https://orcid.org/0000-0001-7558-0669
Figures
Abstract
The peroxisome biogenesis disorders (PBDs) are a group of rare inherited autosomal recessive diseases characterized by motor and cognitive neurological dysfunction, hypotonia, seizures, feeding difficulties, retinopathy, sensorineural hearing loss, hepatic and renal abnormalities, and chondrodysplasia punctata of long bones, and the clinical expression is variable. Exome sequencing and Sanger sequencing were used to identify the genetic defect for PBDs in a two-generation non-consanguineous Han-Chinese pedigree. Compound heterozygous variants, a novel splicing variant c.113-2A>G and a reported substitution c.890T>C (p.Leu297Pro), in the peroxisomal biogenesis factor 10 gene (PEX10) were detected. The splicing variant c.113-2A>G led to a canonical splice acceptor site inactivation, exon 2 skipping, and in-frame deletions (p.Ala39_Gly65del). The three patients had similar phenotypes of milder PBDs, which were further genetically determined as PBD6B. The findings extend the PEX10 variant spectrum and may provide new insights into PBDs causation and diagnosis, with implications for genetic counseling and clinical management.
Citation: Huang X, Deng X, Deng X, Xu H, Deng H, Yuan L (2025) Identification of novel compound heterozygous variants in the PEX10 gene in a Han-Chinese family with PEX10-related peroxisome biogenesis disorders. PLoS ONE 20(4): e0322137. https://doi.org/10.1371/journal.pone.0322137
Editor: Muhammad Farooq,, The Islamia University of Bahawalpur, PAKISTAN
Received: October 31, 2024; Accepted: March 17, 2025; Published: April 23, 2025
Copyright: © 2025 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Data cannot be shared publicly because of privacy and ethical restrictions and legal concerns, regarding sensitive information. Reasonable requests to access the datasets by the qualified researchers can be sent to the Institutional Review Board of the Third Xiangya Hospital, Central South University (xy3irb@163.com) or the correspondence author (hdeng008@163.com).
Funding: This work was supported by grants from National Natural Science Foundation of China (81800219 and 81873686), Natural Science Foundation of Hunan Province (2023JJ30715), Scientific Research Project of Hunan Provincial Health Commission (A202303018385 and C202304019709), Health Research Project of Hunan Provincial Health Commission (W20243024), Distinguished Professor of the Lotus Scholars Award Program of Hunan Province, Sublimation Scholars Project of Central South University, and Wisdom Accumulation and Talent Cultivation Project of the Third Xiangya Hospital of Central South University (YX202109), China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. There was no additional external funding received for this study.
Competing interests: NO authors have competing interests.
Introduction
The peroxisome biogenesis disorders (PBDs) are a group of rare inherited autosomal recessive diseases characterized by neurological and developmental dysfunction with multisystem involvement, manifesting as hypotonia, seizures, mental retardation, feeding difficulties, visual and hearing impairment, and abnormalities in face, skeleton, liver, and kidney, with variable clinical expression [1–6]. According to the clinical manifestations, PBDs can be divided into two main groups, Zellweger spectrum disorders (ZSDs) and rhizomelic chondrodysplasia punctata type 1 (RCDP1). ZSDs include the mild infantile Refsum disease (IRD), the less severe neonatal adrenoleukodystrophy (NALD), and the most severe Zellweger syndrome [1,7–9], in which all three are accompanied by variable neurodevelopmental delay, hearing and vision impairment, and liver dysfunction in the first few months after birth [10]. Zellweger syndrome patients generally die within the first year of life, and NALD and IRD patients may survive to childhood and adulthood [11,12]. Approximately 80% of PBDs patients show phenotypes of ZSDs, and 20% cases have RCDP1 [12,13]. The estimated birth incidence is 0.002% for ZSDs and 0.001% for RCDP1 worldwide, with varied prevalence for both conditions among different populations [14]. Pathological defects of PBDs include impaired peroxisome assembly and function, relating to decreased peroxisome numbers, morphologically abnormal peroxisomes, and impaired peroxisomal alpha- and beta-oxidation, plasmalogen synthesis, and catalase distribution, though the exact mechanism remains unclear [8,14–16].
PBDs are primarily caused by biallelic variants in any of 14 different peroxisomal biogenesis factor (PEX) genes, PEX1, PEX2, PEX3, PEX5, PEX6, PEX7, PEX10, PEX11B, PEX12, PEX13, PEX14, PEX16, PEX19, and PEX26 [1,14]. The PEX10 gene pathogenic variants may be the fifth most common cause of PBDs (3.4%), following PEX1 (48.5%), PEX7 (17.7%), PEX6 (13.1%), and PEX12 (5.9%) based on the reported data worldwide. Laboratory findings of impaired peroxisomal functions and identification of pathogenic variants in genes like PEX are valuable and helpful for definite disease diagnosis [11].
