Characterization of a novel inherited splice-site variant in MAPK8IP3 expands the genetic and phenotypic spectrum of neurodevelopmental disorders

Abstract

Background

The MAPK8IP3 gene encodes JIP3, a kinesin-1 adapter protein crucial for axonal transport and JNK signaling pathway regulation. This gene exhibits extreme intolerance to loss-of-function variants. Heterozygous pathogenic MAPK8IP3 variants are linked to a neurodevelopmental disorder with or without variable brain abnormalities (NEDBA). This study characterizes a novel inherited canonical splice-site variant identified in a three-generation family.

Methods

Exome sequencing was performed on three affected individuals from a single non-consanguineous family with presenting neurological abnormalities. The molecular consequences of the identified variant were evaluated by RNA analysis. Clinical features of the variant carriers were evaluated in detail.

Results

We identified a heterozygous dinucleotide deletion (c.2630-2_2630-1del) at the canonical acceptor splice site of MAPK8IP3. This variant co-segregated with the neurological phenotype in an affected mother and her two children. RNA analysis demonstrated that this variant leads to a partial deletion of exon 22 (r.2630_2673del), which is predicted to cause a frameshift and introduce a premature termination codon (p.Gly877Valfs∗36). Notably, despite carrying an identical genotype, the three affected individuals exhibited marked interindividual variability in clinical severity, ranging from mild specific learning difficulties to global developmental delay with severe intellectual disability and autism.

Conclusion

This represents the first report of a familial, autosomal dominantly inherited pathogenic splice-site variant in MAPK8IP3, extending the established inheritance pattern beyond previously described de novo events. Our findings expand both the mutational and phenotypic spectrum of MAPK8IP3-related disorders, highlighting the complexity of genotype-phenotype correlations and underscoring the necessity of functional assays for accurate variant interpretation.

Highlights

• •Exome sequencing identified a splice-site variant in the MAPK8IP3 gene.
• •Aberrant transcript with a partial exon 22 deletion verified by RNA analysis.
• •The inherited variant exhibits variable expressivity in a family.
• •This variant may lead to a milder phenotypic manifestation.

1. Background

The Mitogen-Activated Protein Kinase 8 Interacting Protein 3 (MAPK8IP3) gene is located on chromosome 16p13.3 and encodes c-Jun NH2-terminal kinase (JNK)-interacting protein 3 (JIP3, also known as SYD2 or JSAP1), which is a member of the kinesin superfamily of proteins and plays a critical role in axonal transport [1,2]. As a scaffold protein, MAPK8IP3/JIP3 interacts with specific components of the JNK pathway, regulating the efficiency and specificity of signal transduction [3,4]. Additionally, it interacts with components of the kinesin-1 motor to mediate anterograde transport of various cargoes along the microtubule network, from the neuronal cell body to the synapse [2,[5], [6], [7]]. This process is crucial for maintaining neuronal health, polarity, and synaptic function.

JIP3 orthologs function as essential regulators of axonal transport; loss-of-function of these orthologs causes disrupted axonal transport and subsequent neuronal degeneration in both vertebrates and invertebrates [1,8,9]. In mouse models, heterozygous loss of Mapk8ip3 (Mapk8ip3^+/−) exhibits normal viability and fertility, without observable anatomical or histological abnormalities. In contrast, homozygous null mutants (Mapk8ip3^−/−) display neonatal lethality caused by respiratory failure [10]. Mice with a double-knockout of Mapk8ip3 and Jlp in the dorsal telencephalon result in severe defects in kinesin-1-dependent axonal transport, leading to axonal dystrophy and progressive neuron degeneration [11]. Similarly, rat models with heterozygous Mapk8ip3 deletion leads to a reduction in the axonal length of hippocampal neurons compared to wild-type controls [6]. In humans, de novo heterozygous variants in the MAPK8IP3 gene have been associated with neurodevelopmental disorder with or without variable brain abnormalities (NEDBA, OMIM #618443). Affected individuals present with global developmental delay apparent from infancy or early childhood, resulting in mildly delayed walking, variably impaired intellectual development, and poor or absent speech [1,8]. Brain imaging reveals structural anomalies in approximately 50% of affected individuals. Additional variable features may involve hypotonia, spasticity, ataxia, seizures, or nonspecific dysmorphic facial features.

