HGNC Approved Gene Symbol: TRIO
Cytogenetic location: 5p15.2 Genomic coordinates (GRCh38) : 5:14,143,342-14,510,204 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 5p15.2 | Intellectual developmental disorder, autosomal dominant 44, with microcephaly | 617061 | Autosomal dominant | 3 |
| Intellectual developmental disorder, autosomal dominant 63, with macrocephaly | 618825 | Autosomal dominant | 3 |
The TRIO protein contains 3 functional domains: a serine/threonine kinase domain and 2 guanine nucleotide exchange factor (GEF) domains for the family of Rho-like GTPases, specific for Rac1 (602048) and RhoA (165390), respectively (Debant et al., 1996). These domains suggest that this enzyme may play a key role in several signaling pathways that control cell proliferation. The TRIO gene is highly expressed in the developing brain (summary by Ba et al., 2016).
Ferraro et al. (2007) showed that some isoforms of kalirin (604605) and Trio colocalized with immature secretory granules in mouse and rat neuroendocrine cells and modulated their cargo secretion. Overexpression of their N-terminal GEF domains enhanced secretion from immature granules, depleting cells of secretory cargo in the absence of secretagogue. This response required GEF activity and was mimicked by kalirin/Trio substrates Rac1 and RhoG (179505). Selective pharmacologic inhibition of endogenous GEF activity decreased secretagogue-independent release of hormone precursors, causing accumulation of product peptide in mature secretory granules. Ferraro et al. (2007) concluded that kalirin/TRIO modulation of cargo secretion from immature granules provides secretory cells with an extra layer of control over the sets of peptides released and enhances the range of physiologic responses that can be elicited.
Liu et al. (1998) described the solution structure of the N-terminal Dbl homology (DH) domain of TRIO (amino acids 1227-1407) that catalyzes nucleotide exchange for Rac1. The all-alpha-helical protein has a very different structure compared to other exchange factors. Based on site-directed mutagenesis, the authors identified functionally important residues of the DH domain. They are all highly conserved and reside in close proximity on 2 alpha helices. In addition, Liu et al. (1998) discovered a unique capability of the pleckstrin homology (PH) domain to enhance nucleotide exchange in DH domain-containing proteins.
By fluorescence in situ hybridization, Taviaux et al. (1997) mapped the TRIO gene to 5p15.1-p14.
Stumpf (2020) mapped the TRIO gene to chromosome 5p12.2 based on an alignment of the TRIO sequence (GenBank BC017268) with the genomic sequence (GRCh38).
Autosomal Dominant Intellectual Developmental Disorder 44 with Microcephaly
In 4 patients from 3 unrelated families with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Ba et al. (2016) identified 3 different heterozygous truncating mutations in the TRIO gene (601893.0001-601893.0003). Two of the mutations occurred de novo. Studies of patient cells were not performed, but knockdown of the Trio gene in rat hippocampal cells resulted in an increase in dendrites and alterations in synaptic transmission, resulting in increased excitatory transmission during development (see ANIMAL MODEL). Ba et al. (2016) noted that premature maturation of excitatory synapses has been observed in several models of autism spectrum disorder, which was observed in these patients.
By exome sequencing in 3 members of a family with MRD44, originally reported by Mercer et al. (2008), Pengelly et al. (2016) identified a heterozygous truncating mutation in the TRIO gene (601893.0004). Exome sequencing subsequently identified de novo heterozygous missense mutations in the TRIO gene in 2 additional unrelated patients with MRD44 (601893.0005-601893.0006). All mutations were confirmed by Sanger sequencing. In vitro functional expression studies in HEK293 cells showed that the truncating mutation and 2 of the missense mutations affecting the GEFD1 domain resulted in decreased RAC1 activation.
