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	80746
Gene name	TRNA splicing endonuclease subunit 2
Gene symbol	TSEN2
Synonyms (NCBI Gene)	PCH2BSEN2SEN2L
Chromosome	3
Chromosome location	3p25.2
Summary	This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseu

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113981920	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Non coding transcript variant, synonymous variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant
rs113994149	A>G	Pathogenic	Non coding transcript variant, missense variant, intron variant, coding sequence variant
rs146117200	G>A,C	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant, missense variant, coding sequence variant, non coding transcript variant
rs730880294	C>T	Pathogenic	Stop gained, intron variant, coding sequence variant, non coding transcript variant
rs755246924	AG>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs797046051	A>G,T	Likely-pathogenic	Non coding transcript variant, downstream transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs797046052	CAA>-	Likely-pathogenic	Inframe deletion, non coding transcript variant, coding sequence variant, genic upstream transcript variant
rs886037738	GTAAG>-	Pathogenic	Splice donor variant, intron variant, non coding transcript variant, coding sequence variant
rs886037739	G>A	Pathogenic	Missense variant, intron variant, non coding transcript variant, coding sequence variant
rs1477347690	A>G	Likely-pathogenic	Missense variant, intron variant, coding sequence variant, non coding transcript variant

103

Show/Hide all (103)

