Alternative titles; symbols
HGNC Approved Gene Symbol: STX3
Cytogenetic location: 11q12.1 Genomic coordinates (GRCh38): 11:59,754,188-59,805,878 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 11q12.1 | Diarrhea 12, with microvillus atrophy | 619445 | Autosomal recessive | 3 |
| Retinal dystrophy and microvillus inclusion disease | 619446 | Autosomal recessive | 3 |
Syntaxins, such as STX3, are conserved SNARE proteins that contain C-terminal transmembrane anchors, which are required for their membrane fusion activity. STX3 also produces a soluble isoform that functions as a nuclear regulator of gene expression (Giovannone et al., 2018).
Ibaraki et al. (1995) cloned mouse cDNAs for 4 different forms of syntaxin-3, which they designated syntaxin-3A, -3B, -3C, and -3D. Ibaraki et al. (1995) stated that these forms of syntaxin-3 were probably generated by alternative splicing of the primary transcript of the mouse syntaxin-3 gene.
To elucidate the mechanisms that regulate neutrophil exocytosis, Martin-Martin et al. (1999) studied the expression of syntaxins in neutrophils. They isolated cDNAs encoding 2 isoforms of human syntaxin-3, which they designated syntaxin-3A and -3B. The 2 isoforms are identical except that syntaxin-3B lacks a 37-amino acid segment. The predicted 289-amino acid syntaxin-3A shares 98% protein sequence identity with rat syntaxin-3. Martin-Martin et al. (1999) noted that the human syntaxin-3B isoform does not correspond to any of the mouse syntaxin-3 isoforms identified by Ibaraki et al. (1995).
Janecke et al. (2021) found that the human STX3B transcript, generated by differential splicing in the same pattern as observed in the mouse, is expressed only in the retina. The STX3A and STX3B isoforms share exons 1 to 8 and differ with respect to exons 9 to 11, which encode the C-terminal SNARE and transmembrane domains. Strong signals for STX3A were detected in human small intestine, kidney, pancreas, and placenta, as well as in retina, with weaker expression levels detected in lung, liver, and heart, and no signals above background detected in human brain and skeletal muscle tissues. Comparison of the relative levels of STX3A and STX3B mRNA in the human retina demonstrated that the STX3B isoform represents approximately 99% of STX3 in human retinal transcripts. Immunohistochemical analysis showed strong STX3 immunolabeling in the photoreceptor and bipolar cell terminals, located in the outer and inner plexiform layers, respectively. Strong STX3 immunolabeling of photoreceptor inner and rhodopsin (180380)-labeled (rod) outer segments was also observed in the human retina, whereas only the inner segments were labeled in mouse photoreceptors. In addition, the inner and outer segments of cone photoreceptors showed immunolabeling for STX3 in human retina specimens.
By EST database analysis and RT-PCR of HEK293T cells, Giovannone et al. (2018) cloned an STX3 splice variant lacking exon 10. The variant produces a soluble isoform lacking the transmembrane domain that the authors termed STX3S. RT-PCR of human kidney showed expression of transcripts for both STX3S and membrane-anchored STX3A. STX3S mRNA was abundantly expressed in human tissues and cell lines, but the protein underwent fast turnover compared with STX3A. STX3S was expressed in a tissue-specific manner and was downregulated in tumor cells in vivo and in rapidly proliferating carcinoma cells in vitro.
Gross (2014) mapped the STX3 gene to chromosome 11q12.1 based on an alignment of the STX3 sequence (GenBank BC007405) with the genomic sequence (GRCh37).
Darios and Davletov (2006) demonstrated that syntaxin-3 has an important role in the growth of neurites and also serves as a direct target for arachidonic acid. By using syntaxin-3 in a screening assay, they determined that the dietary omega-3 linolenic and docosahexaenoic acids can efficiently substitute for arachidonic acid in activating syntaxin-3. Darios and Davletov (2006) concluded that their findings provided a molecular basis for the previously established action of omega-3 and omega-6 polyunsaturated fatty acids in membrane expansion at the growth cones and represented the first identification of a single effector molecule for these essential nutrients.
Using immunofluorescence and immunoelectron microscopy, Galli et al. (1998) demonstrated that human TIVAMP (VAMP7; 300053), STX3A, and SNAP23 (602534), were insensitive to proteolysis by numerous clostridial neurotoxins (NTs). TIVAMP-containing vesicles were concentrated in the apical domain of epithelial cells. STX3A and SNAP23 were codistributed at the apical plasma membrane, where they formed N-ethyl maleimide-dependent SNARE complexes with TIVAMP and cellubrevin (VAMP3; 603657). Galli et al. (1998) proposed that TIVAMP, STX3A, and SNAP23 participate in exocytotic processes at the apical plasma membrane of epithelial cells and in clostridial NT-resistant pathways.
