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	54888
Gene name	NOP2/Sun RNA methyltransferase 2
Gene symbol	NSUN2
Synonyms (NCBI Gene)	MISUMRT5SAKITRM4
Chromosome	5
Chromosome location	5p15.31
Summary	This gene encodes a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. This modification is necessary to stabilize the anticodon-codon pairing and correctly

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs387907190	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs387907191	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs587776908	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1085307575	C>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1085307745	ATCT>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1560982564	C>G	Pathogenic	Intron variant, splice acceptor variant
rs1579360593	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1579368865	T>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1579370234	->T	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1579377990	TT>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

Show/Hide all (63)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022997	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT052294	hsa-let-7b-5p	CLASH	23622248
MIRT051217	hsa-miR-16-5p	CLASH	23622248
MIRT045952	hsa-miR-125b-5p	CLASH	23622248
MIRT045478	hsa-miR-149-5p	CLASH	23622248
MIRT041441	hsa-miR-193b-3p	CLASH	23622248
MIRT052738	hsa-miR-1260b	CLASH	23622248
MIRT439714	hsa-miR-21-5p	HITS-CLIP	22473208
MIRT439714	hsa-miR-21-5p	HITS-CLIP	22473208
MIRT1195401	hsa-miR-2053	CLIP-seq
MIRT1195402	hsa-miR-217	CLIP-seq
MIRT1195403	hsa-miR-329	CLIP-seq
MIRT1195404	hsa-miR-362-3p	CLIP-seq
MIRT1195405	hsa-miR-425	CLIP-seq
MIRT1195406	hsa-miR-4286	CLIP-seq
MIRT1195407	hsa-miR-569	CLIP-seq
MIRT1195408	hsa-miR-642b	CLIP-seq
MIRT1195409	hsa-miR-124	CLIP-seq
MIRT1195410	hsa-miR-1910	CLIP-seq
MIRT1195411	hsa-miR-3192	CLIP-seq
MIRT1195412	hsa-miR-326	CLIP-seq
MIRT1195413	hsa-miR-330-5p	CLIP-seq
MIRT1195414	hsa-miR-3664-5p	CLIP-seq
MIRT1195415	hsa-miR-4274	CLIP-seq
MIRT1195416	hsa-miR-4314	CLIP-seq
MIRT1195417	hsa-miR-4646-5p	CLIP-seq
MIRT1195418	hsa-miR-4714-5p	CLIP-seq
MIRT1195419	hsa-miR-506	CLIP-seq
MIRT1195420	hsa-miR-548an	CLIP-seq
MIRT1195421	hsa-miR-550b	CLIP-seq
MIRT2056682	hsa-miR-944	CLIP-seq
MIRT1195411	hsa-miR-3192	CLIP-seq
MIRT1195412	hsa-miR-326	CLIP-seq
MIRT1195413	hsa-miR-330-5p	CLIP-seq
MIRT1195414	hsa-miR-3664-5p	CLIP-seq
MIRT1195416	hsa-miR-4314	CLIP-seq
MIRT1195417	hsa-miR-4646-5p	CLIP-seq
MIRT1195418	hsa-miR-4714-5p	CLIP-seq
MIRT1195421	hsa-miR-550b	CLIP-seq
MIRT2285137	hsa-miR-1301	CLIP-seq
MIRT1195410	hsa-miR-1910	CLIP-seq
MIRT1195403	hsa-miR-329	CLIP-seq
MIRT1195404	hsa-miR-362-3p	CLIP-seq
MIRT2285138	hsa-miR-380	CLIP-seq
MIRT2285139	hsa-miR-3944-5p	CLIP-seq
MIRT1195405	hsa-miR-425	CLIP-seq
MIRT1195415	hsa-miR-4274	CLIP-seq
MIRT2285140	hsa-miR-4660	CLIP-seq
MIRT2285141	hsa-miR-5047	CLIP-seq
MIRT2285142	hsa-miR-545	CLIP-seq
MIRT2285143	hsa-miR-548p	CLIP-seq
MIRT1195408	hsa-miR-642b	CLIP-seq
MIRT2285137	hsa-miR-1301	CLIP-seq
MIRT1195410	hsa-miR-1910	CLIP-seq
MIRT1195403	hsa-miR-329	CLIP-seq
MIRT1195404	hsa-miR-362-3p	CLIP-seq
MIRT2285139	hsa-miR-3944-5p	CLIP-seq
MIRT1195415	hsa-miR-4274	CLIP-seq
MIRT2285140	hsa-miR-4660	CLIP-seq
MIRT2285141	hsa-miR-5047	CLIP-seq
MIRT1195408	hsa-miR-642b	CLIP-seq
MIRT1195410	hsa-miR-1910	CLIP-seq
MIRT1195415	hsa-miR-4274	CLIP-seq

