Introducing a novel homozygote TRAPPC10 mutation as a potential cause of developmental delay and intellectual disability in an Iranian family

doi:10.21203/rs.3.rs-5054100/v1

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Introducing a novel homozygote TRAPPC10 mutation as a potential cause of developmental delay and intellectual disability in an Iranian family

https://doi.org/10.21203/rs.3.rs-5054100/v1

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published 19 Nov, 2024

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Background

TRAPP complexes are crucial components for intracellular transport and cellular organization. Their role in vesicle trafficking, particularly through their involvement in the secretory pathway, make them more important in neurodevelopmental mechanisms. This study aims to identify a novel genetic variant, associated with developmental delay and intellectual disability by analyzing a consanguineous Iranian family.

Materials and Methods

Here, we performed whole-exome sequencing on an Iranian family, originating from a small population. The patient presented with severe developmental delay, microcephaly, and behavioral abnormalities. Through our analysis, we discovered a new biallelic variant on a previously introduced gene: TRAPPC10 (NM_003274.5): c.3222C > A; p.(Cys1074Ter) that is a potential cause for these specific clinical characteristics.

Results

Previous functional analysis suggest that the mutation causes premature termination of protein translation, likely leading to nonsense-mediated decay because of biallelic loss of functional TRAPPC10 protein which leads to severe developmental delay, microcephaly, and behavioral abnormalities such as aggression and autistic traits.

Conclusion

The aim of this research is to discover a novel variant in the TRAPPC10 gene that is responsible for a particular neurodevelopmental condition, dominantly characterized by developmental delay, intellectual disability, and microcephaly. These findings advance the comprehension of TRAPP-related diseases and emphasize the need for further exploration into the impact of TRAPPC10 on the development of the nervous system.

TRAPPC10

Intellectual Disability

Developmental Delay

Microcephaly

TRAPP II complex

Transport Protein Particles (TRAPPs) are highly conserved eukaryotic binding factor complexes that regulate vesicle-membrane fusion. Yeast was used for the first time to identify these complexes, and they contained multi-subunit structures made up of central and modular subunits[1]. There are three types of TRAPP complexes in yeast with different roles[2]: TRAPP I is involved in ER (Endoplasmic Reticulum)-to-Golgi transport, TRAPP II is involved in late Golgi trafficking, and TRAPP III is involved in autophagy.[3] Orthologues of all of the yeast TRAPP subunits have been identified in mammals and consist of those specific to TRAPP II and TRAPP III[4]. The structures of these complexes include central proteins that self-assemble to form a stable core. The TRAPP core connects to several side proteins to form two complexes known as TRAPP II (core plus TRAPPC9, TRAPPC10, and TRAPPC14[5]) and TRAPP III (core plus TRAPPC8, TRAPPC11, TRAPPC12, and TRAPPC13). Both TRAPP II and TRAPP III have a proven role in the secretory pathway[6]. The main roles of the TRAPP II complex include: the tethering of the coat Protein I (COPI) vesicle to the early Golgi, the activation of Rab1 and Rab18, two small GTP-binding proteins of the Rab family, intra-Golgi traffic, lipid droplet homeostasis, and ciliogenesis[7]. Recently, TRAPPPC14/C7orf43—another protein linked to the TRAPP II complex—was discovered. The TRAPPC14 plays a role in the binding of Rabin 8 to the TRAPP II complex and its tethering of the vesicles to the maternal centrosome during ciliogenesis. It is not required for activation of TRAPP II associated Guanine nucleotide Exchange Factor (GEF), and its absence has no impact on the assembly or stability of the TRAPP II complex. However, we need additional research to clarify the function of the TRAPPC14 subunit in the TRAPP II complex[8].

TRAPPC9 was suggested for having a role in intra‑Golgi and endosome‑to‑Golgi transport [9] such as activation of coat protein II (COP II) vesicle transport and NF-κB signaling[8]. TRAPPC10 interacts with different subunits and also acts as a GEF for key regulator proteins of all membrane trafficking events (Ypt/Rab GTPase) by activating Rab1 [10]. The site-directed mutation of TRAPPC10 highlights that, it might be involved in autophagy and cytoplasmic targeting of vacuoles and autophagy in Saccharomyces cerevisiae[11]. Mutation in various TRAPP subunits causes human inherited diseases, generally known as TRAPPopathies[7].

Symptoms of these diseases include: developmental delay; especially neurodevelopmental delay, severe intellectual disability (ID), spondyloepiphyseal dysplasia tarda (SEDT), primary or progressive microcephaly, hypotonia, craniofacial dysmorphism, and structural brain abnormalities (thinning of the corpus callosum and reduced white matter volume)[7].