The MAPK8IP3 gene exhibits extreme intolerance to heterozygous loss-of-function (LOF) variants in humans, as evidenced by a pLI (probability of being loss-of-function intolerant) score of 1.00 and a LOEUF (LOF observed/expected upper bound fraction) score of 0.41. Consistent with this, the pHaplo (probability of haploinsufficiency) score of 0.93 further supports its haploinsufficiency. Despite the established association between de novo MAPK8IP3 variants and NEDBA, the precise molecular consequences of splice-site variants remain poorly defined. Furthermore, the full genotypic and phenotypic spectrum of MAPK8IP3-related disorders has yet to be fully characterized. To address these knowledge gaps, we conducted comprehensive clinical and molecular investigations in a family segregating a MAPK8IP3 splice-site variant. Functional RNA analysis revealed that this variant causes a partial deletion of exon 22, resulting in a frameshift and a premature termination codon. Notably, the disorder exhibits variable expressivity: the affected mother and her two children, despite sharing the identical splice-site alteration, present with markedly divergent clinical severity ranging from mild learning difficulties to global developmental delay. Together, these findings validate the pathogenic splicing defect of the variant and expand both the mutational and phenotypic spectrum of MAPK8IP3-related disorders.

2. Materials and methods

2.1. Participants and ethical approval

All study participants, including both patients and healthy control individuals, were enrolled from the Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region. The research protocol was reviewed and approved by the Medical Ethics Committee of the Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region (approval number 2024–8/44). Written informed consent was obtained from the parents or legal guardians of all participants prior to inclusion in the study.

2.2. Exome sequencing (ES) and variant analysis

Genomic DNA was extracted from peripheral blood samples of all participants utilizing a Lab-Aid 824s DNA Extraction Kit (ZEESAN Biotech Co., Ltd., Xiamen, China). Library construction was performed using an Agilent SureSelect Human All Exon V6 kit (Agilent Technologies, CA). The resulting libraries underwent paired-end sequencing on an Illumina HiSeq 2500 platform (Illumina, CA). Following the removal of redundant reads, sequencing data were aligned to the human reference genome GRCh37/hg19 using BWA software (http://bio-bwa.sourceforge.net/). Variant calling was subsequently conducted with the Genome Analysis Toolkit (GATK) HaplotypeCaller (https://github.com/broadinstitute/gatk/). Identified variants were annotated and classified using TGex software (LifeMap Sciences, USA). The variant filtering process was performed as follows: (i) variants with a minor allele frequency >1% in public databases (e.g., ESP, 1000 Genomes, gnomAD) or an internal population database were excluded; (ii) exonic variants and canonical or near-canonical splice-site variants (located within ±10 bp of exon-intron boundaries) were retained; (iii) remaining variants were prioritized based on predicted functional impact using multiple in silico tools; and (iv) all prioritized variants were evaluated and classified in accordance with the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines [12]. Splice site variants were assessed using SpliceAI (https://github.com/Illumina/SpliceAI, version 1.3.1) to predict their potential effects on mRNA splicing (threshold ≥0.2). Additionally, the functional consequences of missense variants were evaluated using multiple computational prediction tools, including SIFT (http://sift.bii.a-star.edu.sg/), PROVEAN (http://www.provean.jcvi.org/), MutationTaster (http://www.mutationtaster.org/), and the REVEL tool (https://sites.google.com/site/revelgenomics/).

2.3. Sanger sequencing

PCR amplifications were performed in a reaction volume of 25 μL, which included 2 units of Taq DNA polymerase (Takara Biotechnology, Dalian, China). Subsequently, the purified PCR products were sequenced bidirectionally using both forward and reverse primers on an ABI 3130 Genetic Analyzer (Applied Biosystems, CA, USA).

2.4. RNA sequencing

Total RNA was isolated from peripheral blood samples obtained from the proband, two family members (mother, sister), and three unrelated healthy controls, using the RNAprep Pure High Efficiency Total RNA Extraction Kit (TIANGEN, Beijing, China). RNA-Seq libraries were prepared from 100 ng to 1 μg of DNase-treated RNA through ribodepletion with the Ribo-off Human/Mouse/Rat Globin & rRNA Depletion Kit (Nanjing Novozymes Biotechnology Co., Ltd., Nanjing, China). Library construction was subsequently performed using the DNBSEQ-T7RS High-throughput Sequencing Kit (FCL PE150) V2.0 (BGI Genomics, Shenzhen, China). Sequencing of the prepared libraries was conducted on the DNBSEQ-T7 platform (MGI Tech, China) following the manufacturer's instructions. Quality control was performed on raw sequencing reads using Trimmomatic (v0.36). Clean reads were aligned to the human reference genome GRCh37/hg19 using HISAT2 (v2.2.1). Single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) were identified with GATK (v3.5). Alternative splicing events were analyzed using SplAdder (v2.4.2); and fusion genes were detected using STAR-Fusion (v1.10.1). Gene expression levels were quantified using RSEM (v1.3.0), and differentially expressed genes were identified with EBSeq (v1.26.0).

