Alternative titles; symbols
HGNC Approved Gene Symbol: NOVA2
Cytogenetic location: 19q13.32 Genomic coordinates (GRCh38): 19:45,933,734-45,973,865 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.32 | Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities | 618859 | Autosomal dominant | 3 |
The NOVA2 gene encodes an RNA-binding protein that plays a role in the regulation of alternative mRNA splicing. NOVA2 is primarily expressed in the central nervous system where it is associated with splicing regulation of genes involved in axonal guidance and projection during cortical development (summary by Mattioli et al., 2020).
By exon amplification from cosmids mapping to the glioma tumor suppressor gene candidate region on 19q13.3 (see 137800), Ueki et al. (1997) found an exon with high homology to a portion of the NOVA1 gene (602157), which encodes a neuron-specific RNA-binding protein recognized by the paraneoplastic syndrome antibody anti-Ri. Screening of a human brain cDNA library with this exon identified a 1.9-kb cDNA with extensive homology to NOVA1, including 3 nearly identical KH domains characteristic of a subtype of RNA-binding proteins. Northern blots demonstrated expression of a 2.5-kb mRNA in brain, but no other tissues. In situ hybridization on human cerebral cortex showed mRNA expression restricted to astrocytes. Ueki et al. (1997) therefore named the gene ANOVA, for astrocytic NOVA1-like gene. Southern blotting and SSCP analyses did not show tumor-specific alterations of this gene in gliomas, and RT-PCR studies showed expression in glioma cell lines, suggesting that ANOVA is not the 19q glioma tumor suppressor gene. The authors suggested that, given that 2 cloned paraneoplastic antigens are neuronal RNA-binding proteins and that glial proteins may act as paraneoplastic antigens, the ANOVA product may be a target antigen in one of the undefined human paraneoplastic syndromes.
Yang et al. (1998) cloned NOVA2 by immunoscreening mouse cortical brain regions and screening a small cell lung cancer cDNA library. The deduced 492-amino acid protein is 99% identical to the mouse protein and 75% identical to NOVA1, with 98% identity in the 3 RNA-binding KH domains. Western blot analysis showed strong expression of a 75-kD protein in mouse brain, with much lower expression in lung and no expression in other tissues. Functional analysis showed that both Nova1 and Nova2 bind to similar RNA ligands with high affinity.
Ueki et al. (1997) identified the NOVA2 gene within a region of chromosome 19q13.3 by exon amplification of cosmids.
By analyzing alternative splicing in brains of Nova1 -/- and Nova2 -/- mice, Ule et al. (2005) identified Nova-dependent alternatively spliced transcripts. Of the 40 Nova-spliced transcripts with defined brain function, 34 encoded proteins that act at the synapse (neurotransmitter receptors, cation channels, adhesion and scaffold proteins), and 8 encoded proteins involved in axon guidance. Of the 35 proteins with known interaction partners, 26 (74%) interact with each other.
Ule et al. (2006) combined bioinformatics, biochemistry, and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-mRNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led Ule et al. (2006) to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (180740) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harboring (or closest to) YCAY clusters. Ule et al. (2006) concluded that these results define a genomewide map relating to the position of a cis-acting element to its regulation by an RNA binding protein, namely, that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.
Heinzen et al. (2007) investigated whether the neuronally expressed splice modifier proteins NOVA1 and NOVA2 may contribute to the alternative splicing of exon 5 of SCN1A, which is the site of a polymorphism important in the response to certain antiepileptic drugs (182389.0016). This polymorphism has a dramatic effect on the proportions of neonate and adult alternative transcripts of SCN1A in adult brain tissue, and the effect of the polymorphism appeared to be modified by NOVA2 expression levels. No effect was observed of NOVA2 on the alternative splicing of 17 other neuronally expressed genes.
