SNAPC4 (small nuclear RNA activating complex polypeptide 4)

Gene

• Entrez ID: 6621
• Gene name: Small nuclear RNA activating complex polypeptide 4
• Gene symbol: SNAPC4
• Synonyms (NCBI Gene): NEDRSO, PTFalpha, SNAP190
• Chromosome: 9
• Chromosome location: 9q34.3
• Summary: 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 promote

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT050783	hsa-miR-17-3p	CLASH	23622248
MIRT048015	hsa-miR-30c-5p	CLASH	23622248
MIRT037706	hsa-miR-744-5p	CLASH	23622248
MIRT2111635	hsa-miR-4325	CLIP-seq
MIRT2334793	hsa-miR-3615	CLIP-seq
MIRT2334794	hsa-miR-593	CLIP-seq
MIRT2334795	hsa-miR-626	CLIP-seq
MIRT2394910	hsa-miR-2110	CLIP-seq
MIRT2394911	hsa-miR-3150a-3p	CLIP-seq
MIRT2394912	hsa-miR-4271	CLIP-seq
MIRT2394913	hsa-miR-4725-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000995	Function	RNA polymerase III general transcription initiation factor activity	IDA	9418884
GO:0001006	Function	RNA polymerase III type 3 promoter sequence-specific DNA binding	IBA
GO:0003677	Function	DNA binding	IDA	9418884, 11056176
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	11056176, 28514442, 33961781, 36369505
GO:0005634	Component	Nucleus	IC	11056176
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	7715707
GO:0005654	Component	Nucleoplasm	TAS
GO:0016251	Function	RNA polymerase II general transcription initiation factor activity	IDA	9418884
GO:0019185	Component	SnRNA-activating protein complex	IBA
GO:0019185	Component	SnRNA-activating protein complex	IDA	9418884, 11056176
GO:0042795	Process	SnRNA transcription by RNA polymerase II	IBA
GO:0042795	Process	SnRNA transcription by RNA polymerase II	IDA	9418884
GO:0042796	Process	SnRNA transcription by RNA polymerase III	IBA
GO:0042796	Process	SnRNA transcription by RNA polymerase III	IDA	9418884

Other IDs

• MIM: 602777
• HGNC: 11137
• e!Ensembl: ENSG00000165684

Protein

• UniProt ID: Q5SXM2
• Protein name: snRNA-activating protein complex subunit 4 (SNAPc subunit 4) (Proximal sequence element-binding transcription factor subunit alpha) (PSE-binding factor subunit alpha) (PTF subunit alpha) (snRNA-activating protein complex 190 kDa subunit) (SNAPc 190 kDa su
• Protein function: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TB
• PDB: 7XUR, 7ZWC, 7ZWD, 7ZX7, 7ZX8, 7ZXE, 8ITY, 8IUE, 8IUH, 9FSO, 9FSP, 9FSQ, 9FSR, 9FSS
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13921	Myb_DNA-bind_6	297 → 357		Domain
  PF00249	Myb_DNA-binding	401 → 447	Myb-like DNA-binding domain	Domain
  PF00249	Myb_DNA-binding	453 → 497	Myb-like DNA-binding domain	Domain

• Sequence:

  MDVDAEREKITQEIKELERILDPGSSGSHVEISESSLESDSEADSLPSEDLDPADPPISE
  EERWGEASNDEDDPKDKTLPEDPETCLQLNMVYQEVIQEKLAEANLLLAQNREQQEELMR
  DLAGSKGTKVKDGKSLPPSTYMGHFMKPYFKDKVTGVGPPANEDTREKAAQGIKAFEELL
  VTKWKNWEKALLRKSVVSDRLQRLLQPKLLKLEYLHQKQSKVSSELERQALEKQGREAEK
  EIQDINQLPEEALLGNRLDSHDWEKISNINFEGSRSAEEIRKFWQNSEHPSINKQEWSRE
  EEERLQAIAAAHGHLEWQKIAEELGTSRSAFQCLQKFQQHNKALKRKEWTEEEDRMLTQL
  VQEMRVGSHIPYRRIVYYMEGRDSMQLIYRWTKSLDPGLKKGYWAPEEDAKLLQAVAKYG
  EQDWFKIREEVPGRSDAQCRDRYLRRLHFSLKKGRWNLKEEEQLIELIEKYGVGHWAKIA
  SELPHRSGSQCLSKWKIMMGKKQGLRRRRRRARHSVRWSSTSSSGSSSGSSGGSSSSSSS
  SSEEDEPEQAQAGEGDRALLSPQYMVPDMDLWVPARQSTSQPWRGGAGAWLGGPAASLSP
  PKGSSASQGGSKEASTTAAAPGEETSPVQVPARAHGPVPRSAQASHSADTRPAGAEKQAL
  EGGRRLLTVPVETVLRVLRANTAARSCTQKEQLRQPPLPTSSPGVSSGDSVARSHVQWLR
  HRATQSGQRRWRHALHRRLLNRRLLLAVTPWVGDVVVPCTQASQRPAVVQTQADGLREQL
  QQARLASTPVFTLFTQLFHIDTAGCLEVVRERKALPPRLPQAGARDPPVHLLQASSSAQS
  TPGHLFPNVPAQEASKSASHKGSRRLASSRVERTLPQASLLASTGPRPKPKTVSELLQEK
  RLQEARAREATRGPVVLPSQLLVSSSVILQPPLPHTPHGRPAPGPTVLNVPLSGPGAPAA
  AKPGTSGSWQEAGTSAKDKRLSTMQALPLAPVFSEAEGTAPAASQAPALGPGQISVSCPE
  SGLGQSQAPAASRKQGLPEAPPFLPAAPSPTPLPVQPLSLTHIGGPHVATSVPLPVTWVL
  TAQGLLPVPVPAVVSLPRPAGTPGPAGLLATLLPPLTETRAAQGPRAPALSSSWQPPANM
  NREPEPSCRTDTPAPPTHALSQSPAEADGSVAFVPGEAQVAREIPEPRTSSHADPPEAEP
  PWSGRLPAFGGVIPATEPRGTPGSPSGTQEPRGPLGLEKLPLRQPGPEKGALDLEKPPLP
  QPGPEKGALDLGLLSQEGEAATQQWLGGQRGVRVPLLGSRLPYQPPALCSLRALSGLLLH
  KKALEHKATSLVVGGEAERPAGALQASLGLVRGQLQDNPAYLLLRARFLAAFTLPALLAT
  LAPQGVRTTLSVPSRVGSESEDEDLLSELELADRDGQPGCTTATCPIQGAPDSGKCSASS
  CLDTSNDPDDLDVLRTRHARHTRKRRRLV

• Sequence length: 1469

Pathways

Reactome:

RNA polymerase II transcribes snRNA genes
RNA Polymerase III Transcription Initiation From Type 3 Promoter

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction	Pathogenic; Likely pathogenic	rs754828592, rs2538735580, rs144864297, rs777017571, rs1194239835	RCV003330120 RCV003330121 RCV003330122 RCV003330123 RCV003330124	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANKYLOSING SPONDYLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Ankylosing spondylitis	Ankylosing Spondylitis	BEFREE	20463747, 24334645, 26590821		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Basal Ganglia Diseases	Basal ganglia disease	Pubtator	36965478	Associate	★☆☆☆☆ Found in Text Mining only
Heart Diseases	Heart disease	Pubtator	36965478	Associate	★☆☆☆☆ Found in Text Mining only
Paraparesis	Paraparesis	Pubtator	36965478	Associate	★☆☆☆☆ Found in Text Mining only
Paraparesis Spastic	Paraparesis	Pubtator	36965478	Associate	★☆☆☆☆ Found in Text Mining only