2.5. cDNA sequencing and TA cloning

Total RNA was isolated from leukocyte pellet using TRIzol reagent (ThermoFisher Scientific^Tm, USA). Subsequently, 1 μg of total RNA was reverse-transcribed into cDNA using the RevertAid First Strand cDNA Synthesis Kit (ThermoFisher Scientific^Tm, USA). The resulting cDNA was amplified by PCR using LA Taq DNA polymerase (Takara, Beijing, China) with the following gene-specific primers: forward primer 5′–CCAGTTCACCGTCTGCAAC–3' (E20F) and reverse primer 5′–CTGCTGCTGTCAGGCTCTG–3' (E23R). The PCR products were resolved by electrophoresis on a 2.5% agarose gel and subsequently sequenced using an ABI 3130 genetic analyzer (Applied Biosystems, USA). The amplified cDNA fragments were purified and cloned into the pEASY-T5 Zero Cloning Vector (TransGen Biotech, Beijing, China) via TA cloning. Positive clones identified by colony PCR screening were further validated through Sanger sequencing. All experimental procedures were conducted in accordance with the manufacturers' instructions.

3. Results

3.1. Clinical presentation

The proband (III:2) was a 4-year-old Chinese boy who was the second child of non-consanguineous parents (Fig. 1A). He was born after an uneventful pregnancy and delivered at full term. His developmental milestones were delayed with raising head at 5 months, sitting alone at 8 months, walking at 21 months. Additionally, he displayed deficits in social interaction and communication, such as not responding to his name when being called, avoiding eye contact, not following oral instructions, amusing himself, and avoiding interacting with peers or family members. At the age of two, the individual received a clinical diagnosis of autism and was subsequently enrolled in a rehabilitation program. At the age of 3 years and 11 months, he was administered the Gesell Developmental Scale assessment, which revealed severe global developmental delay: gross motor skills development quotient (DQ) = 51; fine motor skills DQ = 26; adaptive ability DQ = 25; verbal ability DQ = 33; and social ability DQ = 33. The patient and his parents then sought genetic diagnosis at our department. His anthropometric measurements were within normal ranges: height 98 cm (−1.2 SD), weight 17 kg (0.2 SD), and head circumference 52.5 cm (1.7 SD). He could say some simple short sentences, but had no spontaneous speech. Aside from an inguinal hernia, the patient exhibited no congenital malformations or craniofacial anomalies. Diagnostic imaging, including chest and spine X-rays, echocardiography, abdominal ultrasound, electroencephalography (EEG), and brain magnetic resonance imaging (MRI), revealed normal findings. In addition, his mother (II:2) exhibited mild learning difficulties, and his elder sister (III:1) presented with delayed language development and learning difficulties. According to the proband's mother, the maternal grandmother (I:2) has been unable to walk since childhood due to rheumatoid arthritis.

Fig. 1.

Pedigree and DNA sequencing results. (A) Pedigree chart of the family with corresponding phenotypes. RA: rheumatoid arthritis; LD: learning difficulty; SD: speech delay; GDD: global developmental delay; ASD: autism spectrum disorder; ES, exome sequencing; RS, RNA sequencing. Arrows denote the probands. Genotypes are indicated below each individual: +, wild-type allele; –, mutant allele. (B) Identification of variants by Sanger sequencing. Variant site is indicated by red arrows. (C) Mutation spectrum of the MAPK8IP3 gene (NM_001318852.2). RH1 and RH2, Rab-interacting lysosomal protein (RILP) homology 1 and 2; LZ, leucine zipper; WD40, WD40 repeated domain. Missense mutations are represented by dots, nonsense mutations by squares, splicing mutations by diamonds, and frameshift mutations by triangles. The variant identified in this study is highlighted in red.