In 5 unrelated patients (patients 10, 12, 14, 15, and 16) with MRD44, Barbosa et al. (2020) identified de novo heterozygous missense mutations at highly conserved residues in the GEFD1 domain of the TRIO gene (see, e.g., 601893.0005 and 601893.0011). The mutations, which were found by exome sequencing, were not present in the gnomAD database. Immunoblot analysis of HEK293 cells transfected with the mutations showed impaired TRIO binding to RAC1 compared to wildtype. Transfection of the mutations into neuroblastoma cells caused decreased neurite outgrowth and decreased lamellipodia formation compared to controls. The findings were consistent with a loss-of-function effect. Barbosa et al. (2020) also identified heterozygous nonsense or frameshift mutations in 5 additional individuals with a similar disorder (see, e.g., 601893.0012 and 601893.0013). Three of the mutations were demonstrated to occur de novo. Similar in vitro functional studies performed on 1 of the mutations were consistent with a loss-of-function effect.
Autosomal Dominant Intellectual Developmental Disorder 63 with Macrocephaly
In 9 unrelated patients with autosomal dominant intellectual developmental disorder-63 with macrocephaly (MRD63; 618825), Barbosa et al. (2020) identified 5 different heterozygous missense mutations in the TRIO gene (see, e.g., 601893.0007-601893.0010). One of the patients had previously been reported by Pengelly et al. (2016). The mutations, which were found by exome sequencing, were confirmed to occur de novo in 8 patients; inheritance was unknown in the ninth patient. All mutations occurred at highly conserved residues in the seventh spectrin repeat, and none were present in the gnomAD database. Three mutations, found in 6 unrelated patients, affected the same residue (R1078W, R1078G, and R1078Q). Molecular modeling predicted that the mutations could cause steric hindrance and alter the structural organization of the protein or interfere with protein folding. Expression of the mutations into HEK293 cells resulted in increased RAC1 activation, as measured by increased PAK1 (602590) phosphorylation, compared to wildtype. Transfection of the mutations into neuroblastoma cells caused enhanced neurite outgrowth and increased lamellipodia formation compared to controls. The findings were consistent with a gain-of-function effect.
In a large study of 24 individuals with confirmed, mostly de novo heterozygous TRIO mutations, Barbosa et al. (2020) observed a genotype/phenotype correlation involving the location and type of mutation. Patients with mutations affecting the seventh spectrin domain, which resulted in increased RAC1 activation with a gain-of-function effect, tended to have macrocephaly and moderately to severely impaired intellectual development (MRD63). In contrast, patients with mutations in the GEFD1 domain or mutations that resulted in a frameshift or truncated proteins, which resulted in a loss-of-function effect, tended to have microcephaly and mildly to moderately impaired intellectual development or less severe learning disabilities (MRD44). However, there were some exceptions; for example, 2 missense variants in the GEFD1 domain (P1461T, 601893.0006 and P1461L), identified in patients with MRD63, showed no impairment in RAC1 activation compared to wildtype when expressed in HEK293 cells, and both resulted in increased neurite and lamellipodia formation in transfected neuroblastoma cells. Similarly, studies of a frameshift variant (Phe2473fs), predicted to result in a loss of function, showed no effect on RAC1 activation or neurite formation compared to wildtype. The authors suggested that there may be correlation between the types of mutations and their cellular expression or effects on RAC1 activity.
Ba et al. (2016) found expression of the Trio gene during rat hippocampal development. It was expressed during the early postnatal period, but rapidly decreased after postnatal day 11, suggesting a role in early neuronal development. Knockdown of Trio using shRNA in dissociated rat hippocampal neurons resulted in an increase in primary dendrites and branch points during early neuronal development, suggesting that TRIO functions normally to limit dendrite formation. Knockdown of Trio in hippocampal slices resulted in increased AMPA receptor-mediated, but not NMDA receptor-mediated, transmission compared to controls, which was shown to result from a decrease in AMPA receptor endocytosis. These changes were associated with an increase in excitatory currents. These data suggested that Trio negatively regulates hippocampal synaptic strength during development.
Barbosa et al. (2020) found that specific knockdown of the GEFD1 domain of the trio gene in X. tropicalis resulted in abnormal craniofacial development with microcephaly, as well as deformation in the forebrain structure compared to controls.
In a 10-year-old boy with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Ba et al. (2016) identified a de novo heterozygous c.4128G-A transition (c.4128G-A, NM_007118.2) in the TRIO gene, predicted to result in a trp1376-to-ter (W1376X) substitution in the RhoGEF domain. The mutation, which was found by targeted sequencing, was not present in the ExAC database. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a loss of function.