This study sought to reveal the genetic factor giving rise to PBDs in a two-generation non-consanguineous Han-Chinese family. Novel compound heterozygous variants, c.113-2A>G (p.Ala39_Gly65del) and c.890T>C (p.Leu297Pro), in the PEX10 gene (NG_008342.1, NM_153818.2), were identified, which may disrupt peroxisome biogenesis and therefore decrease metabolism, leading to multisystem abnormalities [17].
Materials and methods
Participators and clinical examination
A two-generation Han-Chinese family with PBDs was recruited at the First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China, from June to August, 2023 (Fig 1). Detailed clinical medical histories were collected, and physical, biochemical, and radiological examinations were performed on all participants. Available peripheral venous blood was sampled. Skin biopsy for fibroblast culture and peroxisomal functional analysis was not performed due to the refusal of the family. Written informed consent was obtained from each participant or the legal guardian. This study had received approval from the Institutional Review Board of the Third Xiangya Hospital, Central South University, Changsha, China, which was implemented from June 2023 to February 2025.
(A) Family pedigree of the patients with autosomal recessive PBDs. White square with slash symbol indicates deceased unaffected male family member. White circle symbol represents unaffected female family member. Black circles and black squares denote affected females and males, respectively. Black circle with slash symbol indicates deceased affected female family member. The PEX10 gene variants were indicated under the individuals who had genetic analysis. (B) The PEX10 gene sequence with heterozygous c.113-2A>G variant of patient II:1. (C) The PEX10 gene sequence with heterozygous c.890T>C variant of patient II:1. (D) Conservative analysis of the PEX10 leucine residue at position 297 (p.Leu297). PEX10, the peroxisomal biogenesis factor 10 gene; PBDs, peroxisome biogenesis disorders.
Exome capture and sequencing
Genomic DNA (gDNA) was isolated from sampled peripheral blood lymphocytes via a phenol/chloroform extracting protocol. Exome sequencing was performed to unveil shared genetic causation of PBDs in two affected siblings (II:1 and II:3) of the pedigree by the established method of BGI-Shenzhen (Shenzhen, China) [18]. The “A” base and adaptor were ligated to the fragmented DNA sequentially, and ligated-PCR was used for amplification. Hybridization to the exome array for enrichment was conducted, followed by circularization and amplification for library. The SureSelectXT Human All Exon V6 (Agilent Technologies, Inc., Santa Clara, CA, USA) was used for exome capture, and BGISEQ-500 platform was used to sequence the qualified circular library.
Read mapping and variant analysis
The human reference genome (hg19) was used, and sequencing data were aligned using Burrows-Wheeler Aligner (v0.7.15). Genome Analysis Toolkit (v3.7), Picard (v2.5.0), and SnpEff tool were used for variants’ calling and annotation, including single nucleotide polymorphisms (SNPs) and insertions-deletions (indels) [19]. Common variants or non-pathogenic variants were filtered out using the human gene variant databases, including the Single Nucleotide Polymorphism database (dbSNP, version 141) and 1000 Genomes Project. Variants were further analyzed using the in-house exome databases with 3275 Chinese controls, as well as the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) 6500, Genome Aggregation Database (gnomAD), China Metabolic Analytics Project (ChinaMAP), Human Gene Mutation Database (HGMD), and the ClinVar database. The shared potential disease-causing variants were prioritized. PCR amplification was conducted with the gDNA samples and the designed locus-specific primers, and the presence of potential causative variants was further tested by Sanger sequencing on an Applied Biosystems 3730xl genetic analyzer (Applied Biosystems, Thermo Fisher Scientific Inc., Waltham, MA, USA) [20,21]. The primer sequences were as follows: 5′-CGGAGACAGAAGCAGAGAGG-3′ and 5′-TACCTGCAAGTGTGGTGAGG-3′ for variant 1, 5′-TAAGGTGCACCCACCTTGAC-3′ and 5′-CCACCTCACCTTGCTGCT-3′ for variant 2. Bioinformatics tools including Polymorphism Phenotyping version 2 (PolyPhen-2), Functional Analysis through Hidden Markov Models (FATHMM, v2.3), MutationAssessor, MutationTaster2021, Combined Annotation Dependent Depletion (CADD, v1.6), Berkeley Drosophila Genome Project (BDGP) Splice Site Prediction by Neural Network (v0.9), NetGene2 (v2.4), SpliceAI, and Pangolin were used to evaluate whether amino acid substitutions affected protein structures and functions and the variants’ effects on splicing [22–25].