miRTarBase ID	miRNA	Experiments	Reference
MIRT043908	hsa-miR-378a-3p	CLASH	23622248
MIRT1458434	hsa-miR-3065-5p	CLIP-seq
MIRT1458435	hsa-miR-1184	CLIP-seq
MIRT1458436	hsa-miR-1205	CLIP-seq
MIRT1458437	hsa-miR-1270	CLIP-seq
MIRT1458438	hsa-miR-185	CLIP-seq
MIRT1458439	hsa-miR-1910	CLIP-seq
MIRT1458440	hsa-miR-3158-5p	CLIP-seq
MIRT1458441	hsa-miR-4306	CLIP-seq
MIRT1458442	hsa-miR-4531	CLIP-seq
MIRT1458443	hsa-miR-4644	CLIP-seq
MIRT1458444	hsa-miR-620	CLIP-seq
MIRT1458445	hsa-miR-877	CLIP-seq
MIRT1458446	hsa-miR-103a	CLIP-seq
MIRT1458447	hsa-miR-107	CLIP-seq
MIRT1458448	hsa-miR-1200	CLIP-seq
MIRT1458449	hsa-miR-15a	CLIP-seq
MIRT1458450	hsa-miR-15b	CLIP-seq
MIRT1458451	hsa-miR-16	CLIP-seq
MIRT1458452	hsa-miR-1912	CLIP-seq
MIRT1458453	hsa-miR-195	CLIP-seq
MIRT1458454	hsa-miR-224	CLIP-seq
MIRT1458455	hsa-miR-3074-5p	CLIP-seq
MIRT1458456	hsa-miR-3130-5p	CLIP-seq
MIRT1458457	hsa-miR-331-3p	CLIP-seq
MIRT1458458	hsa-miR-338-3p	CLIP-seq
MIRT1458459	hsa-miR-383	CLIP-seq
MIRT1458460	hsa-miR-3908	CLIP-seq
MIRT1458461	hsa-miR-424	CLIP-seq
MIRT1458462	hsa-miR-4275	CLIP-seq
MIRT1458463	hsa-miR-4292	CLIP-seq
MIRT1458464	hsa-miR-4324	CLIP-seq
MIRT1458465	hsa-miR-4482	CLIP-seq
MIRT1458466	hsa-miR-4524	CLIP-seq
MIRT1458467	hsa-miR-4528	CLIP-seq
MIRT1458468	hsa-miR-4530	CLIP-seq
MIRT1458469	hsa-miR-4646-5p	CLIP-seq
MIRT1458470	hsa-miR-4649-3p	CLIP-seq
MIRT1458471	hsa-miR-4677-3p	CLIP-seq
MIRT1458472	hsa-miR-4747-5p	CLIP-seq
MIRT1458473	hsa-miR-4762-5p	CLIP-seq
MIRT1458474	hsa-miR-497	CLIP-seq
MIRT1458475	hsa-miR-503	CLIP-seq
MIRT1458476	hsa-miR-544b	CLIP-seq
MIRT1458477	hsa-miR-561	CLIP-seq
MIRT1458478	hsa-miR-580	CLIP-seq
MIRT1458479	hsa-miR-646	CLIP-seq
MIRT1458480	hsa-miR-891a	CLIP-seq
MIRT1458435	hsa-miR-1184	CLIP-seq
MIRT1458436	hsa-miR-1205	CLIP-seq
MIRT1458439	hsa-miR-1910	CLIP-seq
MIRT2358419	hsa-miR-3123	CLIP-seq
MIRT2358420	hsa-miR-3126-5p	CLIP-seq
MIRT1458440	hsa-miR-3158-5p	CLIP-seq
MIRT2358421	hsa-miR-4419a	CLIP-seq
MIRT2358422	hsa-miR-4510	CLIP-seq
MIRT2358423	hsa-miR-568	CLIP-seq
MIRT2396402	hsa-miR-4279	CLIP-seq
MIRT2396403	hsa-miR-4287	CLIP-seq
MIRT2396404	hsa-miR-4685-3p	CLIP-seq
MIRT2396405	hsa-miR-4780	CLIP-seq
MIRT2396406	hsa-miR-581	CLIP-seq
MIRT2396407	hsa-miR-623	CLIP-seq
MIRT2462471	hsa-miR-4776-3p	CLIP-seq
MIRT2462472	hsa-miR-4795-3p	CLIP-seq
MIRT1458435	hsa-miR-1184	CLIP-seq
MIRT1458436	hsa-miR-1205	CLIP-seq
MIRT1458437	hsa-miR-1270	CLIP-seq
MIRT2651643	hsa-miR-1827	CLIP-seq
MIRT1458438	hsa-miR-185	CLIP-seq
MIRT1458439	hsa-miR-1910	CLIP-seq
MIRT2651644	hsa-miR-2467-5p	CLIP-seq
MIRT1458440	hsa-miR-3158-5p	CLIP-seq
MIRT2396402	hsa-miR-4279	CLIP-seq
MIRT1458441	hsa-miR-4306	CLIP-seq
MIRT2651645	hsa-miR-4459	CLIP-seq
MIRT1458442	hsa-miR-4531	CLIP-seq
MIRT1458443	hsa-miR-4644	CLIP-seq
MIRT2651646	hsa-miR-4695-5p	CLIP-seq
MIRT2651647	hsa-miR-4722-5p	CLIP-seq
MIRT2651648	hsa-miR-4782-5p	CLIP-seq
MIRT1458444	hsa-miR-620	CLIP-seq
MIRT2651649	hsa-miR-760	CLIP-seq
MIRT1458445	hsa-miR-877	CLIP-seq
MIRT2651650	hsa-miR-940	CLIP-seq
MIRT1458435	hsa-miR-1184	CLIP-seq
MIRT1458436	hsa-miR-1205	CLIP-seq
MIRT1458437	hsa-miR-1270	CLIP-seq
MIRT2651643	hsa-miR-1827	CLIP-seq
MIRT1458438	hsa-miR-185	CLIP-seq
MIRT2651644	hsa-miR-2467-5p	CLIP-seq
MIRT1458440	hsa-miR-3158-5p	CLIP-seq
MIRT1458441	hsa-miR-4306	CLIP-seq
MIRT2651645	hsa-miR-4459	CLIP-seq
MIRT1458442	hsa-miR-4531	CLIP-seq
MIRT1458443	hsa-miR-4644	CLIP-seq
MIRT2651646	hsa-miR-4695-5p	CLIP-seq
MIRT2651647	hsa-miR-4722-5p	CLIP-seq
MIRT2651648	hsa-miR-4782-5p	CLIP-seq
MIRT1458444	hsa-miR-620	CLIP-seq
MIRT2651649	hsa-miR-760	CLIP-seq
MIRT1458445	hsa-miR-877	CLIP-seq
MIRT2651650	hsa-miR-940	CLIP-seq

Show/Hide all (20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000213	Function	TRNA-intron lyase activity	IBA
GO:0000213	Function	TRNA-intron lyase activity	IEA
GO:0000214	Component	TRNA-intron endonuclease complex	IBA
GO:0000214	Component	TRNA-intron endonuclease complex	IEA
GO:0000379	Process	TRNA-type intron splice site recognition and cleavage	IBA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005813	Component	Centrosome	IDA
GO:0005829	Component	Cytosol	IDA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IDA	17495927
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0008033	Process	TRNA processing	IBA
GO:0008033	Process	TRNA processing	IEA
GO:0016829	Function	Lyase activity	IEA

MIM	HGNC	e!Ensembl
608753	28422	ENSG00000154743

Q8NCE0

Protein name

tRNA-splicing endonuclease subunit Sen2 (EC 4.6.1.16) (tRNA-intron endonuclease Sen2) (HsSen2)

Protein function

Constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intr

PDB

7UXA , 7ZRZ , 8HMY , 8HMZ , 8ISS

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02778	tRNA_int_endo_N	265 → 329	tRNA intron endonuclease, N-terminal domain	Domain
PF01974	tRNA_int_endo	339 → 431	tRNA intron endonuclease, catalytic C-terminal domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Isoform 1 and isoform 2 are widely expressed at very low level. {ECO:0000269|PubMed:15109492}.