3.2. Genetic analysis

Exome sequencing of the proband generated 18.2 Gb of clean data, with ≥98% of bases achieving a Q30 score and a uniform base distribution. The mean sequencing depth across the target region was 208.4 × , and 99.21% of the target exome was covered at least 20 × . A total of 108,580 variants were initially detected. After filtering out common variants with a minor allele frequency >1% in public population databases and synonymous variants, 571 rare coding and splice-site variants were retained. No rare recessive variants that fully co-segregated with the clinical phenotype or were predicted to be pathogenic were identified. Clinical phenotype analysis highlighted three candidate heterozygous variants in autosomal dominant genes–NFIB, EP300, and MAPK8IP3–that were of special interest. These variants were subsequently validated by Sanger sequencing of samples obtained from the patient's parents (Table S1). The c.43T > C variant in NFIB was inherited from the proband's unaffected father, whereas the c.5987G > A variant in EP300 and the c.2630–2_2630–1del variant in MAPK8IP3 were derived from the maternal lineage. Further segregation analysis traced the EP300 variant to the proband's unaffected maternal grandfather and the MAPK8IP3 variant to the maternal grandmother. The two missense variants were predicted to be neutral or tolerated by multiple prediction software tools and were inherited from asymptomatic family members; consequently, they were classified as variants of uncertain significance (PM2_supporting; BP4). The dinucleotide deletion in the MAPK8IP3 gene (NM_001318852.2), situated at the splice acceptor site of intron 21, is hypothesized to result in aberrant splicing events. This alteration is regarded as a potential pathogenic mechanism in affected individuals. Segregation analysis by Sanger sequencing revealed that both the proband's grandmother and sister are heterozygous for this variant (Fig. 1B; Table S1). Considering the pronounced phenotypic heterogeneity observed among the four variant carriers within this family, we conducted exome sequencing on additional family members (Fig. 1A). This analysis excluded the presence of other pathogenic variants that might contribute to the observed phenotype.

To assess the effect of this variant on mRNA, total RNA was extracted from the leukocytes of the proband and his family members (Fig. 1A). RNA sequencing analysis indicated that the deletion induces aberrant splicing in approximately half of the transcripts on average (mother: 23/52, 44%; proband: 29/50, 58%; sister: 18/39, 46%) by activating a cryptic splice acceptor site in exon 22, causing a partial deletion of exon 22 (Fig. 2A). Subsequent analysis using RT-PCR and cDNA sequencing verified the presence of an aberrant transcript (Fig. 2B and C). To determine the sequence of the abnormal transcript, the purified PCR products were cloned into a T-vector and sequenced. An aberrant transcript with a partial deletion of exon 22 (r.2630_2673del), observed in approximately 44% of the clones (8 out of 18), was identified (Fig. 2D). This deletion induces a frameshift effect, resulting in the formation of a premature stop codon (p.Gly877Valfs∗36). Based on the ACMG/AMP guidelines, the variant was classified as likely pathogenic, with evidence criteria including PVS1 and PM2_supporting.

Fig. 2.

mRNA analysis of the MAPK8IP3 splice-site variant. (A) Sashimi plot revealed that the variant caused aberrant splicing, resulting in the deletion of part of exon 22 in patients compared with healthy controls. The region of differential RNA splicing is indicated by a gray background. (B) RT-PCR products of MAPK8IP3 mRNA transcripts from patients and healthy controls were separated by electrophoresis on a 2.5% agarose gel. A smaller mutant product (409 bp) is present in family members but absent in controls. (C) Sanger sequencing of the cDNA revealed a double-peak chromatogram pattern starting from position r.2630. (D) Sequencing results of TA clones. The corresponding physical maps are shown above the sequence diagrams; upper panel, wild-type; lower panel, aberrant transcript with partial exon deletion (44 bp of exon 22).

4. Discussion

In this study, we identified a dinucleotide deletion at the canonical acceptor splice site of the MAPK8IP3 gene, which leads to a partial exon 22 deletion. This variant segregates within a family, representing the first documented instance of familial transmission, in contrast to the predominantly de novo variants reported previously. Affected family members, despite carrying the identical variant, exhibited marked intrafamilial phenotypic heterogeneity, ranging from mild learning difficulties to global developmental delay with autism. The proband exhibited only core neurodevelopmental features and had a normal brain MRI. None of the affected individuals exhibited common variable features such as hypotonia, spasticity, ataxia, seizures, or dysmorphic features. This collective profile suggests a milder phenotypic manifestation within the MAPK8IP3-related disease spectrum.

