Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10436
Gene name	EMG1 N1-specific pseudouridine methyltransferase
Gene symbol	EMG1
Synonyms (NCBI Gene)	C2FGrcc2fNEP1
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

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

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miRTarBase ID	miRNA	Experiments
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

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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

MIM	HGNC	e!Ensembl
611531	16912	ENSG00000126749

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

Interactions

View interactions

	KEGG		Reactome
	Ribosome biogenesis in eukaryotes		Major pathway of rRNA processing in the nucleolus and cytosol

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)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Bowen-Conradi syndrome	Pathogenic	rs74435397	RCV000000938	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
EMG1-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (30)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma, Clear Cell	Adenocarcinoma	BEFREE	30826751		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma, Endometrioid	Endometrial Cancer	BEFREE	30826751		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	BEFREE	19463982, 20858271, 20972225, 24240090, 25708872, 27798105		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	GENOMICS_ENGLAND_DG	19463982, 27798105, 30914295		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	ORPHANET_DG	19463982		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	UNIPROT_DG	19463982		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bowen-Conradi syndrome	Bowen-Conradi Syndrome	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Carcinoma, Endometrioid	Endometrioid cancer	BEFREE	30826751		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinosarcoma	Carcinosarcoma	BEFREE	30826751		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	31169192		★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	20047967	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	20858271		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ewings sarcoma	Ewing sarcoma	BEFREE	17154184, 30481065		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	17154184, 26176219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	15254018, 17154184, 29509256, 29552042		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	BEFREE	25708872		★★★★★ ★☆☆☆☆ Found in Text Mining only
NORTH AMERICAN INDIAN CHILDHOOD CIRRHOSIS	Cirrhosis	BEFREE	24240090		★★★★★ ★☆☆☆☆ Found in Text Mining only
Oral cleft	Oral cleft	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sarcoma Ewing	Sarcoma	Pubtator	33230229	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scleroderma	Scleroderma	BEFREE	24240090		★★★★★ ★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	24240090		★★★★★ ★☆☆☆☆ Found in Text Mining only
Vertical Talus	Vertical Talus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Wilms Tumor	Wilms tumor	Pubtator	33230229	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

EMG1 (EMG1 N1-specific pseudouridine methyltransferase)