A Homozygous Missense Variant in HSD17B4 Identified in Two Different Families

Abstract

Background

Perrault syndrome is an inherited disorder with clinical findings that differ according to sex. It is characterized by a variable age of onset and sensorineural hearing loss in both sexes, as well as ovarian dysfunction in females with a 46,XX karyotype. Although it is a rare autosomal recessive syndrome, with approximately 100 affected individuals reported in the literature, it shows both genotypic and phenotypic variations. Mutations in the HSD17B4 gene have been identified as one of the genetic causes of Perrault syndrome.

Case Presentation

A female case and a male case from two different unrelated families with a new variant in the HSD17B4 gene, which were not previously described in the literature and were accompanied by hearing loss, skeletal anomalies, and neurological symptoms, were presented.

Conclusion

We defined Perrault syndrome cases in Turkey caused by a novel mutation in HSD17B4. Whole-exome sequencing is a useful diagnostic technique with varying clinical results due to genetic and phenotypic heterogeneity.

Established Facts

• •Perrault syndrome is characterized by sensorineural hearing loss in men and women.
• •Perrault syndrome can cause skeletal and neurological disorders.
• •Perrault syndrome has been associated with eight genes (CLPP, ERAL1, GGPS1, HARS2, HSD17B4, LARS2, RMND1, and TWNK).

Novel Insights

• •A homozygous missense variant detected in HSD17B4 in the female sex with micrognathia.
• •A homozygous missense variant detected in HSD17B4 in the male sex with psychomotor retardation and motor neuropathy.

Introduction

Perrault syndrome is characterized by sensorineural hearing loss (SNHL) in men and women and ovarian dysfunction in women with a 46,XX karyotype. Diagnosis is confirmed by the presence of biallelic pathogenic variants in one of the eight genes (CLPP, ERAL1, GGPS1, HARS2, HSD17B4, LARS2, RMND1, and TWNK) [Faridi et al., 2022]. However, molecular diagnosis is not possible in approximately 60% of people with Perrault syndrome who have been identified to date [Roberts and Carnivale, 2019].

HSD17B4 (hydroxysteroid 17-beta dehydrogenase 4) encodes multifunctional peroxisomal enzyme, also known as D-bifunctional protein (DBP), acts an important role in fatty acid β-oxidation metabolism [Pierce et al., 2010]. Therefore, besides PRLTS, HSD17B4 is also related to DBP deficiency, characterized by growth failure, neonatal onset encephalopathy, polyneuropathy, hearing and visual impairment, hepatomegaly, and early death in infancy. Compared with DBP deficiency, affected individuals with Perrault syndrome present with both hearing loss and gonadal dysgenesis, while their serum very long-chain fatty acid levels are normal [McMillan et al., 2012].

SNHL in Perrault syndrome is bilateral, and the onset may be congenital or occur in early childhood. When it occurs in early childhood, hearing loss can be progressive. Ovarian dysfunction can range from gonadal dysgenesis, presenting as primary amenorrhea, to secondary ovarian failure, defined as the cessation of menses before the age of 40 years [Jenkinson et al., 2013]. Fertility was mostly reported as normal in affected men, although the number of male patients reported in the literature is small. Neurological features identified in some people with Perrault syndrome include learning difficulties and developmental delay, cerebellar ataxia, pes equinovarus, nystagmus, limited extraocular movements, and motor and sensory peripheral neuropathy. Neurological symptoms are usually progressive and appear later in life. In this article, two different unrelated cases with a variant in the HSD17B4 gene, which has not been previously described in the literature, are described, accompanied by hearing loss, skeletal anomalies, and neurological symptoms.

Material and Methods

Patient and Data Collection

Case Presentation 1

An 18-year-old-female patient presented with complaints of gait and speech disorders and hearing loss that started after the age of six. At 12 months of age, the patient was able to walk and talk. The mother and father were third-degree relatives with no history of similar diseases in the family. Following a normal pregnancy, the patient was delivered vaginally. Her birth weight, length, and head circumference were 3,580 g (75%), 49.5 cm (50%), and 34.5 cm (50%), respectively. On physical examination, dysarthric speech, atypical facial appearance, micrognathia, high palate, marfanoid fingers, nystagmus, ophthalmoplegia, loss of deep tendon reflexes, bilateral pes cavus, hammer toe, ataxic gait, and pubertal development were found to be tanner staging backward (Fig. 1a–c). In this case, SNHL, atrophy of the cerebellar vermis and folia on cranial magnetic resonance imaging (MRI), and chronic neurogenic involvement in L5-S1 myotomes on electromyography were detected (Fig. 1d). Karyotype analysis revealed 46,XX. Biochemical testing revealed hypergonadotropic hypogonadism, while pelvic ultrasonography revealed ovarian dysgenesis (Fig. 1e). Audiometry data revealed the presence of SNHL (Fig. 1f). In light of the clinical findings, whole-exome sequencing (WES) was performed, and a homozygous c.350A>G (p.Asp117Gly) variant, which has not been previously reported in the literature, was found in the HSD17B4 gene (NM_000414.4).