RNA extraction and analysis
To further determine the variants’ effects, total RNA was extracted from the peripheral venous blood of the unaffected mother (I:2) and three patients (II:1, II:3, and II:4) using the RNA-Solv reagent (Omega Bio-Tek Inc., Norcross, GA, USA). Reverse transcription for high-efficient complementary DNA (cDNA) synthesis was performed using the ReverTra Ace qPCR RT Master Mix with gDNA Remover (Toyobo Co., Ltd., Osaka, Japan), and further PCR amplification was completed using the following primer pairs for confirming the variants’ effects: 5′-GGCGCAGAAGGACGAGTA-3′ and 5′-CTGCCTGAAACCGTACAGC-3′ for variant 1, 5′-GAAGGAGTGGAGGCTGCA-3′ and 5′-GAGCTTCTGGGGAGGGAAC-3′ for variant 2. PCR fragments were analyzed by electrophoresis, separation, retraction (only for further evaluation of the splicing variant), and purification, and then sequenced on the genetic analyzer [26]. By comparing the areas under the peaks (AUP) of wild-type and mutant alleles, the nonsense-mediated mRNA decay caused by the variant was evaluated using the direct sequencing results of PCR fragments. The ImageJ software v1.54d (National Institutes of Health, USA) was applied to quantify the AUP, and Microsoft Excel 2021 (Microsoft Corp., Redmond, WA, USA) and GraphPad Prism v8.2.1 (GraphPad Software, LLC, Boston, MA, USA) were used for statistical analysis, in which Student’s t test was applied and P<0.05 was regarded as statistically significant [27]. For further checking the correct splicing caused by the potential splicing variant, primers for amplifying fragments covering both variants were designed, 5′-GCGCAGAAGGACGAGTACTA-3′ and 5′-GGTAGATGAGCTTCTGGGGA-3′, and RNA analysis was performed by TA cloning and sequencing, using pClone007 Versatile Simple Vector Kit (Beijing Tsingke Biotech Co., Ltd., Beijing, China).
Conservative analysis and variant evaluation
National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST) was applied to evaluate the protein’s conservation, and the tertiary structures of wild-type and variant protein were conducted with the online SWISS-MODEL tool (https://swissmodel.expasy.org/) and further visualized using Visual Molecular Dynamics software (version 1.9.4a53) [28]. The variants were further classified following the American College of Medical Genetics and Genomics (ACMG) interpretation guidelines for sequence variants [29].
Results
Clinical findings
Three patients (Fig 1A), including one female (II:1) and two males (II:3 and II:4), manifested similar abnormalities, having cerebellar ataxia, weak tendon reflexes, atrophy of distal muscles, slow neurological deterioration, craniofacial dysmorphism, enamel hypoplasia, osteopenia, chondrodysplasia punctata, scoliosis, pes cavus, and liver dysfunction (Table 1). Brain magnetic resonance imaging showed marked cerebellar atrophy and brain stem atrophy, and chest X-ray indicated scoliosis (Fig 2). Patient II:1 had walk instability and balance problems at about the age of 3 years with a slow progression, and was unable to walk independently at age 13. Patient II:3 had walk instability beginning at the age of 7 years, and his little brother (patient II:4) was found to have the walking difficulty at 2 years.
Brain magnetic resonance imaging of three patients (A, C, and E) showing cerebellar atrophy (thick short arrow) and brain stem atrophy (thin long arrow), and chest X-ray showing scoliosis (B, D, and F).
Variant analysis
The detailed exome sequencing data are shown in S1 Table. The novel compound heterozygous variants in the PEX10 gene, including a novel splicing variant c.113-2A>G and a transition c.890T>C, shared in the two tested patients (II:1 and II:3), were considered as the potential pathogenic causes following the filtering processes and inheritance pattern. No further potential disease-associated variants, including homozygous or compound heterozygous variants, were found. Except the very low frequency (4.72×10-5) of c.890T>C variant in ChinaMAP, which is also deposited in the dbSNP (rs724160000), HGMD (CM090797), and ClinVar (ID 162432, interpreted as likely pathogenic or uncertain significance), the variants were absent in NHLBI ESP6500 and gnomAD, as well as Chinese controls (900 from our in-house exome database and 2375 from the BGI in-house database). The compound heterozygous variants were further validated in three patients by Sanger sequencing, and the heterozygous transition c.890T>C was also found in the unaffected mother (I:2) (Fig 1A–1C, Table 2). The compound heterozygous variants (c.113-2A>G and c.890T>C) co-segregated with the disease phenotype in the family. The novel c.113-2A>G variant was predicted to affect the splicing, by leading to the loss of canonical splice acceptor site. The recurrent c.890T>C variant was predicted to be damaging by in silico analyses (Table 2).