The JNK signaling pathway is integral to numerous physiological and pathological processes, encompassing cell proliferation, differentiation, apoptosis, stress responses, and immune regulation. As a crucial mediator of the JNK pathway, JIP3 coordinates the axonal transport of lysosomes and JNK signaling components. Its deficiency in neuronal cells leads to the accumulation of cargo, ultimately resulting in impairment of the axonal cytoskeleton [[13], [14], [15], [16]]. MAPK8IP3 variants, such as the c.1364A > G (p.Glu455Gly) variant associated with Smith-Magenis-like syndrome and the de novo c.281A > G (p.Tyr94Cys) variant identified in a large autism cohort, collectively underscore the importance of MAPK8IP3 in neurodevelopment [17,18]. Subsequent investigations have confirmed de novo MAPK8IP3 variants as causative factors in NEDBA [1,8,19]. Moreover, the occurrence of compound heterozygous variants in the MAPK8IP3 gene associated with spinal muscular atrophy-like phenotypes have been documented [20]. In addition, studies in murine and human neurons have shown that JIP3 deficiency leads to focal axonal lysosome accumulation and increased Aβ peptide production [15,16,21]. Based on these findings, it has been proposed that JIP3 dysfunction could be a potential contributor to neurodegenerative processes, such as those observed in Alzheimer's and Parkinson's diseases [15,16,21,22]. Typically, pathogenic MAPK8IP3 variants result in loss-of-function effects on endosomal trafficking, leading to cytotoxic cargo accumulation [8]; however, rare gain-of-function mutations, such as c.1732C > T (p.Arg578Cys, R578C), can aberrantly activate the JNK pathway and induce neuronal apoptosis. The toxic gain-of-function effect is supported by in vivo evidence, as expression of the R578C variant in zebrafish neurons recapitulates the axonal varicosity phenotype observed in knockout mice [1,23]. In vitro investigations further revealed that a non-allele-selective antisense oligonucleotide (ASO), which reduces the expression of both mutant and wild-type JIP3, was well tolerated and efficacious in patient-derived neuronal cells. This approach may therefore represent an ideal therapeutic approach for individuals with toxic gain-of-function mutations in JIP3 [23].

The core symptoms of NEDBA, as established in the literature, include global developmental delay and variable intellectual disability (ID), with onset in infancy or early childhood [1,8]. Additionally, four individuals were diagnosed with autism spectrum disorder (ASD). Structural brain anomalies were observed in over half of the reported patients, affecting both cerebral and cerebellar structures. In this study, the proband presented with global developmental delay and ASD, with limited clinical improvement prior to genetic diagnosis. Notably, his brain MRI revealed no structural abnormalities, and physical examination showed no other systemic findings. This contrasts with the high frequency of brain anomalies reported in the general NEDBA population. The other affected family members exhibited milder neurological manifestations compared to the proband. However, cranial MRI was not performed for these individuals; consequently, the presence or absence of structural brain anomalies in these cases remains undetermined. It should be noted that only the proband underwent standardized developmental assessment in this study; formal cognitive and neurological evaluations were not performed in the remaining family members, including the mother, sister, and maternal grandmother. Furthermore, the grandmother's developmental history during childhood is unknown; therefore, discussions regarding clinical phenotypic heterogeneity should be approached with caution.

Notably, seizures were observed exclusively in six individuals with NEDBA who harbored missense variants, suggesting a potential genotype-phenotype correlation. Among these six patients, the R578C variant was the most prevalent, identified in four individuals (Table 1). Furthermore, published data indicate that individuals harboring the R578C or R1146C variants exhibit a more severe disease phenotype compared to those with other MAPK8IP3 variants [1,8]. This severe phenotype is characterized by more pronounced intellectual disability (30% moderate, 60% severe, and 10% profound), marked language impairments ranging from single words to complete non-verbal communication, and a higher incidence of motor deficits, including spastic diplegia and wheelchair dependence. Structural brain abnormalities are also consistently reported in this subgroup. While these findings suggest a potential genotype-phenotype correlation, the limited number of reported patients and the lack of functional evidence for most variants warrant cautious interpretation.

Table 1.

Summary of clinical presentation of individuals with causative MAPK8IP3 variants.