Mutations, truncations, and deletions in the subunits of TRAPPII and TRAPPIII complexes are involved in these diseases[3, 8, 11].

TRAPPC2 protein is the only TRAPP component linked to skeletal dysplasia (Spondyloepiphyseal Dysplasia Tarda-SEDT), and nine other TRAPP subunits are related to neurodevelopmental disorders. Considering the fact that the clinical characteristics of these disorders, are similar[7, 8].

TRAPPC9 mutations impairs the transport of proteins recycled through early endosomes[12] Among the specific subunits of the TRAPP II complex, TRAPPC9 is strongly associated with human disease[2, 8].

Based on recent findings, biallelic TRAPPC10 gene variants Can cause a microcephalic neurodevelopmental disorder with other features like aggressive behavior and impaired speech ability[8, 13].

Here we are reporting a female patient that was born with developmental delay, microcephaly, obesity, and hypotony in 2013 in the Shahrekord, IRAN. Now in addition to that she also has some autistic behaviors and stereotypy.

2.1. Study subjects and Case description

The family enrolled in this study was referred to Sadra Medical Genetics laboratory, Shahrekord, Iran. In this paper we present a 9-year-old girl with developmental delay, microcephaly, autistic and stereotypy behaviors. Both parents are from the same ethnicity with a small population size (less than 50 families in a village). They are distantly related and the proband is their first and only affected child. The three-generation family pedigree was indicative of a disease likely inherited in autosomal recessive pattern (Fig. 1).

Mother reports that baby felt hungry after top feed and she could not stop her from eating. She also describes a history of seizures in the patient that has been controlled by phenobarbital. Unfortunately, there is no documented records regarding the patient's clinical symptoms since birth because the family was settled in a faraway area and they didn't have access to medical facilities. However, information from the child's current neurologist is provided in greater detail in Table 1.

Based on patient's clinical-diagnostic history, she underwent high resolution karyotype analysis and Multiplex Ligation-dependent Probe Amplification (MLPA) test to find out if the child affected with Prader-Willi Syndrome due to significant obesity, hypotony, and ID(when she was under one year old) which are very common amongst individuals with Prader-Willi Syndrome[14].

Table 1

The available clinical manifestations in proband.
Neurology
Any dysarthria	No speech
Cerebellar signs	+
Any gait abnormalities	-
Central tone	Hypotonia
Muscle atrophy	Mild atrophy
Upper limb tone, power and reflexes	DTR + 2
Lower limb tone, power and reflexes
Any history of seizers	+
Any other neurological abnormalities	Hypotony, Microcephaly
Behavioral characteristics	Autistic features, Stereotype behavior
Growth
Birth weight	3200 g
Birth head circumference	Not Available
height	Not Available
weight	Not Available
Head circumference	48 Cm
Development
Intellectual disability-Severity	Mental Retardation
Developmental regression	+
Developmental delay	+
Current gross motor skills	Unable to walk and on purpose movements
Problems with understanding	+
Problems with vision/eye abnormalities	There is no complete information in medical documents, No eye contact
Problem with hearing	+
Other physical findings
Dysmorphic features	Microcephaly
Physical abnormalities	-
Other relevant clinical manifestations	-
Drug history	Phenobarbital

2.2. Whole Exome sequencing and carrier detection

Whole-Exome Sequencing (WES) was advised to be carried out after the genetic counseling. 5 mL of venous blood samples were collected in EDTA-containing tubes. Genomic DNA was extracted using the standard salting-out method.

Genomic DNA was enzymatically fragmented, and regions of interest were selectively enriched using capture probes targeted against coding regions by SureSelect Human All Exon V7. Libraries were produced using Illumina-compatible adaptors and sequenced on an Illumina (HiSeq) platform leading to an average coverage depth of ~ 100X. The evaluation was focused on coding exons along with flanking +/-10 intronic bases within the captured region[15]. An end-to-end in-house bioinformatics workflow was applied, which included base calling, primary filtering of low-quality reads, suspected artifacts, and variant annotation.

2.3. Extending co-segregation to validate the pathogenicity of the causing variant

Variants were classified using multiple databases, including NCBI, OMIM, UCSC, Iranome (http://iranome.com/), PolyPhen, SIFT, and CADD Score. All registered genes in OMIM have been identified through clinical and functional studies in diagnostic laboratories and research centers, we noticed a novel homozygote stop gain variant in TRAPPC10 gene, introduced as a new variant of a previously introduced gene (OMIM#602103), responsible for microcephaly and intellectual disability. Finaly, the TRAPPC10(NM_003274.5 c.3222C > A; p(Cys1074Te) as a single nucleotide homozygous stop-gain variant in association with TRAPPC10 phenotype was suggested to the hospital medical team and after genotype-phenotype correlation confirmation, variant was organized to continue with sanger confirmation and family segregation.

