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.