A Neurodevelopmental Disorder with Intellectual Disability and Autism due to MAP7D3 Haploinsufficiency

We report on a young boy with a neurodevelopmental disorder who is a carrier of a novel frameshift mutation in gene MAP7D3 (MAP7 domain containing 3) of Xq26.3. The protein encoded by this gene belongs to the MAP7 (microtubule associated protein 7) family that is proposed to regulate kinesin-1 (KIF5B)-dependent intracellular transport, by acting as Microtubule (MT)-tethered recruitment factors and activators of this kinesin [1-3]. And as other MT-associated proteins is conceivable the involvement of MAP7D3 in neuronal morphogenesis and therefore in neurodevelopmental disorders.

The findings described here arise from the genomic analysis of an 11-year-old boy under investigation for the last five years for a disorder with Global Developmental Delay (GDD), marked difficulty in language acquisition and learning, as well as Attention-Deficit/Hyperactivity and Autism Spectrum Disorders (ADHD, ASD). He lacks dysmorphic features and additional relevant findings, including those of chromosome studies (normal 46,XY karyotype), a genomic CGH-array (750 K), brain MRI, sleep EEG, and diverse clinical analyses, including that of 5'UTR CGGn sequence of gene FMR1 involved in most cases of fragile X syndrome, with normal results (a sequence of normal size, with 30 CGG triplets). He does not have a family history of interest, being a descendant of healthy fathers, like his twin brother.

Clinical exome analysis

It was undertaken with Illumina NGS (Next Generation Sequencing) procedures, initially (in the year 2018) with the TruSight One Sequencing Panel (for 4.813 genes) and later on (in year 2020) based on WES (Whole Exome Sequencing, with the use of IDT probes) as described in detail at Illumina, https://www.illumina.com. It resulted in the discovery in 2018 of frameshift novel mutation T821RfsX8 (p.Thr821ArgfsTer8) in gene MAP7D3, which is considered the only relevant genomic finding for the evaluation of patient disorder. No other mutations of interest, including exon deletions and duplications, were discovered with the evaluation of numerous genes with proposed association to cardinal features of the patient disorder according to HPO database (> 1700, > 900, > 340, and > 600 genes of GDD, delayed speech and language development, ADHD and ASD, respectively) submitted to WES variant analysis with use of two different pieces of software, of Variant Interpreter (Illumina) and Franklin (Genoox; https://franklin.genoox.com).

As it is depicted by figures 1A-C frameshift mutation T821RfsX8 is due to variant c.2461_2462insGGACA of exon 16 (in reference sequence NM_024597.4), present in a hemizygous pattern in all single sequences in the NGS BAM file of the patient (Figure 1B). The mutation is derived from a maternal allele not inherited by the twin brother (Figure 1C), who, like the mother and the father, is healthy.

Figure 1: T821RfsX8 mutation of gene MAP7D3.
A): The mutation was identified in a young boy with GDD (global developmental delay), no speech, ADHD (attention-deficit/hyperactivity disorder), and ASD (autism spectrum disorder), derived from the mother.
B): It is deduced from variant c.2461_2462insGGACA (in sequence NM_024597.4), observed in the patient with a hemizygous pattern, in all single sequences of NGS BAM viewed with IGV (https://software.broadinstitute.org).
C): Variant c.2461_2462insGGACA viewed with Sanger sequencing.

Further, and as it is shown by figures 2A & B T821RfsX8 mutation is located at the C-terminal end of MAP7D3 protein, far from exon 8 nonsense mutation D304X (p.Asp304Ter) due to variant c.909_910insTA (referred to sequence NM_024597.4) reported by Monies, et al. [4] as a finding of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. It was identified in an 8-year-old boy, a descendant of non-consanguineous healthy parents, affected by GDD, ADHD, no speech, and mild hepatosplenomegaly. The finding of the mutation, described as c.804_805insTA in sequence NM_001173517.1, hemizygous and inherited from the heterozygous mother, led to the authors to propose to MAP7D3 as a candidate gene for the patient disorder considering the nature of the novel and truncating variant identified as well as the probable involvement of MAP7D3 in neurodevelopmental disorder, a speculation supported by the implication of MAP7 protein in neuronal morphogenesis [5], role of MTs in regulating neurons and therefore brain development [6] and growing evidence of association of mutations in MT-associated proteins to different neurodevelopmental disorders, including intellectual disability and ASD [6-10]. In this way, an involvement in intellectual disability has been reported for kinesin genes, motor proteins that control both intracellular cargos transport and MTs cytoskeleton organization. Among them, for KIF4A and KIF5C [11]. In case of KIF4A of Xq13.1 observed in 4 affected males of a family with X-linked mild to moderate mental retardation, poor speech and seizures (described in OMIM as Intellectual developmental disorder, X-linked 100; https://www.omim.org/entry/300923) all carriers of hemizygous KIF4A mutation c.1489-8_1490delins10 (in sequence NM_012310.4) resulting in disruption of the exon 15 acceptor splice site leading to an in-frame deletion of exon 15 from the protein, a genotype that segregated with the disorder in the family [11]. Besides, KIF5B coding for kinesin-1 interacting with that of MAP7D3 has been proposed as a candidate gene for neurological diseases following the identification of homozygous KIF5B missense variant p.His751Arg (NM_004521.3:c.2252A>G) that segregated in two brothers with a disorder including developmental and speech delay [12].

Figure 2: T821RfsX8 and D304X mutations of gene MAP7D3, indicated in schematic representations of genomic exon-intron structure A) and protein B).

Our data would reinforce the concept of a neurodevelopmental disorder due to haploinsufficiency of MAP7D3, according to X-Linked Recessive (XLR) inheritance. It would constitute a disorder associated with a specific function of MAP7D3, excluding redundant functions of MAP7 proteins, whose precise delineation requires necessarily more data from replication studies and gene functions. It would probably be compatible with the continuum of a moderate neurodevelopmental phenotype without congenital cerebral malformations. In this regard, the lack of Autism (ASD) in the Saudi Arabia patient, but present in our patient, may represent genotype-phenotype association differences attributable to the location of mutations and the predicted protein alteration. Nonsense mutation D304X of Saudi Arabia patient would yield truncated short molecules presumably fully defective, at least for interactions with kinesin-1. By contrast, frameshift mutation T821RfsX8 of our patient would yield larger and partially functional MAP7D3 molecules, although defective in the MDCT domain, retaining the MAP or kinesin-1 binding region (MD) but lacking the C-Terminal Tail (CT) that according to results of in vitro assays would have a role in regulating microtubule assembly and stability [1-3].

Authors get parental permission for publication of patient and family data.

They declare that there is no conflict of interests regarding the publication of this paper.

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