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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	283989
Gene name Gene Name - the full gene name approved by the HGNC.	TRNA splicing endonuclease subunit 54
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TSEN54
Synonyms (NCBI Gene) Gene synonyms aliases	PCH2A, PCH4, PCH5, SEN54L, sen54
Disease Acronyms (UniProt) Disease acronyms from UniProt database	PCH2A, PCH4, PCH5
Chromosome Chromosome number	17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	17q25.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypopla

Show/Hide all(19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113994152	G>T	Pathogenic, pathogenic-likely-pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs113994153	C>T	Pathogenic	Coding sequence variant, stop gained
rs113994154	C>T	Pathogenic	Coding sequence variant, stop gained
rs143604970	A>C,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs587784475	G>C,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs587784479	AC>-	Pathogenic	Coding sequence variant, frameshift variant
rs762142684	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs767505004	->GAGCACCACGCGGAGGCCG	Pathogenic	Frameshift variant, coding sequence variant
rs774157225	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs776960594	T>C	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs778884343	C>T	Pathogenic	Stop gained, coding sequence variant
rs797046057	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs886037629	AGAGGAGCCAGCGC>-	Pathogenic	Coding sequence variant, frameshift variant
rs886037740	T>C	Pathogenic	Splice donor variant
rs1012275384	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1057517911	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1337062385	C>T	Pathogenic	Coding sequence variant, stop gained
rs1555644470	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1598477502	G>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all(160)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022257	hsa-miR-124-3p	Microarray	18668037
MIRT042278	hsa-miR-484	CLASH	23622248
MIRT458058	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT458057	hsa-miR-9500	PAR-CLIP	23592263
MIRT458056	hsa-miR-6760-5p	PAR-CLIP	23592263
MIRT458055	hsa-miR-1178-5p	PAR-CLIP	23592263
MIRT458054	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT458053	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT458052	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT458051	hsa-miR-214-3p	PAR-CLIP	23592263
MIRT458050	hsa-miR-3619-5p	PAR-CLIP	23592263
MIRT458049	hsa-miR-761	PAR-CLIP	23592263
MIRT458048	hsa-miR-7515	PAR-CLIP	23592263
MIRT458047	hsa-miR-3202	PAR-CLIP	23592263
MIRT458046	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT458045	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT458044	hsa-miR-6731-5p	PAR-CLIP	23592263
