A case of Smith–Magenis syndrome with skin manifestations caused by a novel locus mutation in the RAI1 gene

Abstract

We report the clinical features and genetic testing of a child with Smith–Magenis syndrome (SMS) to improve the understanding of this disease. The clinical data and molecular genetic test results of a child with SMS caused by a novel mutation in the retinoic acid-induced-1 (RAI1) gene were reviewed. A female patient aged 12 years and 9 months presented to the clinic because her mental and motor development was lagging behind that of her peers. The child had learning difficulties, poor motor coordination, temper tantrums, and self-injurious behaviors, such as skin scratching. She had a peculiar facial appearance, dry skin with scattered eczema, low hairline, wide forehead, flat face, collapsed nasal bridge, turned out upper lip, and deep palmar lines on the right hand through the palm. Wechsler’s IQ test score was 48. Her electroencephalogram was normal. The diagnosis of SMS was confirmed by a heterozygous mutation in exon 3 of the RAI1 gene on chromosome chr-1717696650 at locus c.388C>T (P.Q130X). In addition, this patient had severe eczema on the skin. The RAI1 mutation c.388C>T (P.Q130X) is a newly reported variant that will help in the clinical identification of SMS and the precise localization of more phenotypically related genes.

Keywords

Smith–Magenis syndrome RAI1 gene whole exon child skin eczema

Introduction

Smith–Magenis syndrome ([SMS] OMIM182290) is a complex syndrome associated with intellectual disability.¹ The clinical manifestations of SMS include developmental delay, sleep disturbance, behavioral abnormalities, cognitive impairment and abdominal obesity in childhood.² Infants have feeding difficulties, low reflexes, hypotonia, prolonged lethargy or the need to be woken up for feeding. This disorder is diagnosed late, usually after the age of 1.5 years. Severe anxiety, inattention, impulsivity, hyperactivity, temper tantrums and self-harm are common behavioral abnormalities of SMS³ (Table 1). Most cases of SMS have a common 17p11.2 deletion of approximately 3.5 Mb.⁴ This deletion includes the retinoic acid-induced-1 (RAI1) gene, which is a key gene involved in this disorder. RAI1 (OMIM 607642) regulates the transcription of genes that are involved in transcriptional regulation, cell growth and cell cycle regulation, bone and skeletal development, lipid and glucose metabolism, nervous system development, behavioral function and circadian activity.⁵ RAI1 mutations are a well-established cause of SMS, with a prevalence of about 10% to 30% in diagnosed cases.⁶ Although deletion is more common, an RAI1 mutation should not be overlooked as a potential cause of this syndrome.⁷ Studies have shown that individuals with RAI1 mutations may exhibit milder symptoms than those with deletions.⁸ Sequencing analysis of the RAI1 gene is required for patients who do not have a detectable 17p11.2 deletion, but show a phenotype consistent with SMS.

Table 1.

Phenotypic features of patients with Smith–Magenis syndrome with a 17p11.2 deletion or RAI1 mutation.

Clinical findings	17p11.2 deletion (%)*	RAI1 mutation (%)*	RAI1 mutation c.388C>T (P.Q130X)
Craniofacial/skeletal features
Brachycephaly	89	81.8	−
Midface hypoplasia	92	72.7	+
Prognathism (relative to age)	53	88.8	+
Tented upper lip	73	91.6	+
Broad square face	81	90.9	+
Synophrys	62	33.3	−
Cleft lip/palate	9	0	−
Brachydactyly (short fingers, toes)	85	83.3	−
Short stature	69	9	−
Scoliosis	49–67	36.3	−
Otolaryngological features
Chronic ear infections	85	54.5	−
Hearing loss	68	10	−
Hoarse, deep voice	80	100	+
Neurological/behavioral features
Intellectual disability	100	100	+
Speech delay	>90	70	−
Motor delay	>90	70	+
Hypotonia	>90	61	−
Seizures by history	11–30	16.6	−
Sleep disturbance	70–100	100	+
Self-hugging/hand wringing	70–100	100	−
Attention-seeking	80–100	100	−
Self-injurious behavior	78–96	100	+
Onychotillomania	25–85	80	−
Polyembolokoilmania	25–85	90	+
Head banging/face slapping	71	60	+
Ocular features
Myopia	53	60	−
Strabismus	50	40	−

*Modified from Truong et al.³

+, present; −, absent.

The RAI1 mutation c.388C>T was found in our case.