Fig. 1.

Features of the first case. a–c Facial features and micrognathia. d Atrophy of cerebellar vermis and folia. e Gonadal dysgenesis. f Sensorineural hearing loss.

Case Presentation 2

A 17-year-old male patient presented with complaints of decreased hearing, strabismus, difficulty in walking, and a speech disorder that started after the age of 10 years. Following normal pregnancy, the patient was delivered vaginally. His birth weight, length, and head circumference were 4,750 g (97%), 51.5 cm (75%), and 34.9 cm (50%), respectively. He walked when he was 12 months old and started to form sentences when he was 24 months old. There was a third degree of consanguinity between the parents, and there was still hearing loss in the uncle and grandfather, and psychomotor retardation motor-mental retardation in the cousin. Physical examination revealed intellectual disability, dysarthric speech, atypical facial appearance, marfanoid fingertips, scoliosis, strabismus in the left eye, vivid lower extremity deep tendon reflexes, bilateral pes cavus and hammer thumb, ataxic gait, dysmetria, and dysdiadochokinesia (Fig. 2a, b). Secondary sex characteristics were normal, and the testicular volume was 12–15 mL. In this case, SNHL, motor neuropathy in electromyography, and atrophy of the cerebellar vermis and folios were detected in cranial MRI (Fig. 2c, d). The total intelligence test score was 59, which was considered a mild intellectual disability. A homozygous c.350A>G (p.Asp117Gly) variant was found in the HSD17B4 gene (NM_000414.4) by WES, which has not been previously reported in the literature.

Fig. 2.

Features of the second case. a Facial features and strabismus. b Pes cavus. c Cerebellar vermis and folia atrophy. d Sensorineural hearing loss.

Genetic Analysis

Genomic DNA was extracted from peripheral blood cells according to the manufacturer’s standard procedure (DNeasy Blood & Tissue Kit, QIAGEN). The gDNA was broken into 150–500 bp fragments using a BGI enzyme kit (Segmentase, BGI), and the fragments were collected using magnetic beads. The extracted DNA was amplified by ligation-mediated polymerase chain reaction. A mean exome coverage of >99% was obtained. The sequencing depth was greater than 100× in the capture region. Finally, the qualified products were sequenced with PE100 + 100 on an MGISEQ-2000 (BGI, China). Variants were filtered based on their frequency (≤0.01), inheritance pattern, clinical phenotype, and pathogenicity. A variant filtration threshold of 0.01 was applied for the minimum allele frequency. WES was performed on two affected samples. First, variants with genotype scores lower than 15 and coverage lower than 4 were removed using our in-house script. Second, to filter the variants, we searched publicly available databases, such as gnomAD, ExAC, and 1000 G Project, and our in-house database, consisting of only Turkish samples (n = 3,892). Finally, a nonsynonymous variant in 2 patients with the HSD17B4 gene was selected after filtering. Subsequently, the c.350A>G (p.Asp117Gly) variant was detected in both patients to be homozygous according to the (NM_000414.4) transcript in the HSD17B4 gene, which was considered to explain the patient’s clinical state.

Discussion

In our study, we detected the c.350A>G (p.Asp117Gly) variant as homozygous in the HSD17B4 gene, according to the NM_000414.4 transcript. To the best of our knowledge, this variant is a novel variant. The individuals inherited the variant from their carrier parents, which was confirmed by Sanger sequencing. The identified genetic variations were not found in any databases, including the 1000 Genome projects, esp6500, ExAC, gnomAD, or our in-house database (n = 2,389 Turkish individuals). Bioinformatic prediction analysis with in silico algorithms, such as Mutation Taster, Polyphen-2, CADD, Revel, M-CAP, and SIFT, showed this alteration to be pathogenic and probably disease causing [Adzhubei et al., 2010; Schwarz et al., 2014].

Perrault syndrome is a genetically heterogeneous recessive disorder. New pathogenic variants can be detected because of the increasing application of genetic testing. Genetic heterogeneity is likely related to phenotypic heterogeneity. Eight genes (CLPP, ERAL1, GGPS1, HARS2, HSD17B4, LARS2, RMND1, and TWNK) associated with Perrault syndrome have been identified to date. Seven of these eight genes are mitochondrial proteins, while HSD17B4 is a peroxisomal protein [Faridi et al., 2022].