By reverse transcription, PCR amplification, electrophoresis, and Sanger sequencing, the effects on RNA of identified compound heterozygous variants, c.113-2A>G (p.Ala39_Gly65del) and c.890T>C (p.Leu297Pro), were shown (Fig 3). The potential splicing variant c.113-2A>G was found to cause canonical splice acceptor site inactivation and exon 2 skipping, which can cause in-frame deletions (p.Ala39_Gly65del), a large portion of transmembrane region. No significant difference was shown in the electropherogram AUP for the wild-type (c.113-2A) and c.113-2A>G mutant alleles in three patients (P = 0.2140, S1 Fig). No correct splicing remained which was related to the variant c.113-2A>G (S2 Fig).
(A) cDNA sequence with PEX10 c.113-2A>G variant of patient II:1. (B) cDNA sequence with PEX10 c.890T>C variant of patient II:1. (C) cDNA sequence of the normal splicing in the PEX10 gene of patient II:1. (D) cDNA sequence of the abnormal splicing caused by the PEX10 c.113-2A>G variant of patient II:1. cDNA, complementary DNA; PBDs, peroxisome biogenesis disorders; PEX10, the peroxisomal biogenesis factor 10 gene.
Sequence alignment of multiple orthologous proteins revealed that leucine at position 297 (p.Leu297) of the PEX10 protein, a functionally critical part of zinc-binding motif, near the zinc binding site (p.Cys296), was highly conservative in various organisms (Fig 1D). Structural modelling showed the conformational changes caused by the two variants (Fig 4). According to the ACMG variant interpretation guidelines, c.113-2A>G (p.Ala39_Gly65del) and c.890T>C (p.Leu297Pro) were deemed as “pathogenic”.
(A) The deleted residues at position 39 to 65 (p.Ala39_Gly65del) are colored in the wild-type structure (p.Ala39_Gly65). (B) The residues at position 297, leucine (Leu) and proline (Pro), are indicated with ball-and-stick models. PEX10, peroxisomal biogenesis factor 10.
Discussion
The PEX10 pathogenic variants were reported to be responsible for two definite disorders, PBD6A and PBD6B, in Online Mendelian Inheritance in Man (OMIM) database, variable in clinical severity. PBD6A, a form of Zellweger syndrome, is characterized by neurodevelopmental abnormalities (neuronal migration defects, leukodystrophy, cognitive and psychomotor delay, profound dystonia, and seizures), skeletal abnormalities (craniofacial abnormalities and achondroplasia), and multisystem impairments (eyesight, hearing, liver, and kidney impairments), and the survival of affected infants is usually less than one year [7,15,30–32]. The features of PBD6B are milder than those of PBD6A, corresponding to the phenotypes of NALD and IRD, with a longer disease duration in the sufferers, as well as a slow progression and a later diagnosis [7,11].
The severity of PBDs was reported to be related to disease-causing gene variants which can cause changes in peroxidase function, matrix protein import capacity, and peroxisome numbers, via complete or partial loss-of-function alleles [9,14]. Due to the clinical and genetic overlaps of the subtypes of PBDs, this group of diseases can be divided into independent subtypes of PBDs by disease-causing genes, benefiting to the precise molecular genetic diagnosis [33]. The phenotype spectrum of the PEX10-related PBDs ranges from lethal to mild, and the clinical diagnosis include Zellweger syndrome, NALD, and IRD based on the onset age, symptoms, and signs [34,35]. Variants in important parts of the gene account for severe phenotypes of a certain disorder, while in non-critical parts, variants can result in milder subtypes or increase the disease susceptibility. Thus, based on the underpinning of shared genetic etiology, milder diseases can be classified as less severe subtypes of severe phenotype-related disorders (e.g., PEX10-related PBDs) that exhibit different expressivity [33].