Informed consent

was obtained from probands' parents prior to their inclusion to our study. They were informed about the purpose of study and rights to withdraw at any time. All the protocols were reviewed and approved by Sadra Medical Genetics Laboratory.

Segregation analysis showed that proband is homozygous for c.3222C > A variant (Fig. 2) with both parent heterozygote for it. This finding supports an autosomal recessive inheritance pattern, consistent with the clinical observations and family pedigree (Fig. 1), which represents it as a potential subject for further research. Given the crucial role of TRAPP complexes in intracellular transport processes, these neurological manifestations observed in the patient, all can be well understood.

This novel variant in the TRAPPC10 gene (OMIM# 602103), as a potential cause of the patient's condition opens new avenues for further studies to understand its role in neurodevelopmental disorders. The family has also been informed about the importance of these findings, including the potential genetic risks for future offspring.

TRAPPC10 protein, as a component of the TRAPP II complex, coordinates various cellular processes and is essential for vesicle-membrane fusion (in secretory pathways), and intracellular trafficking. Depletion or dysfunction of TRAPPC10 may led to abnormal Golgi trafficking system and accumulation of numerous secretory vesicles (Fig. 3). Mutations affecting TRAPP complex subunits, is associated with a broad spectrum of developmental disorders.

Here, we have evaluated an Iranian patient with congenital microcephaly and ID. The affected individual has been identified as homozygous for the TRAPPC10 gene (NM_003274.5): c.3222C > A;p. (Cys1074Ter) variant(Fig. 4.c). This stop-gain variant leads to premature translation termination and it is predicted to causes nonsense-mediated mRNA decay of the transcript and subsequent RNA degradation. It is in the 21st exon of the TRAPPC10 gene, located on the chromosome 21q22.3 region (refer to Fig. 4). The location of different variants are summarized in Table 2.

Previous studies have demonstrated that TRAPPC10, a specific component of the TRAPP II complex, has many interactions with other proteins such as TRAPPC9, TRAPPC2L, and TRAPPC2(Fig. 5)[7, 10]. Disruption of each one of them is anticipated to lead to abnormalities in TRAPP II complex activity, indicating that these proteins are likely to create a long and common interface.

As we shall illustrate in schematic view (Fig. 6), TRAPPC10 caps one end of the TRAPPII complex and TRAPPC9 caps the other end, and both are required for TRAPPII function and stabilization. These interactions reveal a tight relationship between two TRAPPII-specific subtypes, TRAPPC9 and TRAPPC10.

It is helpful to follow genotype-phenotype correlations that may contribute to the understanding of TRAPP II complex dysfunctions.

Prior research has extensively examined TRAPPC9 and its variants which is an autosomal recessive neurodevelopmental disorder (OMIM# 613192) characterized by postnatal-onset microcephaly with reduced white matter volume and corpus callosum thinning, ID, dysmorphic features, hypotonia, epilepsy, and raised body mass index and the most common clinical manifestations of the TRAPPC9 mutations are ID, microcephaly, developmental delay, dysmorphic facial features, autistic behaviors, and obesity[18–21]. Previous gene studies on mice with TRAPPC9 mutations, particularly females, exhibit obesity as a characteristic symptom[19].

Considering the effect of deletion either TRAPPC9 or both TRAPPC9 and TRAPPC10 in the manifesting of lipid droplets, it is critical to evaluate the lipid profile and Body Mass Index (BMI) in patients with both TRAPPC9 and TRAPPC10 malfunctions.

As we mentioned earlier, TRAPPC10 has cross-linking with TRAPPC2L (refer to Fig. 6). Mutant TRAPPC2L (P. (Ala2Tyr)) alters TRAPPC10's interaction with the TRAPPII core[10] and causes membrane trafficking delay as the main feature[7].

A prior investigation on TRAPP II complex, documents 2 cases with ID, neurodevelopmental delay, speech impairment, dystonia, and seizure with the TRAPPC2L mutation [10] this study has also mentioned rhabdomyolysis and post-infection encephalopathy as two new clinical manifestations.

The TRAPPC10 mutation-associated phenotype was first identified as a new potential variation responsible for ID in a Pakistani consanguineous family (family number 107)[13] with two affected children, homozygote for missense mutation in TRAPPC10 c.2786C > T; p. (Pro929Leu). In 2022, eight more affected individuals of another consanguineous Pakistani family, all homozygous for a frameshift mutation in TRAPPC10 c.3392delG; p. (Gly1131Valfs*19), have also been incorporated (Table 2)[8].

