RNU4-2 Gene

HGNC Family Non-coding RNAs
Name RNA, U4 small nuclear 2
Description Predicted to enable U6 snRNA binding activity. Predicted to be involved in formation of quadruple SL/U4/U5/U6 snRNP and spliceosomal tri-snRNP complex assembly. Predicted to be part of U4 snRNP and U4/U6 x U5 tri-snRNP complex. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRecent large‐scale genetic studies have revealed that RNU4-2, which encodes the U4 small nuclear RNA—a crucial component of the spliceosome—is essential for proper pre-mRNA splicing and normal neurodevelopment. Disruption of RNU4-2 function through de novo variants has been implicated in a syndrome marked by intellectual disability, microcephaly, short stature, hypotonia, seizures, and motor delay, highlighting its key role in neuronal development and function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nFurther investigation of RNU4-2 has identified an 18-base pair region within its sequence—encompassing structural elements of the U4/U6 snRNA duplex—that is highly conserved in the general population. Notably, recurrent heterozygous variants, including a common single base insertion, disrupt 5′ splice-site usage during spliceosome activation. This disruption correlates with neurodevelopmental disorders and is supported by findings that RNU4-2 is markedly expressed in the developing human brain compared to its homologues. Overall, these alterations in RNU4-2 significantly compromise the efficiency of splicing processes and explain a measurable fraction of neurodevelopmental disorder cases."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Daniel Greene, Chantal Thys, Ian R Berry, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Med (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41591-024-03085-5"}], "href": "https://doi.org/10.1038/s41591-024-03085-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38821540"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38821540"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yuyang Chen, Ruebena Dawes, Hyung Chul Kim, et al. "}, {"type": "b", "children": [{"type": "t", "text": "De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41586-024-07773-7"}], "href": "https://doi.org/10.1038/s41586-024-07773-7"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38991538"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38991538"}]}]}]}
Synonyms RNU4B1, U4C, RNU4-1B, U4A, U4B, RNU4C
NCBI Gene ID 26834
API
Download Associations
Predicted Functions View RNU4-2's ARCHS4 Predicted Functions.
Co-expressed Genes View RNU4-2's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View RNU4-2's ARCHS4 Predicted Functions.

Functional Associations

RNU4-2 has 298 functional associations with biological entities spanning 3 categories (chemical, cell line, cell type or tissue, gene, protein or microRNA) extracted from 6 datasets.

Click the + buttons to view associations for RNU4-2 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of RNU4-2 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of RNU4-2 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations transcription factor perturbations changing expression of RNU4-2 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of RNU4-2 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
GTEx Tissue Sample Gene Expression Profiles tissue samples with high or low expression of RNU4-2 gene relative to other tissue samples from the GTEx Tissue Sample Gene Expression Profiles dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of RNU4-2 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.