Using transfected HEK293T and MDCK renal epithelial cells, Giovannone et al. (2018) found that human STX3S interacted with RANBP5 (IPO5; 602008) and was actively transported to the nucleoplasm. The N-terminal 3-helix bundle motif of STX3S was necessary and sufficient for interaction with RANBP5. STX3S functioned as a signaling protein that regulated gene expression by physically and functionally interacting with transcription factors. STX3S physically interacted with ETV4 (600711) in HEK293T cells and acted as a coactivator of ETV4-regulated transcription. Moreover, STX3S acted as a transcriptional coactivator of ATF2 (123811) and dampened proliferation of HEK293T cells.
Diarrhea 12, with Microvillus Atrophy
In a 1-year-old Dutch girl (patient 1) with intractable diarrhea due to microvillus inclusion disease (DIAR12; 619445), Wiegerinck et al. (2014) identified homozygosity for a nonsense mutation in the STX3 gene (R247X; 600876.0002). Sanger sequencing confirmed the mutation and its segregation with disease in the family. Functional analysis suggested a dominant-negative effect of truncated STX3, disturbing cell polarity.
In a Saudi male infant with DIAR12, Alsaleem et al. (2017) identified homozygosity for the previously identified R247X mutation in the STX3 gene.
Retinal Dystrophy and Microvillus Inclusion Disease
By whole-exome sequencing in an 18-month-old Pakistani boy with intractable diarrhea due to microvillus inclusion disease (MVID), who later developed progressive retinal dystrophy (RDMVID; 619446), Wiegerinck et al. (2014) identified homozygosity for a 2-bp duplication in the STX3 gene (600876.0003). Sanger sequencing confirmed the mutation and its segregation with disease in the family. Functional analysis suggested a dominant-negative effect of truncated STX3, disturbing cell polarity.
In an Afghan male infant with MVID and visual impairment (RDMVID), Julia et al. (2019) identified homozygosity for a del/ins frameshift mutation in the STX3 gene (600876.0004) that was not found in public variant databases.
Janecke et al. (2021) reported 8 patients (P2 to P9) with RDMVID who carried homozygous mutations in the STX3 gene (see, e.g., 600876.0003-600876.0006); see GENOTYPE/PHENOTYPE CORRELATIONS.
Associations Pending Confirmation
For discussion of a possible association between variation in the STX3 gene and congenital cataract with developmental delay, see 600876.0001.
Janecke et al. (2021) studied a cohort of 10 patients from 8 families with MVID, including 8 patients who also displayed early-onset severe retinal dystrophy (RDMVID). Five of the patients had been previously reported (Wiegerinck et al., 2014; Alsaleem et al., 2017; Julia et al., 2019; Maddirevula et al., 2019). All 10 patients had homozygous loss-of-function STX3 variants that segregated with disease in their respective families, and all had onset of persistent diarrhea within the first week of life, with histopathology that demonstrated the characteristic features of MVID. The 8 patients (P2 to P9) with RDMVID had pathogenic variants (see, e.g., 600876.0003-600876.0006) that were located in exons shared between STX3A and STX3B transcripts, with loss of expression of both isoforms. In contrast, the 2 patients (P1 and P10) with only MVID (DIAR12; 619445) carried the same nonsense mutation (R247X; 600876.0002), located in exon 9A and sparing the STX3B transcript, which predominates in the retina.
Janecke et al. (2021) generated a mouse knockout line with rod photoreceptor-specific inactivation of Stx3 and observed progressive photoreceptor degeneration. At 5 weeks of age, an approximately 60% decrease in thickness of the outer nuclear layer (ONL) and in the number of ONL neuronal somata was observed, indicating that a large number of photoreceptors had died. In some of the remaining rods, rhodopsin was appropriately localized to the outer segments, but a marked amount of rhodopsin mislocalized to the outer plexiform layer. At 8 and 12 weeks of age, increasing cell loss and further ectopic expression of rhodopsin were observed. Cone photoreceptor loss and ectopic expression of opsin in cones was also observed, which the authors attributed to a 'bystander effect.' Quantification of the progressive degenerative phenotype revealed a rapid loss in the number of neuronal somata in the ONL, indicative of photoreceptor death, whereas the number of cells in the inner nuclear layer, including horizontal, bipolar, and amacrine cells, was no different from that of controls. The authors concluded that Stx3 expression is essential for the survival of retinal photoreceptors, and suggested that proper trafficking of rhodopsin in the rod is partially affected by lack of Stx3.
This variant is classified as a variant of unknown significance because its contribution to congenital cataract with developmental delay has not been confirmed.