These cases share common clinical features (Table 2), such as ID, hypotonia, speech impairment, and abnormal behaviors with a broad range of different severities. Based on our current analysis of prior studies, the most prevalent clinical symptoms among patients with mutant TRAPPC10 are ID and significant developmental delay in all individuals. Behavioral abnormalities, including autistic features and aggression, are another universal feature in all eleven cases.

Our current case, as well as that of eight other patients, has speech impairment and hypotonia. Severe microcephaly (> 3 standard deviations below the mean) is seen in 9 patients, including ours; however, despite all previous cases of progressive microcephaly in the first year of life, our case has been reported for microcephaly at birth.

Five of all eleven cases have a history of seizures, and four of them, including our current patient, were seizure-free on medication. Considering the role of cellular trafficking proteins in the maintenance of neuronal integrity and nerve conduction [22], the occurrence of seizures and spontaneous movements is likely to be a plausible clinical feature, and all these brain abnormalities emphasize on the role of TRAPPC10 in brain development and function.

Obesity has been described as a common feature among patients with mutant TRAPPC9 but none of the previous ten cases with TRAPPC10 mutations reported it [8, 13] except for our present patient. We must consider that these variations are analyzed with a small sample size, which is a limitation of our investigation.

Table 2

A comparison between individuals with biallelic *TRAPPC10* variants.
	Current study	8 individuals of a family [8]								2 individuals of another family[13]
ID and Developmental Delay	+	+	+	+	+	+	+	+	+	+	+
Behavioral Abnormalities	+	+	+	+	+	+	+	+	+	+	+
Microcephaly	+	-	+	+	+	+	+	+	+	+	+
Speech Impairment	None verbal	< 10 words	None verbal	< 10 words	None verbal	< 10 words	None verbal	< 10 words	< 10 words	impaired speech ability	impaired speech ability
Vision	NL	NL	NL	NL	NL	NL	NL	Strabismus	NL	Strabismus	Strabismus
Seizure	+	+	+	-	+	-	-	-	+	-	-
Obesity	+	-	-	-	-	-	-	-	-	-	-
Gait Abnormality	+	-	+	-	-	-	-	+	+	NK	NK
Hypotonia	+	+	+	+	+	+	+	+	+	NK	NK
HGVS Coding and Protein	c.3222C > A; p(Cys1074Te)	c.3392delG; p.(Gly1131Valfs*19)								c.2786C > T; p.(Pro929Leu)
Transcript	NM_003274.5	NM_003274.5								NM_003274.5
Pathogenicity	Likely pathogenic	Pathogenic								Pathogenic/Likely pathogenic
Location	Exon 21	Exon 22								Exon 18
*NK: Not Known

Mutations at distinct locations within the TRAPPC10 gene may explain the variation in clinical presentations. Clinical manifestations mentioned in this article are frequently observed in individuals with TRAPP protein abnormalities, as such mutations impinge upon Golgi trafficking, thereby contributing to symptomatology.

Based on the data provided here, evaluating different variants depends on clinical presentations. As it mentioned before, more studies warranted for evaluating the effects of different variants.

This study highlights the need for comprehensive genetic screenings in families with a prevalence of neurodevelopmental disorders, particularly in regions with small gene pools and consanguinity which may be facilitated by expanding genetic databases and utilizing advanced sequencing technologies. As a diagnostic laboratory in Iran, we were unable to conduct functional study and more evaluation about this novel nonsense mutation.

Moreover, to understand the genotype-phenotype correlation, further investigations and long-term follow-up studies are also warranted.

Ethical considerations

Informed consent was obtained from probands' parents prior to their inclusion to our study. They were informed about the purpose of currant study and gave written informed consent for publication. All the protocols were reviewed and approved by Sadra Medical Genetics Laboratory ethic committee(ET-1401-58).

Conflicts of interest

Ahoura Nozari, Setareh Banitalebi, Paria Babaahmadi, Narges Jalilian, Taha Sadeghi,and Mahdieh Hasani declare that they have no conflict of interest.

Funding sources

There is no financial support in this study.

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No competing interests reported.

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You are reading this latest preprint version

Introducing a novel homozygote TRAPPC10 mutation as a potential cause of developmental delay and intellectual disability in an Iranian family

Status:

Journal Publication

Version 1

Abstract

Background

Materials and Methods

Results

Conclusion

Figures

1. Introduction

2. Material and Methods

2.1. Study subjects and Case description

2.2. Whole Exome sequencing and carrier detection

2.3. Extending co-segregation to validate the pathogenicity of the causing variant

3. Results

4. Discussion

Declarations

References

Additional Declarations

Status:

Journal Publication

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