 4 years earlier by Rauch et al. [2012] in a cohort study of 51 patients with nonsyndromic intellectual disability. The disease caused by HIVEP2 pathogenic variants has been named autosomal dominant mental retardation type 43 (MRD43). Since then, a total of 15 patients have been reported in the literature. Table 1 summarizes the main clinical features, as well as the HIVEP2 pathogenic variants observed in the 17 patients described thus far, including the 2 patients reported here. Common symptoms shared by all patients include developmental delay/intellectual disability, moderate to severe language impairment, and mild to moderate motor development delay. Hypotonia is also a frequently observed feature, occurring in 65% (11/17) of the patients, as well as abnormal behaviors (hyperactivity, anxiety, aggressivity, and impulsivity) and gastrointestinal problems (like constipation and gastroesophageal reflux), both systems manifestations reported in 59% (10/17) of the patients. A significant number of individuals (7/17; 41%) presented with visual abnormalities, mainly strabismus and hypermetropia. Microcephaly has been described in 5 patients (29%), and brain MRI revealed abnormal findings in 7 individuals (41%); seizures have been reported in only 2 patients (12%) [Srivastava et al., 2016; Steinfeld et al., 2016; Goldsmith et al., 2019; Jain and Atwal, 2019; Park et al., 2019].

Table 1.

Clinical features of reported patients with HIVEP2 pathogenic variants

	This publication		Srivastava et al., 2016			Steinfeld et al., 2016						Goldsmith et al., 2019		Park et al., 2019		Jain and Atwal, 2019	Miyamoto et al., 2021
	Pt 1	Pt 2	Pt 3	Pt 4	Pt 5	Pt 6	Pt 7	Pt 8	Pt 9	Pt 10	Pt 11	Pt 12	Pt 13	Pt 14	Pt 15	Pt 16	Pt 17
Gender	M	M	F	M	F	F	F	M	M	F	M	M	F	F	F	M	F
Age at publication, years	10	11	4	3	21	7	14	10	2	11	6	10	8	27	23	5	4
DD/ID	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Language delay	+ (NV)	+	+	+	+	+	+ (NV)	+ (NV)	+	+	+	+	+	+	+	+	+
Motor delay	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Microcephaly	–	–	–	–	+	+	+	+	–	–	–	+	–	–	–	–	–
Hypotonia	+	–	+	+	+	+	+	Hypertonia	+	+	–	+	+	+	–	–	–
Dysmorphic features	–	–	+	+	+	+	+	+	+	+	+	+	+	+	+	–	–
Behavioural problems	–	+	+	–	+	+	+	+	–	+	+	+	+	–	–	–	–
Brain MRI abnormalities	+	–	+	+	+	–	+	–	–	+	–	–	–	NP	NP	Unknown	+
Seizures	–	–	–	–	–	Possible	+	+	–	–	–	–	–	–	–	–	–
Gastrointestinal problems	+	+	+	–	+	+	+	+	–	–	–	+	+	–	+	–	–
Ophthalmologic anomalies	+			+			+	+			+	+	+
Pathogenic variant	c.2827C>T p. (Arg943*)	c.6667C>T p. (Arg2223*)	c.2827C>T p. (Arg943*)	c.3556C>T p. (Gln1186*)	c.5737del p. (Asp1913 Metfs*15)	c.6475G>T p. (Gly2159*)	c.2857G>T p. (Glu953*)	c.5614dup p. (Glu1872 Glyfs*16)	c.1189G>T p. (Asp397Tyr)	c.6625dup p. (Tyr2209 Leufs*53)	c.3434del p. (Pro1145 Argfs*2)	c.5935C>T p. (Arg1979*)	c.2956_2957del p. (Glu986Argfs*4)	c.6609_6616del p. (Glu2204*)	c.6667C>T p. (Arg2223 *)	c.3742C>T p. (Gln1248*)	c.2827C>T p. (Arg943*)
Inheritance	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo	de novo

Pt, patient; M, male; F, female; DD, developmental delay; ID, intellectual disability; NP, not performed; ΝA, not available; NV, non-verbal; +, present; –, absent.

Concerning the mutational spectrum of HIVEP2, 16 different pathogenic variants have been reported, from which 9 are nonsense, 5 are frameshift, and 2 are missense. As shown in Figure 1, most of the variants occur in exons 5 (7/16), 10 (4/16), and 9 (3/16), which are the longest exons (exon 1 to 4 are not translated to protein). Notably, all pathogenic variants were found to be de novo in the patients.

Fig. 1.

Schematic representation of HIVEP2 protein and location of pathogenic variants. Coding exons are numbered 5 to 10 (exons 1 to 4 are not translated to protein). The 9 nonsense variants (in red, above), the 5 frameshift (in green, bottom), and the 2 missense variants (in blue, bottom) are shown. The protein segment encoded by exon 5 is not drawn to scale.

Furthermore, all patients have been diagnosed based on next-generation sequencing strategies specifically whole-exome sequencing or clinical exome sequencing. This confirms the advantage of such technologies in unraveling the molecular cause of previously undiagnosed patients with neurodevelopmental disorders, bearing in mind the nonspecific manifestations of the majority of such group disorders even when associated with dysmorphic features. In this context, it is particularly difficult to recognize a specific syndrome or clinical phenotype in these patients, leading to a genetic diagnostic odyssey thus postponing, very frequently and for several years, timely reproductive choices.

Statement of Ethics

Informed consent was obtained from the patients' parents for publication of the case reports. This study protocol was approved by the Institutional Review and Data Protection Boards at Centro Hospitalar e Universitário de São João, with approval number RAI-21006217. According to institutional guidelines ethical approval is not required for this type of reuse of clinical data. This work was conducted ethically in accordance with the World Medical Association Declaration of Helsinki.

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Author Contributions

R.Q. wrote the manuscript. R.Q., J.P.B., H.S., and M.L. collected and interpreted clinical data. H.S. and M.L. provided critical revision of the manuscript. All authors reviewed and approved the final manuscript.

Data Availability Statement

All data generated or analyzed during this study are included in this article. Further inquiries can be directed to the corresponding author.

Funding Statement

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.