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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
NOVA2
NOVA alternative splicing regulator 2
Chromosome 19 Β· 19q13.32
NCBI Gene: 4858Ensembl: ENSG00000104967.8HGNC: HGNC:7887UniProt: Q9UNW9
36PubMed Papers
21Diseases
0Drugs
13Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
neuron differentiationregulation of RNA metabolic processregulation of alternative mRNA splicing, via spliceosomeRNA bindingneurodevelopmental disorder with or without autistic features and/or structural brain abnormalitiescomplex neurodevelopmental disorderNeurodevelopmental disorderSevere intellectual disability
✦AI Summary

NOVA2 is a neuron-specific RNA-binding protein that functions as a critical regulator of alternative splicing during brain development and neurodevelopment 1. The protein binds specifically to YCAY sequences on pre-mRNA transcripts to control exon inclusion or exclusion, with binding to exonic YCAY clusters promoting exon skipping while intronic binding enhances exon inclusion 2. NOVA2 exhibits distinct spatiotemporal expression patterns, being predominantly expressed in cortical regions, and regulates alternative splicing of axon guidance genes essential for neural network wiring and cortical development 1. Beyond linear splicing, NOVA2 globally promotes circular RNA biogenesis in the developing brain by binding to YCAY clusters in flanking introns 3. In vascular biology, NOVA2 regulates angiogenesis by controlling alternative splicing of genes like UNC5B in endothelial cells, generating pro-apoptotic isoforms required for proper blood vessel development 4. De novo truncating variants in NOVA2 cause a severe neurodevelopmental disorder characterized by intellectual disability, motor delays, autistic features, and structural brain abnormalities including corpus callosum hypoplasia 21. These mutations disrupt alternative splicing regulation, demonstrating the critical importance of RNA processing in normal neurodevelopment 5.

Sources cited
1
NOVA2 is neuron-specific, binds YCAY sequences, has distinct cortical expression, and truncating variants cause neurodevelopmental disorders
PMID: 40555137
2
NOVA2 binds YCAY sequences to control exon inclusion/exclusion and truncating variants cause severe neurodevelopmental phenotypes
PMID: 35607920
3
NOVA2 globally promotes circular RNA biogenesis in developing brain through binding to flanking intronic YCAY clusters
PMID: 34157123
4
NOVA2 regulates angiogenesis by controlling UNC5B alternative splicing in endothelial cells
PMID: 34381052
5
NOVA2 is a splicing factor associated with autism spectrum disorder pathogenesis
PMID: 38509732
Disease Associationsβ“˜21
neurodevelopmental disorder with or without autistic features and/or structural brain abnormalitiesOpen Targets
0.70Moderate
complex neurodevelopmental disorderOpen Targets
0.46Moderate
Neurodevelopmental disorderOpen Targets
0.37Weak
Severe intellectual disabilityOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.33Weak
genetic disorderOpen Targets
0.19Weak
dementiaOpen Targets
0.06Suggestive
neurodegenerative diseaseOpen Targets
0.03Suggestive
ataxia telangiectasiaOpen Targets
0.02Suggestive
hepatocellular carcinomaOpen Targets
0.01Suggestive
lung adenocarcinomaOpen Targets
0.01Suggestive
Alzheimer diseaseOpen Targets
0.01Suggestive
non-small cell lung carcinomaOpen Targets
0.01Suggestive
neuroblastomaOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
gastric cancerOpen Targets
0.01Suggestive
epilepsyOpen Targets
0.01Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.01Suggestive
spinocerebellar ataxia type 37Open Targets
0.01Suggestive
Nijmegen breakage syndromeOpen Targets
0.01Suggestive
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalitiesUniProt
Pathogenic Variants13
NM_002516.4(NOVA2):c.656del (p.Gly219fs)Likely pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜…β˜†β˜†β˜†2025β†’ Residue 219
NM_002516.4(NOVA2):c.1104_1134del (p.Gly369fs)Likely pathogenic
NOVA2-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 369
NM_002516.4(NOVA2):c.720_721insCCGCGGATGTGCTTCCAGCC (p.Ala241fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 241
NM_002516.4(NOVA2):c.523del (p.Leu175fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜…β˜†β˜†β˜†2022β†’ Residue 175
NM_002516.4(NOVA2):c.987del (p.Tyr330fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜…β˜†β˜†β˜†2022β†’ Residue 330
NM_002516.4(NOVA2):c.755_764del (p.Leu252fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 252
NM_002516.4(NOVA2):c.782del (p.Val261fs)Pathogenic
Severe intellectual disability|Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜…β˜†β˜†β˜†2019β†’ Residue 261
NM_002516.4(NOVA2):c.729del (p.Ala244fs)Pathogenic
Intellectual disability
β˜†β˜†β˜†β˜†2022β†’ Residue 244
NM_002516.4(NOVA2):c.826del (p.Leu276fs)Likely pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜†β˜†β˜†β˜†2021β†’ Residue 276
NM_002516.4(NOVA2):c.781del (p.Val261fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜†β˜†β˜†β˜†2020β†’ Residue 261
NM_002516.4(NOVA2):c.709_748del (p.Val237fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜†β˜†β˜†β˜†2020β†’ Residue 237
NM_002516.4(NOVA2):c.701_720dup (p.Ala241fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜†β˜†β˜†β˜†2020β†’ Residue 241
NM_002516.4(NOVA2):c.710_711dup (p.Leu238fs)Pathogenic
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities
β˜†β˜†β˜†β˜†2020β†’ Residue 238
View on ClinVar β†—
Related Genes
PTBP2Protein interaction89%FAM107BProtein interaction85%HNRNPCProtein interaction73%KCNF1Protein interaction71%SCN1AProtein interaction70%NOVA1Protein interaction57%
Tissue Expression6 tissues
Brain
100%
Lung
36%
Heart
27%
Liver
11%
Ovary
8%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
NOVA2PTBP2FAM107BHNRNPCKCNF1SCN1ANOVA1
PROTEIN STRUCTURE
Preparing viewer…
PDB1DTJ Β· 2.00 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.61LoF Tolerant
pLIβ“˜
0.85Intermediate
Observed/Expected LoF0.29 [0.15–0.61]
RankingsWhere NOVA2 stands among ~20K protein-coding genes
  • #10,826of 20,598
    Most Researched36
  • #2,629of 5,498
    Most Pathogenic Variants13
  • #4,248of 17,882
    Most Constrained (LOEUF)0.61 Β· top quartile
Genes detectedNOVA2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A ligand-insensitive UNC5B splicing isoform regulates angiogenesis by promoting apoptosis.
PMID: 34381052
Nat Commun Β· 2021
1.00
2
Alternative Splicing Changes Promoted by NOVA2 Upregulation in Endothelial Cells and Relevance for Gastric Cancer.
PMID: 37175811
Int J Mol Sci Β· 2023
0.90
3
NOVA2 regulates neural circRNA biogenesis.
PMID: 34157123
Nucleic Acids Res Β· 2021
0.80
4
NOVA1/2 genes and alternative splicing in neurodevelopment.
PMID: 40555137
Curr Opin Genet Dev Β· 2025
0.70
5
De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes.
PMID: 35607920
Hum Mutat Β· 2022
0.60