In a 35-year-old woman with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Ba et al. (2016) identified a de novo heterozygous 1-bp deletion (c.3752del, NM_007118.2) in the TRIO gene, predicted to result in a frameshift and premature termination (Asp1251ValfsTer11) in 1 of the SPEC domains. The mutation, which was found by targeted sequencing, was not present in the ExAC database. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a loss of function.
In a 20-year-old man with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Ba et al. (2016) identified a heterozygous c.649A-T transversion (c.649A-T, NM_007118.2) in the TRIO gene, resulting in an arg217-to-ter (R217X) substitution in the N terminus. The mutation was inherited from his similarly affected father. The mutation, which was found by targeted sequencing, was not present in the ExAC database. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a loss of function.
In 3 members of a family with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), originally reported by Mercer et al. (2008), Pengelly et al. (2016) identified a heterozygous 1-bp deletion (c.4466delA, NM_007118) in exon 30 of the TRIO gene, resulting in a frameshift and premature termination (Gln1489ArgfsTer11) in the GEFD1 domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The mutation was predicted to result in nonsense-mediated mRNA decay. One of the patients also had a pathogenic variant in the KCNJ2 gene (600681), which may have been responsible for ectopic ventricular beats. In vitro functional expression studies in HEK293 cells showed that the mutation strongly reduced Rac1 (602048) activation compared to wildtype.
In a 16-year-old girl with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Pengelly et al. (2016) identified a de novo heterozygous c.4283G-A transition (c.4283G-A, NM_007118) in exon 28 of the TRIO gene, resulting in an arg1428-to-gln (R1428Q) substitution at a highly conserved residue in the GEFD1 domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. In vitro functional expression studies in HEK293 cells showed that the mutation strongly reduced Rac1 (602048) activation compared to wildtype.
Barbosa et al. (2020) identified a de novo heterozygous R1428Q mutation in the TRIO gene in an 8-year-old girl (patient 12) with MRD44. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Immunoblot analysis of HEK293 cells transfected with the mutation showed that the mutation impaired TRIO binding to RAC1 compared to wildtype. Transfection of the mutation into neuroblastoma cells caused decreased neurite outgrowth and decreased lamellipodia formation compared to controls. The findings were consistent with a loss-of-function effect.
In an 8-year-old girl with autosomal dominant mental retardation-44 with microcephaly (MRD44; 617061), Pengelly et al. (2016) identified a de novo heterozygous c.4381C-A transversion (c.4281C-A, NM_007118) in exon 29, resulting in a pro1461-to-thr (P1461T) substitution at a highly conserved residue in the GEFD1 domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. In vitro functional expression studies in HEK293 cells showed that the mutation strongly reduced Rac1 (602048) activation compared to wildtype.
Barbosa et al. (2020) found that transfection of the P1461T mutation into HEK293 cells only slightly impaired RAC1 activation (nonsignificant). Transfection of the variant into neuroblastoma cells did not alter neurite length, but it slightly increased lamellipodia formation.
In a 9-year-old girl with autosomal dominant intellectual developmental disorder-63 with macrocephaly (MRD63; 618825), Pengelly et al. (2016) identified a de novo heterozygous c.3239A-T transversion (c.3239A-T, NM_007118) in exon 19 of the TRIO gene, resulting in an asn1080-to-ile (N1080I) substitution in the spectrin repeat domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. In vitro functional expression studies in HEK293 cells showed that the mutation did not affect RAC1 (602048) activation, which was in contrast to the other TRIO mutations identified by Pengelly et al. (2016). This patient had a slightly different phenotype from the other patients: she did not have microcephaly, but had plagiocephaly, absence of speech, and seizures.
Barbosa et al. (2020) included the patient reported by Pengelly et al. (2016) in their study (referred to as patient 9). Barbosa et al. (2020) found that transfection of the N1080I mutation into HEK293 cells resulted in increased RAC1 (602048) activation, as measured by increased PAK1 (602590) phosphorylation, compared to wildtype. Transfection of the mutation into neuroblastoma cells caused enhanced neurite outgrowth and increased lamellipodia formation compared to controls. The findings were consistent with a gain-of-function effect.