Missense HSD17B4 gene variants are thought to disrupt enzymes and, therefore, cause disease. Our missense variants are located in the hydroxyacyl-CoA-like domain, which has an important function. Our patient’s missense variant resulted in the substitution of a polar aspartate residue for a nonpolar hydrophobic glycine residue at position 117 (p.Asp117Gly), which can affect intracellular interactions.

Parental consanguinity was present in both cases, and the findings included SNHL, ataxia, and neuropathy after early childhood. Neurological findings were progressive, and micrognathia was present in our female patient. The pubertal development of our female patient was delayed, the gonads were dysgenetic, and the pubertal development of our male patient was normal. In addition, while there was no cognitive retardation in our female case, there was a mild intellectual disability in our male case. Cerebellar atrophy was detected on cranial MRI in both cases. In this syndrome, which has very complex clinical heterogeneity, McMillan et al. [2012] reported rod dysfunction and retinal atrophy consistent with retinitis pigmentosa in two siblings aged 16 and 14 years [McMillan et al., 2012]. Pierce et al. [2010] reported that some patients may have mild intellectual disabilities [Pierce et al., 2010].

Perrault’s syndrome may not be uncommon; some cases may go unrecognized, particularly when only one child in a family is affected. Nishi et al. described 21 patients from 8 families, including 16 women with ovarian dysgenesis and deafness, 3 deaf men without gonadal defects, 1 woman with ovarian dysgenesis without deafness, and 1 female patient with deafness whose ovarian function was not evaluated [Nishi et al., 1988]. In addition to SNHL and ovarian dysgenesis, Fiumara et al. [2004] reported short stature, mild intellectual disability, and progressive sensory and motor peripheral neuropathy in two sisters [Fiumara et al., 2004]. The older sister also had significant cerebellar involvement, with dysarthria, intensity tremor, ataxia, and atrophy of the cerebellar hemispheres on MRI. Using WES, the authors identified compound heterozygous variants of HSD17B4 (p.Y217C and p.Y568X) [Fiumara et al., 2004]. Our female patient had clinically similar findings, except that she was short in stature and had no intellectual disabilities. In addition, there were a marfanoid appearance and a syndromic facial appearance accompanied by prominent micrognathia.

Lieber et al. [2014] reported a 35-year-old male patient from Boston with progressive cerebellar atrophy since childhood, with progressive gait disturbance, cognitive impairment, SNHL, nystagmus, progressive ataxia, high-arched feet, hammer toes, exaggerated deep tendon reflexes in the legs, and brain MRI. He had azoospermia with normal secondary sex characteristics and infertility that was developed in adulthood. The described case was similar to our male case, with all of its features. A rare heterozygous missense variant was detected in HSD17B4 (c.587C>T; p.A196V) by WES [Lieber et al., 2014]. In our case, with normal secondary sex characteristics, we could not evaluate infertility because of her age. Variant differences in HSD17B4 may explain the infertility observed in the study by Lieber et al. [2014]. It is necessary to closely monitor our case for azoospermia in adulthood. Infertility in female cases also usually occurs in adulthood.

Approximately 100 affected individuals with Perrault syndrome have been reported in the literature to date [Lerat et al., 2016]. Underdetection is likely, as men without an affected sister will be diagnosed with nonsyndromic deafness rather than Perrault syndrome. Boys with SNHL and prepubertal female patients with SNHL should be carefully screened for variants of genes associated with Perrault syndrome [Pan et al., 2020]. Due to genetic and phenotypic heterogeneity, single gene testing is often ineffective, and WES emerges as an effective diagnostic test [Lieber et al., 2013; Demain et al., 2017].

Conclusion

In conclusion, we defined Perrault syndrome cases in Turkey caused by a novel mutation in HSD17B4. We emphasize that WES can be an important diagnostic method for rare cases with atypical courses.

Statement of Ethics

Written informed consent was obtained from the patients and their parents for the publication of the details of their medical case and any accompanying images. Ethical approval was not required for this study, in accordance with the local/national guidelines.

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

The authors declare that this study received no financial support.

Author Contributions

Pınar Özkan Kart analyzed the data and wrote the manuscript. Nihal Yildiz and Gülnur Esenulku analyzed the data. Yavuz Sahin studied the genetic analysis of the first case. Alper Han Cebi performed the genetic analysis of the second case. Ali Cansu designed the study, cared for the patients, analyzed the data, and wrote the manuscript.

Funding Statement

The authors declare that this study received no financial support.

Data Availability Statement

The data supporting the findings of this study are available upon request from the corresponding author. The data are not publicly available because of privacy or ethical restrictions.