This study identified compound heterozygous variants c.113-2A>G (p.Ala39_Gly65del) and c.890T>C (p.Leu297Pro) in the PEX10 gene in a non-consanguineous Han-Chinese family with PBDs, which co-segregated with the disease phenotype. The deceased father (I:1) was supposed to be an obligate heterozygote of c.113-2A>G variant. In addition to the absence of c.113-2A>G variant in public and in-house exome databases, and a low frequency of c.890T>C variant in public databases, the in silico predicted deleterious effect and RNA analysis further supported that both variants were pathogenic factors for PBDs in our family. The splicing variant c.113-2A>G may not induce nonsense-mediated mRNA decay, as well as retaining correct splicing. Our three patients have the milder presentations of PBDs, and the clinical features include cerebellar ataxia, weak tendon reflexes, atrophy of distal muscles, slow neurological deterioration, craniofacial dysmorphism, enamel hypoplasia, osteopenia, chondrodysplasia punctata, scoliosis, and pes cavus, which are consistent with the reported manifestations of PBD6B cases [7,35–37].
The PEX10 gene, located on chromosome 1q36.32, consisting of 6 exons, can encode an integral peroxisomal membrane protein, which is known as a multi-pass membrane protein with a zinc-binding motif in the C-terminus [11,36]. There are two main transcripts due to the alterative splice acceptor site in intron 3, leading to the 346-amino acid (39.2-kDa) and 326-amino acid (37-kDa) isoform, in which the shorter one may be more abundant and the identified substitution was previously reported as c.830T>C (p.Leu277Pro) [11,35,38]. In drosophila, pex10 variants had peroxisomal protein import defect, increased very-long-chain fatty acids levels, and growth restriction, similar to features of PBDs in humans [39]. Pex10Cys294Tyr/Cys294Tyr mice displayed neurological deficits with progressive locomotion defects, peroxisomal biochemical abnormalities, and neonatal death [40].
To date, at least 34 PEX10 gene variants, in the homozygous or compound heterozygous state, have been reported to be responsible for PBDs in published literature and in the HGMD, as well as our study. A total of 13 missense, 9 frameshift (including 4 small insertions, 4 small deletions, and 1 small indel), 7 nonsense, and 2 splicing variants, as well as 3 variants leading to the loss of the start codon, were identified in 60 cases. Variants are mainly in exon 3 (11/34) and involving in 5 coding exons (Table 3) [7,41–47]. The homozygous c.874_875del (p.Leu292Valfs*66) variant is the most common reported variant (15/30 homozygotes, 32/120 alleles), and the c.764dup (p.Leu256Alafs*103) variant is the second one (10/120 alleles). Genotype-phenotype association may be revealed for the PEX10 deficiency, which can be partially veiled by the limited PBD phenotype description in the literature. Generally, in homozygotes, missense variant, p.(Leu177Arg), retaining residual function, is related to milder phenotypes (i.e., PBD6B), and missense variant, p.(Cys296Phe), interrupting the formation of critical C-terminal zinc-binding domain, and truncations relating to splicing, nonsense, and frameshift variants, c.600+1G>A (p.Gly65Alafs*36), p.Arg264*, and p.Leu292Valfs*66, affecting large portions of the coding region, are associated with severe phenotypes (i.e., PBD6A) [5–7,9,38,43,48]. Compound heterozygotes, modifier genes, and other confounding factors can complicate the genotype-phenotype relationship [5,7,11,14,32,35–37,43–48]. In our study, the novel identified splicing variant c.113-2A>G led to exon 2 skipping and the loss of transmembrane region (p.Ala39_Gly65del). The identified missense variant c.890T>C (p.Leu297Pro), with hydrophobic property, involving a functionally critical part of zinc-binding motif, near the zinc binding site (p.Cys296), was previously reported in two unrelated patients, responsible for the milder phenotype of PBDs (i.e., PBD6B) in a compound heterozygous state with a missense variant, c.209G>A, p.(Gly70Glu), and a frameshift variant, c.337del, p.(Leu113Trpfs*40), respectively [7,35]. The compound heterozygous variants may lead to the milder phenotype, PBD6B, in our family via a loss-of-function mechanism (predicted by LoGoFunc predictor in https://itanlab.shinyapps.io/goflof/) [49]. Due to the autosomal recessive inheritance pattern, newborn screening for PBDs or prenatal genetic testing for at-risk fetus, or even preimplantation genetic testing, is recommended, especially for those with affected siblings [50,51]. It is a pity that peroxisomal functional studies were not performed in this study. Further studies like peroxisomal activity in patient-related materials and variants’ functional study may reveal the exact pathogenicity and disease mechanism [14,17].