MIRT458043	hsa-miR-8085	PAR-CLIP	23592263
MIRT458042	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT458041	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT458039	hsa-miR-8073	PAR-CLIP	23592263
MIRT458055	hsa-miR-1178-5p	PAR-CLIP	26701625
MIRT458054	hsa-miR-128-3p	PAR-CLIP	26701625
MIRT458051	hsa-miR-214-3p	PAR-CLIP	26701625
MIRT458053	hsa-miR-216a-3p	PAR-CLIP	26701625
MIRT458042	hsa-miR-27a-3p	PAR-CLIP	26701625
MIRT458041	hsa-miR-27b-3p	PAR-CLIP	26701625
MIRT458047	hsa-miR-3202	PAR-CLIP	26701625
MIRT458050	hsa-miR-3619-5p	PAR-CLIP	26701625
MIRT458052	hsa-miR-3681-3p	PAR-CLIP	26701625
MIRT458046	hsa-miR-4747-5p	PAR-CLIP	26701625
MIRT458045	hsa-miR-5196-5p	PAR-CLIP	26701625
MIRT458058	hsa-miR-6510-5p	PAR-CLIP	26701625
MIRT458044	hsa-miR-6731-5p	PAR-CLIP	26701625
MIRT458056	hsa-miR-6760-5p	PAR-CLIP	26701625
MIRT458048	hsa-miR-7515	PAR-CLIP	26701625
MIRT458049	hsa-miR-761	PAR-CLIP	26701625
MIRT458039	hsa-miR-8073	PAR-CLIP	26701625
MIRT458043	hsa-miR-8085	PAR-CLIP	26701625
MIRT458057	hsa-miR-9500	PAR-CLIP	26701625
MIRT458058	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT458057	hsa-miR-9500	PAR-CLIP	23592263
MIRT458056	hsa-miR-6760-5p	PAR-CLIP	23592263
MIRT458055	hsa-miR-1178-5p	PAR-CLIP	23592263
MIRT458054	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT458053	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT458052	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT458051	hsa-miR-214-3p	PAR-CLIP	23592263
MIRT458050	hsa-miR-3619-5p	PAR-CLIP	23592263
MIRT458049	hsa-miR-761	PAR-CLIP	23592263
MIRT458048	hsa-miR-7515	PAR-CLIP	23592263
MIRT458047	hsa-miR-3202	PAR-CLIP	23592263
MIRT458046	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT458045	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT458044	hsa-miR-6731-5p	PAR-CLIP	23592263
MIRT458043	hsa-miR-8085	PAR-CLIP	23592263
MIRT458042	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT458041	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT458039	hsa-miR-8073	PAR-CLIP	23592263
MIRT1458528	hsa-miR-1200	CLIP-seq
MIRT1458529	hsa-miR-1203	CLIP-seq
MIRT1458530	hsa-miR-125a-5p	CLIP-seq
MIRT1458531	hsa-miR-125b	CLIP-seq
MIRT1458532	hsa-miR-127-5p	CLIP-seq
MIRT1458533	hsa-miR-128	CLIP-seq
MIRT1458534	hsa-miR-1324	CLIP-seq
MIRT1458535	hsa-miR-146a	CLIP-seq
MIRT1458536	hsa-miR-146b-5p	CLIP-seq
MIRT1458537	hsa-miR-1915	CLIP-seq
MIRT1458538	hsa-miR-193a-3p	CLIP-seq
MIRT1458539	hsa-miR-193b	CLIP-seq
MIRT1458540	hsa-miR-214	CLIP-seq
MIRT1458541	hsa-miR-2276	CLIP-seq
MIRT1458542	hsa-miR-27a	CLIP-seq
MIRT1458543	hsa-miR-27b	CLIP-seq
MIRT1458544	hsa-miR-3176	CLIP-seq
MIRT1458545	hsa-miR-3180-5p	CLIP-seq
MIRT1458546	hsa-miR-3714	CLIP-seq
MIRT1458547	hsa-miR-3918	CLIP-seq
MIRT1458548	hsa-miR-3922-3p	CLIP-seq
