SPOUT1 (SPOUT domain containing methyltransferase 1)

Gene

• Entrez ID: 51490
• Gene name: SPOUT domain containing methyltransferase 1
• Gene symbol: SPOUT1
• Synonyms (NCBI Gene): C9orf114, CENP-32, CENP32, HSPC109, NEDGSB
• Chromosome: 9
• Chromosome location: 9q34.11

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT722625	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT722624	hsa-miR-29b-1-5p	HITS-CLIP	19536157
MIRT722623	hsa-miR-6837-3p	HITS-CLIP	19536157
MIRT722622	hsa-miR-219b-5p	HITS-CLIP	19536157
MIRT722621	hsa-miR-181b-2-3p	HITS-CLIP	19536157
MIRT722620	hsa-miR-181b-3p	HITS-CLIP	19536157
MIRT722619	hsa-miR-4420	HITS-CLIP	19536157
MIRT722618	hsa-miR-653-3p	HITS-CLIP	19536157
MIRT722617	hsa-miR-3977	HITS-CLIP	19536157
MIRT722616	hsa-miR-29b-2-5p	HITS-CLIP	19536157
MIRT456675	hsa-miR-7112-5p	PAR-CLIP	23592263
MIRT456674	hsa-miR-6804-5p	PAR-CLIP	23592263
MIRT456673	hsa-miR-505-5p	PAR-CLIP	23592263
MIRT456672	hsa-miR-363-5p	PAR-CLIP	23592263
MIRT456671	hsa-miR-6745	PAR-CLIP	23592263
MIRT456670	hsa-miR-6880-5p	PAR-CLIP	23592263

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000776	Component	Kinetochore	IBA
GO:0000776	Component	Kinetochore	IDA	25657325
GO:0000776	Component	Kinetochore	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	21750715
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IEA
GO:0005819	Component	Spindle	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006364	Process	RRNA processing	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0010608	Process	Post-transcriptional regulation of gene expression	IMP	28431233
GO:0016740	Function	Transferase activity	IEA
GO:0031616	Component	Spindle pole centrosome	IBA
GO:0031616	Component	Spindle pole centrosome	IDA	25657325
GO:0032259	Process	Methylation	IEA
GO:0035196	Process	MiRNA processing	IBA
GO:0035196	Process	MiRNA processing	IMP	28431233
GO:0035198	Function	MiRNA binding	IBA
GO:0035198	Function	MiRNA binding	IDA	28431233
GO:0051301	Process	Cell division	IEA
GO:0051661	Process	Maintenance of centrosome location	IBA
GO:0051661	Process	Maintenance of centrosome location	IMP	25657325
GO:0070042	Function	RRNA (uridine-N3-)-methyltransferase activity	IDA	39671501
GO:0070475	Process	RRNA base methylation	IDA	39671501
GO:0072686	Component	Mitotic spindle	IBA
GO:0072686	Component	Mitotic spindle	IDA	25657325
GO:1904047	Function	S-adenosyl-L-methionine binding	IDA	39671501

Other IDs

• MIM: 617614
• HGNC: 26933
• e!Ensembl: ENSG00000198917

Protein

• UniProt ID: Q5T280
• Protein name: 28S rRNA (uridine-N(3))-methyltransferase (EC 2.1.1.-) (Centromere protein 32) (CENP-32) (Kinetochore-associated protein) (Methyltransferase C9orf114) (Ribosomal RNA methyltransferase SPOUT1) (SPOUT domain-containing methyltransferase 1)
• Protein function: S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N3 position of a uridine in 28S rRNA (PubMed:39671501). Required for association of the centrosomes with the poles of the bipolar mitotic spindle during metapha
• PDB: 4RG1, 8QSU, 8QSV, 8QSW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02598	Methyltrn_RNA_3	74 → 364	Putative RNA methyltransferase	Family

• Sequence:

  MAERGRKRPCGPGEHGQRIEWRKWKQQKKEEKKKWKDLKLMKKLERQRAQEEQAKRLEEE
  EAAAEKEDRGRPYTLSVALPGSILDNAQSPELRTYLAGQIARACAIFCVDEIVVFDEEGQ
  DAKTVEGEFTGVGKKGQACVQLARILQYLECPQYLRKAFFPKHQDLQFAGLLNPLDSPHH
  MRQDEESEFREGIVVDRPTRPGHGSFVNCGMKKEVKIDKNLEPGLRVTVRLNQQQHPDCK
  TYHGKVVSSQDPRTKAGLYWGYTVRLASCLSAVFAEAPFQDGYDLTIGTSERGSDVASAQ
  LPNFRHALVVFGGLQGLEAGADADPNLEVAEPSVLFDLYVNTCPGQGSRTIRTEEAILIS
  LAALQPGLIQAGARHT

• Sequence length: 376

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	Likely pathogenic	rs2490935545, rs771013793, rs771869476, rs1830177686, rs374919043, rs756797528	RCV004555923 RCV004555924 RCV004555925 RCV004555926 RCV004555927 RCV004586461	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental disorder with poor growth, seizures, and brain abnormalities	Likely pathogenic	rs2490935545, rs771869476	RCV005254904 RCV005254905	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Undetermined early-onset epileptic encephalopathy	Likely pathogenic	rs771869476	RCV005100827	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC EARLY-ONSET EPILEPTIC ENCEPHALOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPOUT1 Associated Development delay Microcephaly Seizures Short stature	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPOUT1-associated neurodevelopmental disorder	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPOUT1-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Glycosuria Renal	Renal glycosuria	Pubtator	20663906	Associate	★☆☆☆☆ Found in Text Mining only