The global prevalence of ID is estimated at approximately 1% of the general population and is etiologically heterogeneous, with genetic factors playing a major role [24,25]. Establishing a molecular diagnosis is therefore critical, as it can inform prognosis, guide clinical management, and enable accurate recurrence risk counseling. In the present case, the proband's mother completed junior high school, but reported experiencing academic challenges during childhood and has no history of employment in adulthood. Although she exhibited no significant communication deficits, her accounts of the family history are somewhat vague. She reported unverified conditions among her maternal relatives, including macrocephaly, speech impairment, and esophageal malformations. The potential relationship between these family-reported abnormalities and the identified genetic variant in the proband remains unclear, as the relatives were not available for evaluation. Beyond the primary genetic variant, additional factors such as the individual's genetic background, epigenetic regulation, and environmental exposures may also contribute to the observed intrafamilial phenotypic variability. Although no secondary variants directly impacting neurodevelopment were identified in the proband's exome data, our understanding of these other potential contributors remains incomplete.

We acknowledge several important limitations of this study. First, as a single-family case report, the generalizability of our findings is inherently limited, and the observed phenotypic variability may not represent the broader spectrum of MAPK8IP3-related disorders. Second, while we assessed mutant transcript levels, our study lacks comprehensive functional validation, such as experiments in patient-derived cells or animal models, which are necessary to confirm the underlying disease mechanism. Third, our RNA analysis did not provide definitive evidence for nonsense-mediated mRNA decay (NMD); more robust RNA expression studies, such as allele-specific expression analysis and quantitative PCR with and without NMD inhibition, were not performed. The absence of evidence for pre-mRNA degradation leaves open the possibility that haploinsufficiency, if present, may not be the sole or fully penetrant mechanism. This is consistent with reports of asymptomatic carriers of loss-of-function variants [20], suggesting that genotype-phenotype correlations remain highly uncertain. Therefore, although truncating MAPK8IP3 variants are suspected to cause disease, the precise pathogenic mechanism-and its variable expressivity within families-has yet to be elucidated. Future studies involving larger cohorts and integrated functional assays are essential to establish more accurate genotype-phenotype correlations.

5. Conclusion

Through extended pedigree exome sequencing and RNA analysis, this study identified and characterized an inherited splice-site variant in MAPK8IP3 in a family exhibiting a broad spectrum of neurological phenotypes. This study expands the known mutational spectrum of the MAPK8IP3 gene (Fig. 1C). Further case studies and functional investigations are required to elucidate the precise pathogenic mechanisms underlying MAPK8IP3-related disorders and to clarify genotype-phenotype correlations.

CRediT authorship contribution statement

Conceptualization and visualization: Sheng Yi, Zailong Qin, Jingsi Luo; Software: Shang Yi; Data curation: Sheng Yi, Limei Huang; Resources: Xiong Song, Qi Yang, Jingsi Luo; Formal analysis: Sheng Yi, Shang Yi; Supervision: Zailong Qin, Jingsi Luo; Funding acquisition: Sheng Yi, Jingsi Luo; Investigation and validation: Sheng Yi, Qi Yang, Limei Huang; Methodology: Sheng Yi, Shang Yi, Zailong Qin, Jingsi Luo; Writing – original draft and review & editing: Sheng Yi, Zailong Qin, Jingsi Luo; Project administration: Zailong Qin, Jingsi Luo.

Ethics approval and consent to participate

The study was approved by the ethics committee of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region. Written informed consents were obtained from parents or guardians of all patients. All methods were performed in accordance with the ethical standards as laid down in the Declaration of Helsinki and its later amendments or comparable ethical standards.

Funding

This work is funded by Guangxi Medical and Health Appropriate Technology Development and Application Project (S2024083), Guangxi Science and Technology Program (21-220-22 and GuiKe LT2600640039), and Health Department of Guangxi Zhuang Autonomous Region (Z20200678 and Z–A20220314).

Declaration of competing interest

The authors declare that they have no competing interests.

Abbreviations

NEDBA

neurodevelopmental disorder with or without variable brain abnormalities

MAPK8IP3

The Mitogen-Activated Protein Kinase 8 Interacting Protein 3

JNK

c-Jun NH2-terminal kinase

JIP3

JNK-interacting protein 3

LOF

loss-of-function

pLI

probability of being loss-of-function intolerant

LOEUF

the LOF observed/expected upper bound fraction

pHaplo

the probability of haploinsufficiency

ES

exome sequencing

GATK

Genome Analysis Toolkit

ACMG/AMP

American College of Medical Genetics and Genomics and the Association for Molecular Pathology

EEG

electroencephalography

MRI

magnetic resonance imaging

MAF

minor allele frequencies

NMD

nonsense-mediated mRNA decay

ID

intellectual disability

Appendix A. Supplementary data

The following is the Supplementary data to this article:

Data availability

Data will be made available on request.