MIRT1458549	hsa-miR-3922-5p	CLIP-seq
MIRT1458550	hsa-miR-4251	CLIP-seq
MIRT1458551	hsa-miR-4269	CLIP-seq
MIRT1458552	hsa-miR-4319	CLIP-seq
MIRT1458553	hsa-miR-4324	CLIP-seq
MIRT1458554	hsa-miR-4449	CLIP-seq
MIRT1458555	hsa-miR-4463	CLIP-seq
MIRT1458556	hsa-miR-4494	CLIP-seq
MIRT1458557	hsa-miR-4682	CLIP-seq
MIRT1458558	hsa-miR-4685-5p	CLIP-seq
MIRT1458559	hsa-miR-4690-5p	CLIP-seq
MIRT1458560	hsa-miR-4708-3p	CLIP-seq
MIRT1458561	hsa-miR-4732-3p	CLIP-seq
MIRT1458562	hsa-miR-4746-5p	CLIP-seq
MIRT1458563	hsa-miR-4757-5p	CLIP-seq
MIRT1458564	hsa-miR-4773	CLIP-seq
MIRT1458565	hsa-miR-4783-3p	CLIP-seq
MIRT1458566	hsa-miR-520a-5p	CLIP-seq
MIRT1458567	hsa-miR-525-5p	CLIP-seq
MIRT1458568	hsa-miR-544b	CLIP-seq
MIRT1458569	hsa-miR-548v	CLIP-seq
MIRT1458570	hsa-miR-552	CLIP-seq
MIRT1458571	hsa-miR-589	CLIP-seq
MIRT1458572	hsa-miR-670	CLIP-seq
MIRT1458528	hsa-miR-1200	CLIP-seq
MIRT2137617	hsa-miR-1224-3p	CLIP-seq
MIRT2137618	hsa-miR-124	CLIP-seq
MIRT1458532	hsa-miR-127-5p	CLIP-seq
MIRT1458533	hsa-miR-128	CLIP-seq
MIRT1458534	hsa-miR-1324	CLIP-seq
MIRT2137619	hsa-miR-1343	CLIP-seq
MIRT2137620	hsa-miR-1910	CLIP-seq
MIRT2137621	hsa-miR-1913	CLIP-seq
MIRT1458537	hsa-miR-1915	CLIP-seq
MIRT1458538	hsa-miR-193a-3p	CLIP-seq
MIRT1458539	hsa-miR-193b	CLIP-seq
MIRT1458540	hsa-miR-214	CLIP-seq
MIRT1458541	hsa-miR-2276	CLIP-seq
MIRT1458542	hsa-miR-27a	CLIP-seq
MIRT1458543	hsa-miR-27b	CLIP-seq
MIRT1458544	hsa-miR-3176	CLIP-seq
MIRT1458545	hsa-miR-3180-5p	CLIP-seq
MIRT2137622	hsa-miR-3183	CLIP-seq
MIRT2137623	hsa-miR-3189-5p	CLIP-seq
MIRT2137624	hsa-miR-324-3p	CLIP-seq
MIRT2137625	hsa-miR-361-5p	CLIP-seq
MIRT2137626	hsa-miR-3664-5p	CLIP-seq
MIRT1458546	hsa-miR-3714	CLIP-seq
MIRT2137627	hsa-miR-3909	CLIP-seq
MIRT1458547	hsa-miR-3918	CLIP-seq
MIRT1458548	hsa-miR-3922-3p	CLIP-seq
MIRT1458549	hsa-miR-3922-5p	CLIP-seq
MIRT1458551	hsa-miR-4269	CLIP-seq
MIRT1458553	hsa-miR-4324	CLIP-seq
MIRT1458555	hsa-miR-4463	CLIP-seq
MIRT2137628	hsa-miR-4484	CLIP-seq
MIRT1458556	hsa-miR-4494	CLIP-seq
MIRT2137629	hsa-miR-4639-3p	CLIP-seq
MIRT2137630	hsa-miR-4677-3p	CLIP-seq
MIRT2137631	hsa-miR-4679	CLIP-seq
MIRT1458557	hsa-miR-4682	CLIP-seq
MIRT1458558	hsa-miR-4685-5p	CLIP-seq
MIRT1458559	hsa-miR-4690-5p	CLIP-seq
MIRT1458560	hsa-miR-4708-3p	CLIP-seq
MIRT2137632	hsa-miR-4723-3p	CLIP-seq
MIRT2137633	hsa-miR-4727-5p	CLIP-seq
MIRT1458563	hsa-miR-4757-5p	CLIP-seq
MIRT2137634	hsa-miR-4758-3p	CLIP-seq
MIRT2137635	hsa-miR-496	CLIP-seq
MIRT2137636	hsa-miR-506	CLIP-seq
MIRT1458566	hsa-miR-520a-5p	CLIP-seq
MIRT1458567	hsa-miR-525-5p	CLIP-seq
MIRT1458568	hsa-miR-544b	CLIP-seq
MIRT2137637	hsa-miR-548an	CLIP-seq
MIRT2137617	hsa-miR-1224-3p	CLIP-seq
MIRT2137619	hsa-miR-1343	CLIP-seq
MIRT2137621	hsa-miR-1913	CLIP-seq
MIRT2137623	hsa-miR-3189-5p	CLIP-seq
MIRT2137624	hsa-miR-324-3p	CLIP-seq
MIRT2137634	hsa-miR-4758-3p	CLIP-seq