In 4 unrelated boys (patients 2-5) with autosomal dominant intellectual developmental disorder-63 with macrocephaly (MRD63; 618825), Barbosa et al. (2020) identified a de novo heterozygous c.3232C-T transition (c.3232C-T, NM_007118) in the TRIO gene, resulting in an arg1078-to-trp (R1078W) substitution at a highly conserved residue in the seventh spectrin repeat domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Molecular modeling predicted that the mutation could cause steric hindrance and alter the structural organization of the protein or protein folding. Expression of the mutation into HEK293 cells resulted in increased RAC1 (602048) activation, as measured by increased PAK1 (602590) phosphorylation, compared to wildtype. Transfection of the mutation into neuroblastoma cells caused enhanced neurite outgrowth and increased lamellipodia formation compared to controls. The findings were consistent with a gain-of-function effect.
In a 6-year-old boy (patient 6) with autosomal dominant intellectual developmental disorder-63 with macrocephaly (MRD63; 618825), Barbosa et al. (2020) identified a de novo heterozygous c.3232C-G transversion (c.3232C-G, NM_007118) in the TRIO gene, resulting in an arg1078-to-gly (R1078G) substitution at a highly conserved residue in the seventh spectrin repeat domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Molecular modeling predicted that the mutation could cause steric hindrance and alter the structural organization of the protein or protein folding. Expression of the mutation into HEK293 cells resulted in increased RAC1 (602048) activation, as measured by increased PAK1 (602590) phosphorylation, compared to wildtype. Transfection of the mutation into neuroblastoma cells caused enhanced neurite outgrowth and increased lamellipodia formation compared to controls. The findings were consistent with a gain-of-function effect.
In 2 unrelated patients (patients 7 and 8) with autosomal dominant intellectual developmental disorder-63 with macrocephaly (MRD63; 618825), Barbosa et al. (2020) identified a de novo heterozygous c.3233G-A transition (c.3233G-A, NM_007118) in the TRIO gene, resulting in an arg1078-to-gln (R1078Q) substitution at a highly conserved residue in the seventh spectrin repeat domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Molecular modeling predicted that the mutation could cause steric hindrance and alter the structural organization of the protein or protein folding. Expression of the mutation into HEK293 cells resulted in increased RAC1 (602048) activation, as measured by increased PAK1 (602590) phosphorylation, compared to wildtype. Transfection of the mutation into neuroblastoma cells caused enhanced neurite outgrowth and increased lamellipodia formation compared to controls. The findings were consistent with a gain-of-function effect.
In a 20-month-old boy (patient 10) with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Barbosa et al. (2020) identified a de novo heterozygous c.3895G-A transition (c.3895G-A, NM_007118) in the TRIO gene, predicted to result in a glu1299-to-lys (E1299K) substitution at a highly conserved residue in the GEFD1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Immunoblot analysis of HEK293 cells transfected with the mutation showed that the mutation impaired TRIO binding to RAC1 (602048) compared to wildtype. Transfection of the mutation into neuroblastoma cells caused decreased neurite outgrowth and decreased lamellipodia formation compared to controls. The findings were consistent with a loss-of-function effect.
In a 14-year-old girl (patient 18) with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Barbosa et al. (2020) identified a heterozygous c.2302C-T transition (c.2302C-T, NM_007118) in the TRIO gene, predicted to result in a gln768-to-ter (Q768X) substitution. The mutation was found by exome sequencing; parental DNA was not available to confirm de novo occurrence. The mutation was predicted to result in nonsense-mediated mRNA decay and haploinsufficiency, but functional studies of the variant and studies of patient cells were not performed.
In a 16-year-old boy (patient 20) with autosomal dominant intellectual developmental disorder-44 with microcephaly (MRD44; 617061), Barbosa et al. (2020) identified a de novo heterozygous 1-bp duplication in the TRIO gene (c.6092dup, NM_007118), predicted to result in a frameshift and premature termination (Leu2031PhefsTer9). The mutation was found by exome sequencing. Immunoblot analysis of HEK293 cells transfected with the mutation showed that the mutation impaired TRIO binding to RAC1 (602048) compared to wildtype. However, transfection of the mutation into neuroblastoma cells showed no effect on neurite outgrowth or lamellipodia formation compared to controls. The findings were suggestive of a loss-of-function effect.