Conclusions
In summary, compound heterozygous PEX10 variants, c.113-2A>G (p.Ala39_Gly65del) and c.890T>C (p.Leu297Pro), were likely the responsible variants for the multisystem abnormalities in a Han-Chinese family with PBD6B, the milder subtype of the PEX10-related PBDs. Exome sequencing provides a cost-effective and expedited approach to identify pathogenic variants responsible for highly heterogeneous disorders. This is the first known report of PEX10 c.113-2A>G variant, with the exon 2-skipping effect first confirmed by RNA analysis. Our finding may provide new insights and approaches into the genetic cause and diagnosis of PBDs, and may also have implications for genetic counseling and clinical intervention. Because of the limited number of patients in this study and the relative rarity of the disease, more cases confirmed by genetic analysis in other families and the evaluation of gene variants’ pathogenicity are warranted. More in-depth research including variants’ functional analyses in vitro and animal models with genetic defects in vivo, and the discovery of variants in the affected families will help to discover the cause and provide assistance for gene therapy of PBDs intervention.
Supporting information
S1 Table. The summarized exome sequencing data of the two patients.
https://doi.org/10.1371/journal.pone.0322137.s001
(PDF)
S1 Fig. RNA analysis of PEX10 c.113-2A>G variant.
https://doi.org/10.1371/journal.pone.0322137.s002
(PDF)
S2 Fig. RNA analysis of PEX10 c.113-2A>G variant and c.890T>C variant.
https://doi.org/10.1371/journal.pone.0322137.s003
(PDF)
Acknowledgments
We would like to thank all the enrolled individuals for their participation in this study.
References
- 1. Zaki MS, Issa MY, Thomas MM, Elbendary HM, Rafat K, Al Menabawy NM, et al. A founder mutation in PEX12 among Egyptian patients in peroxisomal biogenesis disorder. Neurol Sci. 2021;42(7):2737–45. pmid:33123925
- 2. Zeharia A, Ebberink MS, Wanders RJA, Waterham HR, Gutman A, Nissenkorn A, et al. A novel PEX12 mutation identified as the cause of a peroxisomal biogenesis disorder with mild clinical phenotype, mild biochemical abnormalities in fibroblasts and a mosaic catalase immunofluorescence pattern, even at 40 degrees C. J Hum Genet. 2007;52(7):599–606. pmid:17534573
- 3. O’Bryhim BE, Kozel BA, Lueder GT. Novel retinal findings in peroxisomal biogenesis disorders. Ophthalmic Genet. 2018;39(3):377–9. pmid:29377746
- 4. Gootjes J, Elpeleg O, Eyskens F, Mandel H, Mitanchez D, Shimozawa N, et al. Novel mutations in the PEX2 gene of four unrelated patients with a peroxisome biogenesis disorder. Pediatr Res. 2004;55(3):431–6. pmid:14630978
- 5. Warren DS, Morrell JC, Moser HW, Valle D, Gould SJ. Identification of PEX10, the gene defective in complementation group 7 of the peroxisome-biogenesis disorders. Am J Hum Genet. 1998;63(2):347–59. pmid:9683594
- 6. Shimozawa N, Nagase T, Takemoto Y, Ohura T, Suzuki Y, Kondo N. Genetic heterogeneity of peroxisome biogenesis disorders among Japanese patients: evidence for a founder haplotype for the most common PEX10 gene mutation. Am J Med Genet A. 2003;120A(1):40–3. pmid:12794690
- 7. Zhang C, Zhan F-X, Tian W-T, Xu Y-Q, Zhu Z-Y, Wang Y, et al. Ataxia with novel compound heterozygous PEX10 mutations and a literature review of PEX10-related peroxisome biogenesis disorders. Clin Neurol Neurosurg. 2019;177:92–6. pmid:30640048
- 8. Honsho M, Okumoto K, Tamura S, Fujiki Y. Peroxisome biogenesis disorders. Adv Exp Med Biol. 2020;1299:45–54. pmid:33417206
- 9. Krause C, Rosewich H, Thanos M, Gärtner J. Identification of novel mutations in PEX2, PEX6, PEX10, PEX12, and PEX13 in Zellweger spectrum patients. Hum Mutat. 2006;27(11):1157. pmid:17041890
- 10. Barth PG, Gootjes J, Bode H, Vreken P, Majoie CB, Wanders RJ. Late onset white matter disease in peroxisome biogenesis disorder. Neurology. 2001;57(11):1949–55. pmid:11769739
