EMG1 (EMG1 N1-specific pseudouridine methyltransferase)

Gene

• Entrez ID: 10436
• Gene name: EMG1 N1-specific pseudouridine methyltransferase
• Gene symbol: EMG1
• Synonyms (NCBI Gene): C2F, Grcc2f, NEP1
• Chromosome: 12
• Chromosome location: 12p13.31
• Summary: This gene encodes an essential, conserved eukaryotic protein that methylates pseudouridine in 18S rRNA. The related protein in yeast is a component of the small subunit processome and is essential for biogenesis of the ribosomal 40S subunit. A mutation in

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs74435397	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT961940	hsa-miR-1265	CLIP-seq
MIRT961941	hsa-miR-144	CLIP-seq
MIRT961942	hsa-miR-148a	CLIP-seq
MIRT961943	hsa-miR-148b	CLIP-seq
MIRT961944	hsa-miR-152	CLIP-seq
MIRT961945	hsa-miR-2355-5p	CLIP-seq
MIRT961946	hsa-miR-298	CLIP-seq
MIRT961947	hsa-miR-376a	CLIP-seq
MIRT961948	hsa-miR-376b	CLIP-seq
MIRT961949	hsa-miR-3913-3p	CLIP-seq
MIRT961950	hsa-miR-3942-3p	CLIP-seq
MIRT961951	hsa-miR-421	CLIP-seq
MIRT961952	hsa-miR-4264	CLIP-seq
MIRT961953	hsa-miR-4501	CLIP-seq
MIRT961954	hsa-miR-4504	CLIP-seq
MIRT961955	hsa-miR-4696	CLIP-seq
MIRT961956	hsa-miR-4709-5p	CLIP-seq
MIRT961957	hsa-miR-4764-5p	CLIP-seq
MIRT961958	hsa-miR-4773	CLIP-seq
MIRT961959	hsa-miR-4797-3p	CLIP-seq
MIRT961960	hsa-miR-489	CLIP-seq
MIRT961961	hsa-miR-542-3p	CLIP-seq
MIRT961962	hsa-miR-548p	CLIP-seq
MIRT961963	hsa-miR-664	CLIP-seq
MIRT961940	hsa-miR-1265	CLIP-seq
MIRT961945	hsa-miR-2355-5p	CLIP-seq
MIRT961947	hsa-miR-376a	CLIP-seq
MIRT961948	hsa-miR-376b	CLIP-seq
MIRT961949	hsa-miR-3913-3p	CLIP-seq
MIRT961951	hsa-miR-421	CLIP-seq
MIRT961953	hsa-miR-4501	CLIP-seq
MIRT961954	hsa-miR-4504	CLIP-seq
MIRT961956	hsa-miR-4709-5p	CLIP-seq
MIRT961957	hsa-miR-4764-5p	CLIP-seq
MIRT961960	hsa-miR-489	CLIP-seq
MIRT961961	hsa-miR-542-3p	CLIP-seq
MIRT961963	hsa-miR-664	CLIP-seq
MIRT961940	hsa-miR-1265	CLIP-seq
MIRT961942	hsa-miR-148a	CLIP-seq
MIRT961943	hsa-miR-148b	CLIP-seq
MIRT961944	hsa-miR-152	CLIP-seq
MIRT961945	hsa-miR-2355-5p	CLIP-seq
MIRT961949	hsa-miR-3913-3p	CLIP-seq
MIRT961951	hsa-miR-421	CLIP-seq
MIRT961952	hsa-miR-4264	CLIP-seq
MIRT961953	hsa-miR-4501	CLIP-seq
MIRT961954	hsa-miR-4504	CLIP-seq
MIRT961956	hsa-miR-4709-5p	CLIP-seq
MIRT961957	hsa-miR-4764-5p	CLIP-seq
MIRT961959	hsa-miR-4797-3p	CLIP-seq
MIRT961960	hsa-miR-489	CLIP-seq
MIRT961961	hsa-miR-542-3p	CLIP-seq
MIRT961962	hsa-miR-548p	CLIP-seq
MIRT961945	hsa-miR-2355-5p	CLIP-seq
MIRT961945	hsa-miR-2355-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001824	Process	Blastocyst development	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	ISS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IDA
GO:0005730	Component	Nucleolus	IDA
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	ISS
GO:0005737	Component	Cytoplasm	ISS
GO:0006364	Process	RRNA processing	IEA
GO:0006364	Process	RRNA processing	ISS
GO:0008168	Function	Methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0017126	Process	Nucleologenesis	IEA
GO:0019843	Function	RRNA binding	IBA
GO:0019843	Function	RRNA binding	IEA
GO:0032040	Component	Small-subunit processome	IBA
GO:0032040	Component	Small-subunit processome	IDA	34516797
GO:0032259	Process	Methylation	IEA
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042274	Process	Ribosomal small subunit biogenesis	IDA	34516797
GO:0042274	Process	Ribosomal small subunit biogenesis	ISS
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0070037	Function	RRNA (pseudouridine) methyltransferase activity	IBA
GO:0070037	Function	RRNA (pseudouridine) methyltransferase activity	IDA	20047967
GO:0070037	Function	RRNA (pseudouridine) methyltransferase activity	IEA
GO:0070475	Process	RRNA base methylation	IBA
GO:0070475	Process	RRNA base methylation	IEA

Other IDs

• MIM: 611531
• HGNC: 16912
• e!Ensembl: ENSG00000126749

Protein

• UniProt ID: Q92979
• Protein name: Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.-) (18S rRNA (pseudouridine(1248)-N1)-methyltransferase) (18S rRNA Psi1248 methyltransferase) (Nucleolar protein EMG1 homolog) (Protein C2f) (Ribosome biogenesis protein NEP1)
• Protein function: S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1248 (Psi1248) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1a
• PDB: 5FAI, 7MQ8, 7MQ9, 7MQA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03587	EMG1	45 → 238	EMG1/NEP1 methyltransferase	Family

• Sequence:

  MAAPSDGFKPRERSGGEQAQDWDALPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKT
  YELLNCDKHKSILLKNGRDPGEARPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEV
  NPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKVGTSFSI
  PVVSDVRELVPSSDPIVFVVGAFAHGKVSVEYTEKMVSISNYPLSAALTCAKLTTAFEEV
  WGVI

• Sequence length: 244

Pathways

KEGG:

Ribosome biogenesis in eukaryotes

Reactome:

Major pathway of rRNA processing in the nucleolus and cytosol

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Bowen-Conradi syndrome	Pathogenic	rs74435397	RCV000000938

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
EMG1-related disorder	Likely benign	rs782249279, rs2542785102, rs147457308	RCV003923999 RCV003897414 RCV003934520

Associations from Text Mining
Disease Name	Relationship Type	References
Bowen Conradi syndrome	Associate	20047967, 20972225, 27798105
Developmental Disabilities	Associate	20047967
Sarcoma Ewing	Associate	33230229
Wilms Tumor	Associate	33230229