In addition, patients with SMS have some associated cutaneous features. Some of these features are the result of neurobehavioral features, but others are abnormalities of cutaneous features and appendages⁹ (Table 2). In addition to the well-known bites, abrasions, atrophic scars, limited hyperkeratotic plaques, nail abnormalities and leukoplakia, papular dermatoses and fissured foot keratoses are common. Some patients with SMS have persistent skin thickening and dryness with extensive follicular keratosis.¹⁰ Older patients often have dermatofibromas.¹¹ A small number of patients with SMS suffer from alopecia, hairline abnormalities and tinea pedis.^3,12 These features have rarely been described in the literature and are not even described in the GeneReviews database.

Table 2.

Cutaneous features of patients with Smith–Magenis syndrome.

Clinical findings	SMS (%)*	RAI1 c.388C>T (P.Q130X)
Cutaneous features
Skin thickening,	85	−
Xerosis	100	+
Hyperhidrosis	35	+
Keratoderma	50	+
Dystrophic scars	50	+
Spots of hyperkeratosis	45	−
Onychotillomania	40	−
Pachyonychia	25	−
Keratosis pilaris	65	−
Folliculitis	55	−

*Modified from Guérin-Moreau et al.⁹

+, present; −, absent.

The RAI1 mutation c.388C>T was found in our case.

We report a case of SMS due to a heterozygous mutation in exon 3 of the RAI1 gene, and this was not a 17p11.2 deletion. In this child with SMS, we performed a thorough examination of the skin and took skin tissue for a pathological biopsy. Hopefully a summary of the skin features of this patient will contribute to the early clinical recognition and diagnosis of SMS in future patients.

Case presentation

Patient and examinations

A 12-year-old girl presented to the clinic with mental and motor development, which was lagging behind that of her peers since childhood. She had normal physical development, slept for short periods of time, was irritable, and showed self-injurious behaviors, such as scratching skin, pulling nails and banging her head. Additionally, she was insensitive to pain and danger, lagged behind in school performance, did not get along with her classmates and was often truant from school. The patient was born spontaneously at 38 + 3 weeks of gestation and weighed 2.75 kg at birth, and had no history of resuscitation or asphyxia. She showed delayed motor development since birth. She lifted her head at 7 months, turned over at 9 months, crawled at 1 year and walked unaided at 2 years. The patient’s parents were not in a consanguineous union. The mother was healthy during pregnancy and denied exposure to drugs, radiation or toxins during pregnancy. The father is in good health and has no family history of relevant diseases.

A physical examination (Figure 1) showed a height of 155.5 cm, weight of 50 kg, exceptional facial features, clear consciousness, low voice and answers to questions were relevant. She also had dry skin with desquamation all over the body, a papular rash and skin keratinization, a low hairline, a wide forehead, a flat face, a collapsed nasal bridge, a turned out upper lip, and deep palmar lines on the right hand through the palm. No enlargement of superficial lymph nodes was palpable throughout the body, the skull was normal in appearance and her hair distribution was normal. Her eyes were not protruding or sunken, and the reflex to light was acute bilaterally. There was no deformity of the auricle, no pressure on the mastoid process and her nose was normal in appearance. There were no abnormalities on an examination of both lungs. The heart sounds were strong, no pathological murmurs were heard in the valve areas and no pericardial friction sounds were heard. The abdomen was soft, and the liver and spleen were not palpable. There was no deformity in the limbs, and muscle tone was normal. A neurological examination was normal, and there were no “milk coffee” spots on the body.

Figure 1.

Phenotypic features of the patient.

Auxiliary investigations were also performed. Routine blood, liver and kidney function and electrolyte examinations showed no abnormalities. Magnetic resonance imaging of the head showed fullness of the supratentorial ventricles with no closure of the hyaline septal space. Wechsler’s IQ test score was 48. An electroencephalogram was normal. A sample of the patient’s skin was stained with hematoxylin and eosin for pathological analysis to detect skin lesions.

Genetic analysis

Approximately 2 mL of peripheral blood was drawn from each family member in tubes containing EDTA as an anticoagulant for whole-exome analysis and sequencing of the RAI1 gene. Full-exon sequencing was performed by MyGenostics Company (Beijing, China).^3,12 To make a definite diagnosis, we performed whole-exome sequencing of the proband of each family included. We fragmented 1 to 3 μg of genomic DNA, which was extracted from each sample, to an average size of 180 base pairs (bp) using a Bioruptor sonicator (Diagenode, Liège, Belgium). Paired-end sequencing libraries were then prepared using a DNA sample-prep reagent set 1 (New England Biolabs UK Ltd., Hitchin, UK). Library preparations, including end repair, adapter ligation, and polymerase chain reaction enrichment, were performed following Illumina (San Diego, CA, USA) protocols. Amplified DNA was captured using the GenCap Short-statue Capture Kit (MyGenostics GenCap Enrichment Technologies, Chongqing, China). The capture experiment was conducted in accordance with the manufacturer’s protocol. The polymerase chain reaction product was purified using SPRI beads (Beckman Coulter, Brea, CA, USA) by following manufacturer’s instructions. The enrichment libraries were next sequenced using an Illumina Nova6000 sequencer (Illumina) for paired reads of 150 bp.