Saito et al. (2019) generated functional maps of Nova2-RNA interactions from different neuronal populations in mouse brain. Combining this data with data from conditional Nova2-knockout mice, they found that Nova2 regulated unique alternative splicing programs on the same transcripts in different types of neurons. Nova2 acted as an essential factor for development of laminar structure in cortical excitatory, but not inhibitory, neurons and for proper motor coordination and synapse formation in cerebellar Purkinje cells. Further analysis revealed that Nova2 regulated intron retention by functioning as a cis-acting scaffold for the trans-acting alternative splicing factor Ptbp2 (608449).
Crystal Structure
Lewis et al. (2000) determined the structure of the KH3 domain of NOVA2 interacting with single-stranded RNA at 2.4-angstrom resolution. The structure of the KH3 domain bound to a stem loop RNA resembled a molecular vise, with 5-prime-UCAC-3-prime pinioned between an invariant gly-X-X-gly motif and the variable loop. Tetranucleotide recognition was supported by an aliphatic alpha-helix/beta-sheet RNA-binding platform, which mimicked 5-prime-UG-3-prime by making Watson-Crick-like hydrogen bonds with 5-prime-CA-3-prime.
In 6 unrelated patients with neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified de novo heterozygous frameshift mutations in the NOVA2 gene (601991.0001-601991.0006). The mutations, which were found by exome sequencing through different laboratories, were not found in public databases, including gnomAD. All the mutations occurred in the last exon, exon 4, and were predicted to escape nonsense-mediated mRNA decay (NMD), although studies of patient cells were not performed. Expression of 1 of the mutations (Mut1) (601991.0001) in HeLa cells showed that the mutant protein was expressed at normal levels and showed normal nuclear localization, consistent with escape from NMD. All the mutations, which clustered near one another, resulted in frameshifts leading to the same alternative frame, and the resulting truncated proteins shared a common region of 133 residues before premature termination between residues 394-401. The full-length protein contains 492 residues. The mutations were predicted to remove the third KH domain (residues 406-473), which binds RNA loops composed of the tetranucleotide YCAY. siRNA-mediated knockdown of NOVA2 in human neuronal cells resulted in an increase in the proportion of cells with multiple neurites and a decrease in the proportion of undifferentiated cells compared to controls. The abnormalities in neurite outgrowth could be rescued by wildtype NOVA2, but not by the Mut1 mutation. Transcriptome analysis of human neural stem cells treated with siRNA causing a 50% reduction in NOVA2 expression showed that a set of genes had differences in alternative splicing. Gene ontology analysis showed that affected genes were related to transmembrane proteins, the extracellular matrix, cytoskeleton organization, and neuron projection/dendrite development. Genes affected included several that have been shown to undergo alternative splicing in the mouse cortex, such as SGCE (604149), NEO1 (601907), SORBS1 (605264), and DAB1 (603448). In vitro studies showed that Mut1 had a reduction in RNA binding capacity for the YCAY motif compared to wildtype, and expression of Mut1 in HeLa cells resulted in abnormal regulation of splicing of certain genes, although the findings were more consistent with a partial loss of function than a complete loss of function. There was no evidence of a dominant-negative effect.
Mattioli et al. (2020) found that knockdown of the NOVA2 ortholog (nova1a) in zebrafish resulted in a reduction in the number of axonal tracts formed between optic tecta, as well as a reduction in tecta size. The morpholino phenotype could be rescued by wildtype NOVA2 mRNA, but not by NOVA2 mutant (Mut1) mRNA. However, injection of either wildtype or Mut1 NOVA2 alone did not significantly affect axonal tracts.