Show/Hide all(8)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000214	Component	TRNA-intron endonuclease complex	IBA	21873635
GO:0000379	Process	TRNA-type intron splice site recognition and cleavage	IBA	21873635
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IEA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IDA	17495927
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	TAS
GO:0006397	Process	MRNA processing	IEA

MIM	HGNC	e!Ensembl
608755	27561	ENSG00000182173

Protein

UniProt ID

Q7Z6J9

Protein name

tRNA-splicing endonuclease subunit Sen54 (SEN54 homolog) (HsSEN54) (tRNA-intron endonuclease Sen54)

Protein function

Non-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 intron. The products are an

PDB

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

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12928	tRNA_int_end_N2	63 → 130	tRNA-splicing endonuclease subunit sen54 N-term	Domain

Sequence

MEPEPEPAAVEVPAGRVLSARELFAARSRSQKLPQRSHGPKDFLPDGSAAQAERLRRCRE
ELWQLLAEQRVERLGSLVAAEWRPEEGFVELKSPAGKFWQTMGFSEQGRQRLHPEEALYL
LECGSIHLFHQDLPLSIQEAYQLLLTDHTVTFLQYQVFSHLKRLGYVVRRFQPSSVLSPY
ERQLNLDASVQHLEDGDGKRKRSSSSPRSINKKAKALDNSLQPKSLAASSPPPCSQPSQC
PEEKPQESSPMKGPGGPFQLLGSLGPSPGPAREGVGCSWESGRAENGVTGAGKRRWNFEQ
ISFPNMASDSRHTLLRAPAPELLPANVAGRETDAESWCQKLNQRKEKLSRREREHHAEAA
QFQEDVNADPEVQRCSSWREYKELLQRRQVQRSQRRAPHLWGQPVTPLLSPGQASSPAVV
LQHISVLQTTHLPDGGARLLEKSGGLEIIFDVYQADAVATFRKNNPGKPYARMCISGFDE
PVPDLCSLKRLSYQSGDVPLIFALVDHGDISFYSFRDFTLPQDVGH

Sequence length

526

Interactions

View interactions

	Reactome
			tRNA processing in the nucleus

Show/Hide Causal Diseases (7)

Disease term	Disease name	dbSNP ID	References
Causal
Arthrogryposis multiplex congenita	Arthrogryposis	rs1586285494, rs80358233, rs137853305, rs1559154278, rs398124167, rs398124172, rs587780399, rs786204576, rs786204430, rs769345284, rs749355583, rs793888524, rs793888525, rs878854368, rs555445835 View all (138 more)
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Mental retardation	Profound Mental Retardation, Mental deficiency, Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)	18711368
Microcephaly	Microcephaly	rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019 View all (280 more)	18711368
Microlissencephaly	Microlissencephaly	rs771116788	18711368
Pontoneocerebellar hypoplasia	Pontocerebellar Hypoplasia Type 1, Pontocerebellar Hypoplasia Type 2A, Pontocerebellar hypoplasia type 4, Pontocerebellar hypoplasia type 2, Pontocerebellar hypoplasia type 1, Congenital pontocerebellar hypoplasia	rs63749985, rs113994152, rs113994153, rs113994154, rs113994150, rs137853063, rs267607036, rs267607035, rs886037629, rs147391618, rs141138948, rs672601331, rs387907196, rs672601332, rs397515426 View all (108 more)	21468723, 18711368, 21368912, 27570394, 23177318, 24886362, 23307886, 29410950, 20803644, 20952379
Amyloidosis	PONTOCEREBELLAR HYPOPLASIA TYPE 4 (disorder)	rs63750567, rs63750560, rs387906821, rs387906822, rs387906823, rs1561123748, rs140352180, rs770211260, rs763065333, rs1554300664, rs747723062, rs773435101	20952379, 18711368, 24886362, 23177318, 21824568, 21368912

Show/Hide Unknown Diseases (2)

Disease term	Disease name	Source
Unknown
Congenital contracture	Congenital contracture	ClinVar
Cerebellar Hypoplasia	pontocerebellar hypoplasia type 5	GenCC

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References
Associations from Text Mining
Atrophy	Associate	26701950
Carcinoma Hepatocellular	Stimulate	37059591
Cerebellar Hypoplasia	Associate	26701950
Death	Associate	20952379
Dyskinesia Drug Induced	Associate	20952379, 26701950
Dystonia	Associate	20952379
Dystonic Disorders	Associate	24886362
Hearing Loss Sensorineural	Associate	32697043
Heart Defects Congenital	Associate	32697043
Microcephaly	Associate	26701950
Muscle Spasticity	Associate	20952379
Olivopontocerebellar hypoplasia fetal onset	Associate	21368912
Pain	Associate	29156912
Pneumonia Ventilator Associated	Associate	20952379
Pontocerebellar Hypoplasia	Associate	20952379, 21368912, 22452838, 32697043, 37059591
Pontocerebellar Hypoplasia Type 2	Associate	20803644, 22452838, 24886362, 26701950, 27430971
Pontocerebellar Hypoplasia Type 2A	Associate	26701950
Pulmonary Disease Chronic Obstructive	Associate	26423011
Seizures	Associate	26701950
Stiff Person Syndrome	Associate	26701950
Stomach Neoplasms	Associate	34413861
Young McKeever Squier syndrome	Associate	20952379

TSEN54 (tRNA splicing endonuclease subunit 54)