Show/Hide all (53)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IBA
GO:0000049	Function	TRNA binding	IEA
GO:0001510	Process	RNA methylation	IEA
GO:0001701	Process	In utero embryonic development	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	33961781
GO:0005576	Component	Extracellular region	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA	17071714
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	17071714
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	31276587, 31287866
GO:0005739	Component	Mitochondrion	IEA
GO:0005819	Component	Spindle	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006397	Process	MRNA processing	IDA	22395603, 28418038, 31358969
GO:0006397	Process	MRNA processing	IEA
GO:0006400	Process	TRNA modification	TAS
GO:0007283	Process	Spermatogenesis	IEA
GO:0007286	Process	Spermatid development	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008173	Function	RNA methyltransferase activity	IEA
GO:0008757	Function	S-adenosylmethionine-dependent methyltransferase activity	IEA
GO:0010793	Process	Regulation of mRNA export from nucleus	IDA	28418038
GO:0016428	Function	TRNA (cytidine-5-)-methyltransferase activity	EXP	17071714
GO:0016428	Function	TRNA (cytidine-5-)-methyltransferase activity	IBA
GO:0016428	Function	TRNA (cytidine-5-)-methyltransferase activity	IDA	17071714, 31287866, 34556860
GO:0016428	Function	TRNA (cytidine-5-)-methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030488	Process	TRNA methylation	IBA
GO:0030488	Process	TRNA methylation	IDA	17071714, 31287866
GO:0030488	Process	TRNA methylation	IEA
GO:0032259	Process	Methylation	IEA
GO:0033313	Process	Meiotic cell cycle checkpoint signaling	IEA
GO:0033391	Component	Chromatoid body	IEA
GO:0036416	Process	TRNA stabilization	IEA
GO:0036416	Process	TRNA stabilization	ISS
GO:0048820	Process	Hair follicle maturation	IEA
GO:0048820	Process	Hair follicle maturation	ISS
GO:0051301	Process	Cell division	IEA
GO:0062152	Function	MRNA (cytidine-5-)-methyltransferase activity	IDA	22395603, 28418038, 31358969
GO:0062152	Function	MRNA (cytidine-5-)-methyltransferase activity	IEA
GO:0070062	Component	Extracellular exosome	IDA	28341602
GO:2000736	Process	Regulation of stem cell differentiation	IEA
GO:2000736	Process	Regulation of stem cell differentiation	ISS

MIM	HGNC	e!Ensembl
610916	25994	ENSG00000037474

Q08J23

Protein name

RNA cytosine C(5)-methyltransferase NSUN2 (EC 2.1.1.-) (Myc-induced SUN domain-containing protein) (Misu) (NOL1/NOP2/Sun domain family member 2) (Substrate of AIM1/Aurora kinase B) (mRNA cytosine C(5)-methyltransferase) (EC 2.1.1.-) (tRNA cytosine C(5)-me

Protein function

RNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs (lncRNAs) (PubMed:17071714, PubMed:22995836, PubMed:31199786, PubMed:31358969). Involved i

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01189	Methyltr_RsmB-F	169 → 369	16S rRNA methyltransferase RsmB/F	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in adult and fetal brain and in lymphoblastoid cells. {ECO:0000269|PubMed:22541559}.

Sequence

MGRRSRGRRLQQQQRPEDAEDGAEGGGKRGEAGWEGGYPEIVKENKLFEHYYQELKIVPE
GEWGQFMDALREPLPATLRITGYKSHAKEILHCLKNKYFKELEDLEVDGQKVEVPQPLSW
YPEELAWHTNLSRKILRKSPHLEKFHQFLVSETESGNISRQEAVSMIPPLLLNVRPHHKI
LDMCAAPGSKTTQLIEMLHADMNVPFPEGFVIANDVDNKRCYLLVHQAKRLSSPCIMVVN
HDASSIPRLQIDVDGRKEILFYDRILCDVPCSGDGTMRKNIDVWKKWTTLNSLQLHGLQL
RIATRGAEQLAEGGRMVYSTCSLNPIEDEAVIASLLEKSEGALELADVSNELPGLKWMPG
ITQWKVMTKDGQWFTDWDAVPHSRHTQIRPTMFPPKDPEKLQAMHLERCLRILPHHQNTG
GFFVAVLVKKSSMPWNKRQPKLQGKSAETRESTQLSPADLTEGKPTDPSKLESPSFTGTG
DTEIAHATEDLENNGSKKDGVCGPPPSKKMKLFGFKEDPFVFIPEDDPLFPPIEKFYALD
PSFPRMNLLTRTTEGKKRQLYMVSKELRNVLLNNSEKMKVINTGIKVWCRNNSGEEFDCA
FRLAQEGIYTLYPFINSRIITVSMEDVKILLTQENPFFRKLSSETYSQAKDLAKGSIVLK
YEPDSANPDALQCPIVLCGWRGKASIRTFVPKNERLHYLRMMGLEVLGEKKKEGVILTNE
SAASTGQPDNDVTEGQRAGEPNSPDAEEANSPDVTAGCDPAGVHPPR