In a 9.5-year-old boy (patient 1) with neurodevelopmental disorder with autistic features and structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 1-bp deletion (c.782del, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Val261GlyfsTer135). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Expression of the mutation in HeLa cells showed that the truncated protein was expressed normally and localized normally to the nucleus. The authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
In a 3.5-year-old boy (patient 2) with neurodevelopmental disorder with autistic features without structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 2-bp duplication (c.710_711dup, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Leu238CysfsTer159). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
In a 4-year-old girl (patient 3) with neurodevelopmental disorder without autistic features and with structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 20-bp duplication (c.701_720dup, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Ala241ProfsTer162). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
In a 2.7-year-old girl (patient 4) with neurodevelopmental disorder with autistic features and structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 40-bp deletion (c.709_748del, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Val237ProfsTer146). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
In a 22-year-old man (patient 5) with neurodevelopmental disorder with autistic features and structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 1-bp deletion (c.781del, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Val261TrpfsTer135). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
In a 5.5-year-old girl (patient 6) with neurodevelopmental disorder with autistic features without structural brain abnormalities (NEDASB; 618859), Mattioli et al. (2020) identified a de novo heterozygous 20-bp insertion (c.720_721insCCGCGGATGTGCTTCCAGCC, NM_002516.3) in exon 4 of the NOVA2 gene, predicted to result in a frameshift and premature termination (Ala241ProfsTer162). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. The mutation was predicted to remove the third KH domain of the protein, which binds certain RNA loops. Since the mutation occurs in the last exon, it likely escapes nonsense-mediated mRNA decay, but NOVA2 is not expressed in blood cells, precluding confirmation. Functional studies of the variant and studies of patient cells were not performed, but the authors postulated that the mutation results in a partial loss-of-function rather than a dominant-negative effect.
Heinzen, E. L., Yoon, W., Tate, S. K., Sen, A., Wood, N. W., Sisodiya, S. M., Goldstein, D. B. Nova2 interacts with a Cis-acting polymorphism to influence the proportions of drug-responsive splice variants of SCN1A. Am. J. Hum. Genet. 80: 876-883, 2007. [PubMed: 17436242] [Full Text: https://doi.org/10.1086/516650]
Lewis, H. A., Musunuru, K., Jensen, K. B., Edo, C., Chen, H., Darnell, R. B., Burley, S. K. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell 100: 323-332, 2000. [PubMed: 10676814] [Full Text: https://doi.org/10.1016/s0092-8674(00)80668-6]
Mattioli, F., Hayot, G., Drouot, N., Isidor, B., Courraud, J., Hinckelmann, M.-V., Mau-Them, F. T., Sellier, C., Goldman, A., Telegrafi, A., Boughton, A., Gamble, C., and 16 others. De novo frameshift variants in the neuronal splicing factor NOVA2 result in a common C-terminal extension and cause a severe form of neurodevelopmental disorder. Am. J. Hum. Genet. 106: 438-452, 2020. [PubMed: 32197073] [Full Text: https://doi.org/10.1016/j.ajhg.2020.02.013]
Saito, Y., Yuan, Y., Zucker-Scharff, I., Fak, J. J., Jereb, S., Tajima, Y., Licatalosi, D. D., Darnell, R. B. Differential NOVA2-mediated splicing in excitatory and inhibitory neurons regulates cortical development and cerebellar function. Neuron 101: 707-720, 2019. [PubMed: 30638744] [Full Text: https://doi.org/10.1016/j.neuron.2018.12.019]
Ueki, K., Ramaswamy, S., Billings, S. J., Mohrenweiser, H. W., Louis, D. N. ANOVA, a putative astrocytic RNA-binding protein gene that maps to chromosome 19q13.3. Neurogenetics 1: 31-36, 1997. [PubMed: 10735272] [Full Text: https://doi.org/10.1007/s100480050005]
Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., Darnell, R. B. An RNA map predicting Nova-dependent splicing regulation. Nature 444: 580-586, 2006. [PubMed: 17065982] [Full Text: https://doi.org/10.1038/nature05304]
Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.-S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., Zeeberg, B. R., Kane, D., Weinstein, J. N., Blume, J., Darnell, R. B. Nova regulates brain-specific splicing to shape the synapse. Nature Genet. 37: 844-852, 2005. [PubMed: 16041372] [Full Text: https://doi.org/10.1038/ng1610]
Yang, Y. Y. L., Yin, G. L., Darnell, R. B. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia. Proc. Nat. Acad. Sci. 95: 13254-13259, 1998. [PubMed: 9789075] [Full Text: https://doi.org/10.1073/pnas.95.22.13254]