- 11. Waterham HR, Ebberink MS. Genetics and molecular basis of human peroxisome biogenesis disorders. Biochim Biophys Acta. 2012;1822(9):1430–41. pmid:22871920
- 12. Yik WY, Steinberg SJ, Moser AB, Moser HW, Hacia JG. Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders. Hum Mutat. 2009;30(3):E467-80. pmid:19105186
- 13. Grønborg S, Krätzner R, Rosewich H, Gärtner J. Lymphoblastoid cell lines for diagnosis of peroxisome biogenesis disorders. JIMD Rep. 2011;1:29–36. pmid:23430824
- 14. Argyriou C, D’Agostino MD, Braverman N. Peroxisome biogenesis disorders. Transl Sci Rare Dis. 2016;1(2):111–44. pmid:29152457
- 15. Ge M-M, Hu L, Li Z, Cheng G, Yan K, Kong Y, et al. Novel compound heterozygous mutations in the PEX1 gene in two Chinese newborns with Zellweger syndrome based on whole exome sequencing. Clin Chim Acta. 2017;470:24–8. pmid:28432012
- 16. Nuebel E, Morgan JT, Fogarty S, Winter JM, Lettlova S, Berg JA, et al. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. EMBO Rep. 2021;22(10):e51991. pmid:34351705
- 17. Warren DS, Wolfe BD, Gould SJ. Phenotype-genotype relationships in PEX10-deficient peroxisome biogenesis disorder patients. Hum Mutat. 2000;15(6):509–21. pmid:10862081
- 18. Huang X, Deng X, Xu H, Wu S, Yuan L, Yang Z, et al. Identification of a novel mutation in the COL2A1 gene in a Chinese family with spondyloepiphyseal dysplasia congenita. PLoS One. 2015;10(6):e0127529. pmid:26030151
- 19. Yuan L, Deng X, Song Z, Deng S, Zheng W, Mao P, et al. Systematic analysis of genetic variants in patients with essential tremor. Brain Behav. 2018;8(10):e01100. pmid:30252209
- 20. Huang X, Yuan L, Xu H, Zheng W, Cao Y, Yi J, et al. Identification of a novel mutation in the ABCA4 gene in a Chinese family with retinitis pigmentosa using exome sequencing. Biosci Rep. 2018;38(2):BSR20171300. pmid:29437900
- 21. Yuan L, Yi J, Lin Q, Xu H, Deng X, Xiong W, et al. Identification of a PRX variant in a Chinese family with congenital cataract by exome sequencing. QJM. 2016;109(11):731–5. pmid:27081207
- 22. Yu X, Yuan L, Deng S, Xia H, Tu X, Deng X, et al. Identification of DNAH17 variants in Han-Chinese patients with left-right asymmetry disorders. Front Genet. 2022;13:862292. pmid:35692830
- 23. Wu S, Guo Y, Liu C, Liu Q, Deng H, Yuan L. Identification of a de novo TSC2 variant in a Han-Chinese family with tuberous sclerosis complex. J Chin Med Assoc. 2021;84(1):46–50. pmid:33177398
- 24. Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, et al. Predicting splicing from primary sequence with deep learning. Cell. 2019;176(3):535-548.e24. pmid:30661751
- 25. Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 2022;23(1):103. pmid:35449021
- 26. Fan K, Guo Y, Song Z, Yuan L, Zheng W, Hu X, et al. The TSC2 c.2742+5G>A variant causes variable splicing changes and clinical manifestations in a family with tuberous sclerosis complex. Front Mol Neurosci. 2023;16:1091323. pmid:37152430
- 27. Gao Y, Yuan L, Yuan J, Yang Y, Wang J, Chen Y, et al. Identification of COL4A4 variants in Chinese patients with familial hematuria. Front Genet. 2023;13:1064491. pmid:36699462
- 28. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–8, 27–8. pmid:8744570
- 29. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24. pmid:25741868
- 30. Rydzanicz M, Stradomska TJ, Jurkiewicz E, Jamroz E, Gasperowicz P, Kostrzewa G, et al. Mild Zellweger syndrome due to a novel PEX6 mutation: correlation between clinical phenotype and in silico prediction of variant pathogenicity. J Appl Genet. 2017;58(4):475–80. pmid:29047053
- 31. Barillari MR, Karali M, Di Iorio V, Contaldo M, Piccolo V, Esposito M, et al. Mild form of Zellweger Spectrum Disorders (ZSD) due to variants in PEX1: detailed clinical investigation in a 9-years-old female. Mol Genet Metab Rep. 2020;24:100615. pmid:32596134
- 32. Berendse K, Engelen M, Linthorst GE, van Trotsenburg ASP, Poll-The BT. High prevalence of primary adrenal insufficiency in Zellweger spectrum disorders. Orphanet J Rare Dis. 2014;9:133. pmid:25179809