In 3 sibs from a consanguineous Tunisian family with congenital cataract and developmental delay, Chograni et al. (2015) performed homozygosity mapping and found 2 regions of shared homozygosity, at chromosome 11p11.2-p11.12 and 11q11-q13.1. Analysis of 4 candidate genes within those regions revealed that the 3 affected sibs were homozygous for a c.122A-G transition (c.122A-G, NM_004177) in exon 3 of the STX3 gene, resulting in a glu41-to-gly (E41G) substitution at a highly conserved residue within the syntaxin N-terminal domain. The STX3 missense mutation was present in heterozygosity in their unaffected parents and was not found in 50 ethnically matched controls; variants detected in the 3 other candidate genes did not segregate with disease. According to medical records, all 3 sibs had bilateral posterior polar opacification present at birth and underwent cataract removal early in life. Visual acuity was preserved in all 3 patients, and spectral domain optical coherence tomography (OCT) and electrophysiologic testing were normal. There was significant psychomotor disability in the 3 sibs, who all failed to walk by the age of 15 to 18 months, had significant delay in speech development, and exhibited mild to moderate intellectual disability. They had no dysmorphic features, and brain MRIs were normal.
By whole-exome sequencing in a 1-year-old Dutch girl (patient 1), born of consanguineous parents, with intractable diarrhea due to microvillus inclusion disease (DIAR12; 619445), Wiegerinck et al. (2014) identified homozygosity for a c.739C-T transition in exon 9 of the STX3 gene, resulting in an arg247-to-ter (R247X) substitution. Sanger sequencing confirmed the mutation and its segregation with disease in the family. The mutation was predicted to cause protein depletion and truncation, which was supported by Western blot of STX3 on patient organoids. Stable expression of a truncated version of STX3 corresponding to the R247X mutant protein in Caco2 cell cultures recapitulated all histologic hallmarks of the disease, including a statistically significant increase of both microvillus inclusions and basolateral microvilli. Scanning and transmission electron microscopy of the mutant Caco2 cells further demonstrated disruption of cell polarity, with formation of intercellular lumina within the cell multilayer. Confocal laser-scanning microscopy revealed mislocalization of the R247X mutant, which was found throughout the cytoplasm rather than showing the strictly apical localization of wildtype STX3. In addition, 3-dimensional organoids derived from patient duodenal biopsy specimens were devoid of syntaxin-3 staining and recapitulated morphologic characteristics of the disease.
In a Saudi male infant with DIAR12, Alsaleem et al. (2017) identified homozygosity for the previously identified R247X mutation in the STX3 gene.
By whole-exome sequencing in an 18-month-old Pakistani boy (patient 2) with intractable diarrhea due to microvillus inclusion disease, who later developed progressive retinal dystrophy (RDMVID; 619446), Wiegerinck et al. (2014) identified homozygosity for a 2-bp duplication (c.372_373dup) in exon 6 of the STX3 gene, causing a frameshift predicted to result in a premature termination codon (Arg125LeufsTer7). Sanger sequencing confirmed the mutation and its segregation with disease in the family. The mutation was predicted to cause protein depletion and truncation, which was supported by Western blot of STX3 on patient organoids. Stable expression of a truncated version of STX3 corresponding to the patient's mutant protein in Caco2 cell cultures recapitulated all histologic hallmarks of the disease, including a statistically significant increase of both microvillus inclusions and basolateral microvilli. Scanning and transmission electron microscopy of the mutant Caco2 cells further demonstrated disruption of cell polarity, with formation of intercellular lumina within the cell multilayer.
In an Afghan male infant with visual impairment and intractable diarrhea due to microvillus inclusion disease (RDMVID; 619446), Julia et al. (2019) identified homozygosity for a deletion/insertion (c.363_366delinsGA) in exon 6 of the STX3 gene, causing a frameshift predicted to result in a premature termination codon (Val122fs). The variant was identified by massively parallel sequencing, and confirmed by Sanger sequencing. The proband's parents were heterozygous for the variant.
Janecke et al. (2021) noted the effect of the mutation as Val122fsTer14.
In 2 Arab cousins (P4 and P5) with retinal dystrophy and microvillus inclusion disease (RDMVID; 619446), Janecke et al. (2021) identified homozygosity for a splicing mutation (c.115-2A-G, NM_004177.5) in intron 2 of the STX3 gene, predicted to cause skipping of exon 3 and result in a premature termination codon (Ile39LysfsTer6). The unaffected parents of the female cousin (P4) were heterozygous for the mutation; the male cousin's parents were not tested.
In a Lebanese sister and brother (P8 and P9) who had retinal dystrophy and microvillus inclusion disease (RDMVID; 619446) and died at 10 months and 5 months of age, respectively, Janecke et al. (2021) identified homozygosity for a 2-bp deletion (c.177_178delCT, NM_004177.5) in exon 3 of the STX3 gene, causing a frameshift predicted to result in a premature termination codon (Tyr60GlnfsTer16). The mutation was identified by genomewide autozygosity mapping analysis followed by direct sequencing of STX3, which confirmed segregation of the variant with disease in the family.
