SNAPC4 Gene

HGNC Family	SANT/Myb domain containing
Name	small nuclear RNA activating complex, polypeptide 4, 190kDa
Description	This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRecent genome‐wide association studies have implicated SNAPC4 in the pathogenesis of ankylosing spondylitis (AS). In several independent case–control investigations (including studies in European, Iranian, and Chinese populations), a non‐synonymous single‐nucleotide polymorphism in SNAPC4 (rs3812571) was found to be modestly but significantly associated with AS risk. Despite these associations, the precise mechanistic contribution of SNAPC4 to AS remains to be fully delineated, with some studies noting a closer correlation between the strongest genetic signals and altered expression of related immune regulators."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAt the molecular level, SNAPC4 serves as an essential subunit of the snRNA‐activating protein complex (SNAPc), which is central to the transcription of small nuclear RNA (snRNA) genes by both RNA polymerase II and III. In this context, SNAPC4 (also referred to as SNAP190) binds to snRNA gene promoters to facilitate pre‐initiation complex assembly. Notably, phosphorylation by protein kinase CK2 of specific regions within SNAPC4 negatively modulates its DNA‐binding ability and subsequently reduces transcription from U6 snRNA promoters. In contrast, for U1 snRNA gene transcription, CK2-mediated phosphorylation similarly impedes promoter binding by SNAPc, underscoring a regulatory mechanism that differentially impacts snRNA gene expression based on promoter context."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn a clinical context, bi-allelic deleterious variants in SNAPC4 have been shown to markedly diminish SNAPC4 protein levels, leading to reduced expression of several snRNAs and a global disruption of alternative splicing. This molecular disruption is associated with a neurodevelopmental phenotype characterized by delayed motor skills, developmental regression, progressive spasticity, and neuroanatomical abnormalities such as cerebral and cerebellar volume loss. These findings underscore the critical role of SNAPC4 in maintaining proper snRNA transcription and splicing homeostasis, which is essential for normal neural development and function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "J J Pointon, D Harvey, T Karaderi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Elucidating the chromosome 9 association with AS; CARD9 is a candidate gene."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Immun (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/gene.2010.17"}], "href": "https://doi.org/10.1038/gene.2010.17"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20463747"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20463747"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Parisa Momenzadeh, Mahdi Mahmoudi, Maani Beigy, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Determination of IL1 R2, ANTXR2, CARD9, and SNAPC4 single nucleotide polymorphisms in Iranian patients with ankylosing spondylitis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Rheumatol Int (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00296-015-3391-1"}], "href": "https://doi.org/10.1007/s00296-015-3391-1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26590821"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26590821"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Xiaochun Ma, Yongchao Liu, Hua Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Evidence for genetic association of CARD9 and SNAPC4 with ankylosing spondylitis in a Chinese Han population."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Rheumatol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3899/jrheum.130519"}], "href": "https://doi.org/10.3899/jrheum.130519"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24334645"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24334645"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Liping Gu, Rhonda Husain-Ponnampalam, Susanne Hoffmann-Benning, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The protein kinase CK2 phosphorylates SNAP190 to negatively regulate SNAPC DNA binding and human U6 transcription by RNA polymerase III."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M702269200"}], "href": "https://doi.org/10.1074/jbc.M702269200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17670747"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17670747"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Liping Gu, Walter J Esselman, R William Henry "}, {"type": "b", "children": [{"type": "t", "text": "Cooperation between small nuclear RNA-activating protein complex (SNAPC) and TATA-box-binding protein antagonizes protein kinase CK2 inhibition of DNA binding by SNAPC."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M503206200"}], "href": "https://doi.org/10.1074/jbc.M503206200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15955816"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15955816"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "F Graeme Frost, Marie Morimoto, Prashant Sharma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Hum Genet (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ajhg.2023.03.001"}], "href": "https://doi.org/10.1016/j.ajhg.2023.03.001"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36965478"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36965478"}]}]}]}
Synonyms	SNAP190, PTFALPHA
Proteins	SNPC4_HUMAN
NCBI Gene ID	6621
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SNAPC4 has 5,736 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 114 datasets.

Click the + buttons to view associations for SNAPC4 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SNAPC4 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by SNAPC4 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SNAPC4 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SNAPC4 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SNAPC4 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SNAPC4 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SNAPC4 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SNAPC4 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SNAPC4 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SNAPC4 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SNAPC4 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of SNAPC4 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SNAPC4 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SNAPC4 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with SNAPC4 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SNAPC4 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SNAPC4 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SNAPC4 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SNAPC4 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SNAPC4 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SNAPC4 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing SNAPC4 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SNAPC4 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SNAPC4 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing SNAPC4 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SNAPC4 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with SNAPC4 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with SNAPC4 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with SNAPC4 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SNAPC4 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SNAPC4 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SNAPC4 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with SNAPC4 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at SNAPC4 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SNAPC4 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of SNAPC4 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing SNAPC4 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with SNAPC4 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with SNAPC4 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of SNAPC4 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with SNAPC4 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.