After sequencing, the raw data were saved in the FASTQ format and analyzed. Illumina sequencing adapters and low-quality reads (<80 bp) were filtered according to the Cutadapt quality-controlled process (version 1.16, https://cutadapt.readthedocs.io/en/stable/guide.html). After quality control, the clean reads were mapped to the UCSC hg19 human reference genome using Burrows–Wheeler Aligner (version 0.7.12-r1044; https://github.com/lh3/bwa) software. Duplicated reads were removed using Picard tools (version 2.2.3; https://broadinstitute.github.io/picard/) and mapped reads were used for detecting variation. Furthermore, variants were annotated by ANNOVAR software (https://annovar.openbioinformatics.org/) and associated with multiple databases, such as the 1000 Genomes dataset, ESP6500, NCBI dbSNP, EXAC and HGMD. Prediction was then implemented by software, including SIFT (Sorting Intolerant From Tolerant, https://sift.bii.a-star.edu.sg/), PolyPhen-2 (Polymorphism Phenotyping v2, http://genetics.bwh.harvard.edu/pph2/), Mutation Taster (http://www.mutationtaster.org/) and GERP++ (http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html). The candidate variants were validated by Sanger sequencing, and their pathogenicity was graded in accordance with the American College of Medical Genetics and Genomics guidelines.^3,12

Guidelines

The reporting of this study conforms to the CARE guidelines.¹³

Results

Whole exon detection and RAI1 gene sequencing

The patient’s full exon test and sequencing of the RAI1 gene showed a heterozygous mutation in exon 3 of the RAI1 gene at chromosome chr-1717696650, with the mutation site c.388C > T (P.Q130X). Moreover, there were no abnormalities in the sequencing of the RAI1 gene in the patient’s parents (Figure 2a). The novelty of the RAI1 variants was confirmed in genetic variant databases (Centogene, Franklin, ClinVar, Varsome and InterVar). According to the American College of Medical Genetics and Genomics guidelines, the detected genetic variation NM_030665:c.388C > T is likely pathogenic (PVS1 +PS2 + PM2_Supporting). PVS1 indicates that the variant is a zero-effect variant (nonsense mutation), which may lead to loss of gene function. PS2 indicates no variation at this locus in the father of the subject and no variation at this locus in the mother of the subject, as analyzed by lineage verification; therefore, this variation is a spontaneous mutation. The frequency of PM2_Supporting in the normal population database is negative, which indicates a low-frequency variant. No correlation has been reported for this locus in the HGMD database. The bioinformatics protein function prediction software SIFT, PolyPhen_2, and REVEL predicted unknown, unknown, and unknown, respectively.

Figure 2.

Genetic sequencing results and histopathology. (a) Genetic sequencing results of the patient and her parents and (b) Histopathological sections of skin tissue from the patient.

Histopathological sections of the skin

A histopathological section of the skin showed incomplete keratinization, hyperplasia of the spinous layer with spongy edema and a chronic inflammatory cell infiltrate with a lymphocytic, histiocytic predominance in the superficial mid-dermis. The final diagnosis was eczema (Figure 2b).

Discussion

The worldwide prevalence of SMS is approximately 1:15,000 to 1:25,000, and more than 100 cases have been reported since its discovery. Of these cases, 90% are associated with 17p11.2 deletions, and of these deletions, mutations in the RAI1 gene are the second most common molecular cause.^14,15 We report a case of a newly identified nonsense mutation at the c.388C > T (P.Q130X) locus of the RAI gene. The RAI1 gene is located on chromosome 17p11.2.¹⁶ This gene consists of six exons containing a 470-bp 5′ UTR (the first 2 exons and the first 16 nucleotides of exon 3) and a 3′ UTR of 1452 bp (corresponding to exon 6). The nuclear protein encoded by the RAI1 gene contains a plant zinc finger homology structural domain that is associated with the transcriptional regulation of the gene.¹⁷ This finding implies that the RAI1 gene is associated with transcriptional regulation.¹⁸ Currently, all reported mutation sites in the RAI1 gene occur in exon 3, which encodes almost 98% of the protein.⁵ Furthermore, any deleterious mutation could lead to the disruption of protein translation. Interestingly, there is no evidence to confirm the existence of a mutational hotspot in exon 3, which will require further study in the future.