Ba, W., Yan, Y., Reijnders, M. R. F., Schuurs-Hoeijmakers, J. H. M., Feenstra, I., Bongers, E. M. H. F., Bosch, D. G. M., De Leeuw, N., Pfundt, R., Gilissen, C., De Vries, P. F., Veltman, J. A., Hoischen, A., Mefford, H. C., Eichler, E. E., Vissers, L. E. L. M., Kasri, N. N., De Vries, B. B. A. TRIO loss of function is associated with mild intellectual disability and affects dendritic branching and synapse function. Hum. Molec. Genet. 25: 892-902, 2016. [PubMed: 26721934] [Full Text: https://doi.org/10.1093/hmg/ddv618]
Barbosa, S., Greville-Heyate, S. Bonnet, M., Godwin, A., Fagotto-Kaufmann, C., Kajava, A. V., Laouteouet, D., Mawby, R., Wai, H. A., Dingemans, A. J. M., Hehir-Kwa, J., Willems, M., and 32 others. Opposite modulation of RAC2 by mutations in TRIO is associated with distinct, domain-specific neurodevelopmental disorders. Am. J. Hum. Genet. 106: 338-355, 2020. [PubMed: 32109419] [Full Text: https://doi.org/10.1016/j.ajhg.2020.01.018]
Debant, A., Serra-Pages, C., Seipel, K., O'Brien, S., Tang, M., Park, S.-H., Streuli, M. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains. Proc. Nat. Acad. Sci. 93: 5466-5471, 1996. [PubMed: 8643598] [Full Text: https://doi.org/10.1073/pnas.93.11.5466]
Ferraro, F., Ma, X.-M., Sobota, J. A., Eipper, B. A., Mains, R. E. Kalirin/Trio Rho guanine nucleotide exchange factors regulate a novel step in secretory granule maturation. Molec. Biol. Cell 18: 4813-4825, 2007. [PubMed: 17881726] [Full Text: https://doi.org/10.1091/mbc.e07-05-0503]
Liu, X., Wang, H., Eberstadt, M., Schnuchel, A., Olejniczak, E. T., Meadows, R. P., Schkeryantz, J. M., Janowick, D. A., Harlan, J. E., Harris, E. A. S., Staunton, D. E., Fesik, S. W. NMR structure and mutagenesis of the N-terminal DBl homology domain of the nucleotide exchange factor Trio. Cell 95: 269-277, 1998. [PubMed: 9790533] [Full Text: https://doi.org/10.1016/s0092-8674(00)81757-2]
Mercer, C. L., Keeton, B., Dennis, N. R. Familial multiple ventricular extrasystoles, short stature, craniofacial abnormalities and digital hypoplasia: a further case of Stoll syndrome? Clin. Dysmorph. 17: 91-93, 2008. [PubMed: 18388777] [Full Text: https://doi.org/10.1097/MCD.0b013e3282efefc9]
Pengelly, R. J., Greville-Heygate, S., Schmidt, S., Seaby, E. G., Jabalameli, M. R., Mehta, S. G. Parker, M. J., Goudie, D., Fagotto-Kaufmann, C., Mercer, C., the DDD Study, Debant, A., Ennis, S., Baralle, D. Mutations specific to the Rac-GEF domain of TRIO cause intellectual disability and microcephaly. J. Med. Genet. 53: 735-742, 2016. [PubMed: 27418539] [Full Text: https://doi.org/10.1136/jmedgenet-2016-103942]
Stumpf, A. M. Personal Communication. Baltimore, Md. 04/03/2020.
Taviaux, S., Diriong, S., Bellanger, J.-M., Streuli, M., Debant, A. Assignment of TRIO, the trio gene (PTPRF interacting) to human chromosome bands 5p15.1-p14 by in situ hybridization. Cytogenet. Cell Genet. 76: 107-108, 1997. [PubMed: 9154137] [Full Text: https://doi.org/10.1159/000134524]