Alsaleem, B. M. R., Ahmed, A. B. M., Fageeh, M. A. Microvillus inclusion disease variant in an infant with intractable diarrhea. Case Rep. Gastroent. 11: 647-651, 2017. [PubMed: 29282386] [Full Text: https://doi.org/10.1159/000479624]
Chograni, M., Alkuraya, F. S., Ourteni, I., Maazoul, F., Lariani, I., Chaabouni, H. B. Autosomal recessive congenital cataract, intellectual disability phenotype linked to STX3 in a consanguineous Tunisian family. Clin. Genet. 88: 283-287, 2015. [PubMed: 25358429] [Full Text: https://doi.org/10.1111/cge.12489]
Darios, F., Davletov, B. Omega-3 and omega-6 fatty acids stimulate cell membrane expansion by acting on syntaxin 3. Nature 440: 813-817, 2006. [PubMed: 16598260] [Full Text: https://doi.org/10.1038/nature04598]
Galli, T., Zahraoui, A., Vaidyanathan, V. V., Raposo, G., Tian, J. M., Karin, M., Niemann, H., Louvard, D. A novel tetanus neurotoxin-insensitive vesicle-associated membrane protein in SNARE complexes of the apical plasma membrane of epithelial cells. Molec. Biol. Cell 9: 1437-1448, 1998. [PubMed: 9614185] [Full Text: https://doi.org/10.1091/mbc.9.6.1437]
Giovannone, A. J., Winterstein, C., Bhattaram, P., Reales, E., Low, S. H., Baggs, J. E., Xu, M., Lalli, M. A., Hogenesch, J. B., Weimbs, T. Soluble syntaxin 3 functions as a transcriptional regulator. J. Biol. Chem. 293: 5478-5491, 2018. [PubMed: 29475951] [Full Text: https://doi.org/10.1074/jbc.RA117.000874]
Gross, M. B. Personal Communication. Baltimore, Md. 5/21/2014.
Ibaraki, K., Horikawa, H. P. M., Morita, T., Mori, H., Sakimura, K., Mishina, M., Saisu, H., Abe, T. Identification of four different forms of syntaxin 3. Biochem. Biophys. Res. Commun. 211: 997-1005, 1995. [PubMed: 7598732] [Full Text: https://doi.org/10.1006/bbrc.1995.1910]
Janecke, A. R., Liu, X., Adam, R., Punuru, S., Viestenz, A., Strauss, V., Laass, M., Sanchez, E., Adachi, R., Schatz, M. P., Saboo, U. S., Mittal, N., and 13 others. Pathogenic STX3 variants affecting the retinal and intestinal transcripts cause an early-onset severe retinal dystrophy in microvillus inclusion disease subjects. Hum. Genet. 140: 1143-1156, 2021. [PubMed: 33974130] [Full Text: https://doi.org/10.1007/s00439-021-02284-1]
Julia, J., Shui, V., Mittal, N., Heim-Hall, J., Blanco, C. L. Microvillus inclusion disease, a diagnosis to consider when abnormal stools and neurological impairments run together due to a rare syntaxin 3 gene mutation. J. Neonatal Perinatal Med. 12: 313-319, 2019. [PubMed: 30909251] [Full Text: https://doi.org/10.3233/NPM-1852]
Maddirevula, S., Alzahrani, F., Al-Owain, M., Al Muhaizea, M. A., Kayyali, H. R., AlHashem, A., Rahbeeni, Z., Al-Otaibi, M., Alzaidan, H. I., Balobaid, A., El Khashab, H. Y., Bubshait, D. K., and 36 others. Autozygome and high throughput confirmation of disease genes candidacy. Genet. Med. 21: 736-742, 2019. [PubMed: 30237576] [Full Text: https://doi.org/10.1038/s41436-018-0138-x]
Martin-Martin, B., Nabokina, S. M., Lazo, P. A., Mollinedo, F. Co-expression of several human syntaxin genes in neutrophils and differentiating HL-60 cells: various isoforms and detection of syntaxin 1. J. Leuko. Biol. 65: 397-406, 1999. [PubMed: 10080545] [Full Text: https://doi.org/10.1002/jlb.65.3.397]
Wiegerinck, C. L., Janecke, A. R., Schneeberger, K., Vogel, G. F., van Haaften-Visser, D. Y., Escher, J. C., Adam, R., Thoni, C. E., Pfaller, K., Jordan, A. J., Weis, C.-A., Nijman, I. J., and 13 others. Loss of syntaxin 3 causes variant microvillus inclusion disease. Gastroenterology 147: 65-68, 2014. [PubMed: 24726755] [Full Text: https://doi.org/10.1053/j.gastro.2014.04.002]