The downstream targets of the transcription factor RAI1 are involved in transcriptional regulation (RXRB, ZNF236, ZIC1, RUNX1T1, AKR7A3 and FBLN1), cell growth and cell cycle regulation (SPTBN1, POLDIP3, PPP1R14D, GLI3, KMT2A and ADD3), skeletal development (PSTPIP2 and ANGH), lipid biosynthesis and cholesterol metabolism (LIPE, HMGCS1, and INSIG1), neurological development (ZIC1, PSEN2, RXRB, CLN8, SMA4, NF1 and KMT2A), behavioral function (SCN12A), circadian activity (NR1D2, PER2, PER3, CRY1 and ARNTL) and insulin regulation (INSIG1, PIK3R1, ZNF236 and LIPE).¹⁹ As a result, patients with SMS caused by RAI1 mutations often have obesity, intellectual disability, behavioral abnormalities, sleep disturbances, hyperlipidemia and hypercholesterolemia.²⁰ Different phenotypes may also exist depending on the mutation site or the length of the CAG repeat sequence. A small proportion of patients with SMS and RAI1 mutations only present with atypical manifestations, such as obesity, and even patients with the same mutation in the same family may have different phenotypes.²¹

In our case, there were common clinical manifestations of intellectual disability, irritability, sleep disturbance, self-injurious behavior and insensitivity to pain. There were also some typical cutaneous manifestations, such as dry skin with flaking, papular rash, atrophic scarring and skin keratinization. The diagnosis of eczema was confirmed by a histopathological examination of the skin, which has not been previously reported. Ludovic Martin et al. reported similar cutaneous manifestations, but the diagnosis was not confirmed because of a lack of pathology.⁹ Previous studies have suggested that the skin manifestations of patients with SMS are mostly due to psychobehavioral abnormalities and that repeated self-injurious behavior may cause localized skin manifestations, such as atrophic scarring and keratinization.²² However, generalized dry, flaky and itchy skin cannot be explained by psychobehavioral abnormalities.

The RAI1 gene encodes retinoic acid-inducible protein 1, which is a metabolite of vitamin A.²³ Retinoic acid plays an important role in the nuclear receptor signaling pathway. Retinoic acid is not only involved in the development of the nervous system, cardiovascular system, skeletal system and urinary system, but is also associated with the proliferation of mucus-secreting cells and the secretion of collagen in skin tissue.²⁴ A deficiency of retinoic acid may lead to dry and itchy skin, which could explain the dry and itchy skin of patients with SMS and mutations in the RAI1 gene.²⁵ From a therapeutic point of view, moisturizers and vitamin A supplementation may reduce dry skin and pruritus,²⁶ and a reduction in skin itchiness is likely to indirectly reduce the occurrence of self-injurious behavior. However, these speculations need to be confirmed by further clinical trials.

In summary, patients with SMS have common clinical manifestations, but they also present with other skin features. These skin features can be caused by psychobehavioral abnormalities,²⁷ but nonpsychobehavioral-related skin features may also provide an important basis for the diagnosis of this disorder. Our case report provides a new molecular and clinical basis for the diagnosis of SMS, but the small number of cases leads to a low level of confidence. The finding of eczema in patients with SMS may just be a coincidence because eczema is a common condition. In the future, more patients with SMS and skin characteristics need to be studied to provide more information regarding the diagnosis of SMS.

Supplemental Material

sj-pdf-1-imr-10.1177_03000605231190553 - Supplemental material for A case of Smith–Magenis syndrome with skin manifestations caused by a novel locus mutation in the RAI1 gene

Supplemental material, sj-pdf-1-imr-10.1177_03000605231190553 for A case of Smith–Magenis syndrome with skin manifestations caused by a novel locus mutation in the RAI1 gene by Xiaobin Wu, Li Zhang, Sisi Chen and Yanxi Li in Journal of International Medical Research

Footnotes

Availability of data and material

All data generated or analyzed during this study are included in the published article.

Author contributions

YXL, LZ and SSC wrote the manuscript. XBW reviewed the manuscript. All authors have read and approved the manuscript.

Declaration of conflicting interest

The authors declare that there is no conflict of interest.

Ethics statement

The study was approved by the Chongqing Traditional Chinese Medicine Hospital ethics committee (20221011). The parents of the patient signed an informed consent form for all examinations and publication of this report. We have de-identified all of the patient’s details.

Funding

This study was supported by the Natural Science Foundation of Chongqing (no. cstc2020jcyj-msxmX0327 and no. jxyn2020-7), the High-level Medical Reserved Personnel Training Project of Chongqing, the Senior Medical Talents Program of Chongqing for Young and Middle-aged and the Program for Scientific Institutions of Chongqing (no. 2022GDRC015).

ORCID iD

Xiaobin Wu

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