Sequence

MAEAVFHAPKRKRRVYETYESPLPIPFGQDHGPLKEFKIFRAEMINNNVIVRNAEDIEQL
YGKGYFGKGILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQHSVEWAAELMRRQGQ
DESTVRRILKDYTKPLEHPPVKRNEEAQVHDKLNSGMVSNMEGTAGGERPSVVNGDSGKS
GGVGDPREPLGCLQEGSGCHPTTESFEKSVREDASPLPHVCCCKQDALILQRGLHHEDGS
QHIGLLHPGDRGPDHEYVLVEEAECAMSEREAAPNEELVQRNRLICRRNPYRIFEYLQLS
LEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGL
KYGTDLLLYRKGPPFYHASYSVIIELVDDHFEGSLRRPLSWKSLAALSRVSVNVSKELML
CYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL

Sequence length

465

Interactions

View interactions

	Reactome
			tRNA processing in the nucleus

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 (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hemolytic-uremic syndrome	Likely pathogenic	rs759981027	RCV003484423	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pontocerebellar hypoplasia type 2B	Pathogenic; Likely pathogenic	rs2054534882, rs1553587071, rs886037738, rs886037739, rs730880294, rs797046052, rs797046051, rs774323175, rs760722955, rs755246924, rs1477347690, rs201467485	RCV001333264 RCV001814953 RCV000157627 RCV000157628 RCV000157629 View all (7 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontoneocerebellar hypoplasia	Likely pathogenic; Pathogenic	rs886037738, rs774323175, rs760722955, rs755246924	RCV003226220 RCV003479893 RCV004587864 RCV003226332	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (23)

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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEGLUTITION DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTROPHIC CARDIOMYOPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC OSTEONECROSIS OF THE FEMORAL HEAD	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOVEMENT DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-ALCOHOLIC FATTY LIVER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTAL DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PONTOCEREBELLAR HYPOPLASIA TYPE 2	—	Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PONTOCEREBELLAR HYPOPLASIA, TYPE 2B	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TSEN2-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 1 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VISION DISORDERS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (29)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital pontocerebellar hypoplasia	Pontoneocerebellar hypoplasia	GENOMICS_ENGLAND_DG	20952379		★★★★★ ★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	CTD_human_DG	18711368		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	30956117	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	30956117		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Dysphagia	Esophageal Dysphagia	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Etat Marbre	Status marmoratus	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Extrapyramidal dyskinesia	Extrapyramidal dyskinesia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemeralopia	Hemeralopia	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	CTD_human_DG	18711368		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental deficiency	Mental retardation	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	CTD_human_DG	18711368		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microlissencephaly	Microlissencephaly	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	CTD_human_DG	18711368		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Oropharyngeal Dysphagia	Oropharyngeal Dysphagia	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pontocerebellar Hypoplasia Type 2	Pontocerebellar hypoplasia	Pubtator	20803644	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar Hypoplasia Type 2	Pontoneocerebellar hypoplasia	BEFREE	23562994		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar Hypoplasia Type 2	Pontoneocerebellar hypoplasia	ORPHANET_DG	23562994		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar hypoplasia type 2	Pontoneocerebellar hypoplasia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar Hypoplasia Type 2A	Pontoneocerebellar hypoplasia	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pontocerebellar Hypoplasia Type 2B	Pontoneocerebellar hypoplasia	UNIPROT_DG	18711368		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontocerebellar Hypoplasia Type 2B	Pontoneocerebellar hypoplasia	GENOMICS_ENGLAND_DG	20952379		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontocerebellar Hypoplasia Type 2B	Pontoneocerebellar hypoplasia	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontocerebellar Hypoplasia Type 2B	Pontoneocerebellar hypoplasia	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Profound Mental Retardation	Mental retardation	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe Congenital Microcephaly	Congenital Microcephaly	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only
Vision Disability	Vision Disability	CTD_human_DG	18711368		★★★★★ ★☆☆☆☆ Found in Text Mining only

TSEN2 (tRNA splicing endonuclease subunit 2)