Sequence length

767

Interactions

View interactions

	Reactome
			tRNA modification in the nucleus and cytosol

169

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive non-syndromic intellectual disability	Likely pathogenic; Pathogenic	rs1377452635, rs868442196	RCV003331119 RCV003226479
Intellectual disability	Pathogenic	rs1579368865	RCV004798882
Intellectual disability, autosomal recessive 5	Likely pathogenic; Pathogenic	rs1377452635, rs1403893283, rs2477413153, rs1737230745, rs2477508063, rs2477448485, rs2126481981, rs387907190, rs387907191, rs2126499522, rs587776908, rs1560982564, rs1579370234, rs1579377990, rs1579368865, rs762288077, rs1041431561 View all (2 more)	RCV001332181 RCV001543353 RCV002283598 RCV002305693 RCV003226540 RCV003223501 RCV003486332 RCV000024355 RCV000024356 RCV000024357 RCV000024358 RCV000030682 RCV000984498 RCV000991432 RCV001027963 RCV003147576 RCV004783922
Phenylketonuria	Pathogenic	rs1579368865	RCV005860176
See cases	Likely pathogenic; Pathogenic	rs1221890051	RCV002252421

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs10051208, rs76534720	RCV005921944 RCV005923425
Cholangiocarcinoma	Benign	rs368018490	RCV005868262
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Uncertain significance	rs202085420	RCV005899884
Familial cancer of breast	Benign; Likely benign	rs6887702, rs139131959	RCV005915664 RCV005869376
Gastric cancer	Benign; Likely benign	rs139131959	RCV005869377
Intellectual Disability, Recessive	Conflicting classifications of pathogenicity; Likely benign; Benign; Uncertain significance	rs8192122, rs147269098, rs200230801, rs139131959, rs779027908, rs886060730, rs8192125, rs139145592, rs4702373, rs562817249, rs569790049, rs8192123, rs8192124, rs778200969	RCV000329185 RCV000321887 RCV000385790 RCV000318971 RCV000274142 RCV000380109 RCV000282075 RCV000298290 RCV000355528 RCV000325617 RCV000376517 RCV000365128 RCV000270497 RCV000285782
Lung cancer	Likely benign; Benign	rs16877643, rs76534720	RCV005915996 RCV005923426
Malignant lymphoma, large B-cell, diffuse	Benign	rs368018490	RCV005868261
Malignant tumor of esophagus	Benign	rs10051208	RCV005921943
NSUN2-related disorder	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs13181449, rs184594943, rs150809074, rs143551642, rs140673211, rs527650370, rs141912087, rs756450204, rs181415619, rs147958833, rs138016489	RCV003975030 RCV003915155 RCV003958814 RCV003973403 RCV003917762 RCV003967503 RCV003912509 RCV003912508 RCV003912510 RCV003938063 RCV003965478
Ovarian serous cystadenocarcinoma	Uncertain significance	rs202085420	RCV005899882
Uterine carcinosarcoma	Benign	rs13181449	RCV005889171
Uterine corpus endometrial carcinoma	Likely benign; Benign; Uncertain significance	rs16877643, rs76534720, rs202085420	RCV005915997 RCV005923427 RCV005899883

Show/Hide Text Mining Associations (37)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Inhibit	33337366
Aortic Aneurysm Abdominal	Associate	34856760
Ataxia Telangiectasia	Associate	38183111
Autism Spectrum Disorder	Associate	31209396
Breast Neoplasms	Associate	40555775
Carcinogenesis	Associate	37586363, 38065062
Carcinoma Non Small Cell Lung	Associate	37161388
Corneal Diseases	Associate	36862118
Developmental Disabilities	Associate	33002343
Disease	Associate	37226891
Drug Related Side Effects and Adverse Reactions	Associate	38183111
Dubowitz syndrome	Associate	33098347
Endometrial Neoplasms	Stimulate	38042059
Facial Dysmorphism with Multiple Malformations	Associate	33002343
Foot Deformities	Associate	33002343
Growth Disorders	Associate	33002343
Hallux Valgus	Associate	33002343
Intellectual Disability	Associate	33002343
Leukemia	Associate	38065062
Lymphoma	Associate	33858292
Lymphoma Non Hodgkin	Associate	33400376
Microcephaly	Associate	33002343
Neoplasm Metastasis	Associate	34504059
Neoplasm Metastasis	Stimulate	36632452
Neoplasms	Associate	31957540, 34504059, 36169095, 37161388, 37228185, 37769000, 38042059, 38183111, 39742570, 40555775
Osteosarcoma	Associate	36792587
Precancerous Conditions	Associate	34504059
Prostatic Neoplasms	Associate	36169095
Retinoblastoma	Associate	37228185
Squamous Cell Carcinoma of Head and Neck	Associate	31887619
Stomach Neoplasms	Stimulate	34504059
Stomach Neoplasms	Associate	37582794
Thyroid Carcinoma Anaplastic	Associate	37983928
Thyroid Neoplasms	Associate	37983928
Tooth Mobility	Associate	33002343
Uterine Cervical Neoplasms	Associate	36632452
Uveal melanoma	Associate	35757999

NSUN2 (NOP2/Sun RNA methyltransferase 2)