- 33. Deng H, Huang X, Yuan L. Molecular genetics of the COL2A1-related disorders. Mutat Res Rev Mutat Res. 2016;768:1–13. pmid:27234559
- 34. Gould SJ, Valle D. Peroxisome biogenesis disorders: genetics and cell biology. Trends Genet. 2000;16(8):340–5. pmid:10904262
- 35. Steinberg SJ, Snowden A, Braverman NE, Chen L, Watkins PA, Clayton PT, et al. A PEX10 defect in a patient with no detectable defect in peroxisome assembly or metabolism in cultured fibroblasts. J Inherit Metab Dis. 2009;32(1):109–19. pmid:19127411
- 36. Renaud M, Guissart C, Mallaret M, Ferdinandusse S, Cheillan D, Drouot N, et al. Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia. J Neurol. 2016;263(8):1552–8. pmid:27230853
- 37. Régal L, Ebberink MS, Goemans N, Wanders RJA, De Meirleir L, Jaeken J, et al. Mutations in PEX10 are a cause of autosomal recessive ataxia. Ann Neurol. 2010;68(2):259–63. pmid:20695019
- 38. Okumoto K, Itoh R, Shimozawa N, Suzuki Y, Tamura S, Kondo N, et al. Mutations in PEX10 is the cause of Zellweger peroxisome deficiency syndrome of complementation group B. Hum Mol Genet. 1998;7(9):1399–405. pmid:9700193
- 39. Chen H, Liu Z, Huang X. Drosophila models of peroxisomal biogenesis disorder: peroxins are required for spermatogenesis and very-long-chain fatty acid metabolism. Hum Mol Genet. 2010;19(3):494–505. pmid:19933170
- 40. Hanson MG, Fregoso VL, Vrana JD, Tucker CL, Niswander LA. Peripheral nervous system defects in a mouse model for peroxisomal biogenesis disorders. Dev Biol. 2014;395(1):84–95. pmid:25176044
- 41. Ebberink MS, Mooijer PAW, Gootjes J, Koster J, Wanders RJA, Waterham HR. Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder. Hum Mutat. 2011;32(1):59–69. pmid:21031596
- 42. Steinberg S, Chen L, Wei L, Moser A, Moser H, Cutting G, et al. The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum. Mol Genet Metab. 2004;83(3):252–63. pmid:15542397
- 43. Havali C, Dorum S, Akbaş Y, Görükmez O, Hirfanoglu T. Two different missense mutations of PEX genes in two similar patients with severe Zellweger syndrome: an argument on the genotype-phenotype correlation. J Pediatr Endocrinol Metab. 2020;33(3):437–41. pmid:32069232
- 44. Nava E, Hartmann B, Boxheimer L, Capone Mori A, Nuoffer J-M, Sargsyan Y, et al. How to detect isolated PEX10-related cerebellar ataxia? Neuropediatrics. 2022;53(3):159–66. pmid:35038753
- 45. Benkirane M, Marelli C, Guissart C, Roubertie A, Ollagnon E, Choumert A, et al. High rate of hypomorphic variants as the cause of inherited ataxia and related diseases: study of a cohort of 366 families. Genet Med. 2021;23(11):2160–70. pmid:34234304
- 46. Yamashita T, Mitsui J, Shimozawa N, Takashima S, Umemura H, Sato K, et al. Ataxic form of autosomal recessive PEX10-related peroxisome biogenesis disorders with a novel compound heterozygous gene mutation and characteristic clinical phenotype. J Neurol Sci. 2017;375:424–9. pmid:28320181
- 47. Kaya Özçora GD, Miyatake S, Matsumoto N, Canpolat M, Erdoğan M, Bayramov R, et al. PEX10-related autosomal recessive cerebellar ataxia with hearing loss. Acta Neurol Belg. 2020;120(2):429–32. pmid:30022445
- 48. Blomqvist M, Ahlberg K, Lindgren J, Ferdinandusse S, Asin-Cayuela J. Identification of a novel mutation in PEX10 in a patient with attenuated Zellweger spectrum disorder: a case report. J Med Case Rep. 2017;11(1):218. pmid:28784167
- 49. Sevim Bayrak C, Stein D, Jain A, Chaudhary K, Nadkarni GN, Van Vleck TT, et al. Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. Am J Hum Genet. 2021;108(12):2301–18. pmid:34762822
- 50. Klouwer FCC, Berendse K, Ferdinandusse S, Wanders RJA, Engelen M, Poll-The BT. Zellweger spectrum disorders: clinical overview and management approach. Orphanet J Rare Dis. 2015;10:151. pmid:26627182
- 51. Lu P, Ma L, Sun J, Gong X, Cai C. A Chinese newborn with Zellweger syndrome and compound heterozygous mutations novel in the PEX1 gene: a case report and literature review. Transl Pediatr. 2021;10(2):446–53. pmid:33708531