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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	83480
Gene name	Pseudouridine synthase 3
Gene symbol	PUS3
Synonyms (NCBI Gene)	2610020J05RikDEG1FKSG32MRT55NEDMIGS
Chromosome	11
Chromosome location	11q24.2
Summary	The protein encoded by this gene catalyzes the formation of tRNA pseudouridine from tRNA uridine at position 39 in the anticodon stem and loop of transfer RNAs. Two transcript variants encoding different isoforms have been found for this gene. [provided b

Show/Hide all (57)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022366	hsa-miR-124-3p	Microarray	18668037
MIRT042525	hsa-miR-423-3p	CLASH	23622248
MIRT665105	hsa-miR-6512-5p	HITS-CLIP	23824327
MIRT665104	hsa-miR-6815-5p	HITS-CLIP	23824327
MIRT665103	hsa-miR-6865-5p	HITS-CLIP	23824327
MIRT665102	hsa-miR-6800-5p	HITS-CLIP	23824327
MIRT665101	hsa-miR-6802-5p	HITS-CLIP	23824327
MIRT635980	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT635979	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT635978	hsa-miR-4652-3p	HITS-CLIP	23824327
MIRT635984	hsa-miR-3606-3p	HITS-CLIP	23824327
MIRT635983	hsa-miR-513a-3p	HITS-CLIP	23824327
MIRT635982	hsa-miR-513c-3p	HITS-CLIP	23824327
MIRT635981	hsa-miR-627-3p	HITS-CLIP	23824327
MIRT635980	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT635979	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT635978	hsa-miR-4652-3p	HITS-CLIP	23824327
MIRT564502	hsa-miR-624-3p	PAR-CLIP	20371350
MIRT564501	hsa-miR-3159	PAR-CLIP	20371350
MIRT564500	hsa-miR-300	PAR-CLIP	20371350
MIRT564499	hsa-miR-381-3p	PAR-CLIP	20371350
MIRT564498	hsa-miR-873-5p	PAR-CLIP	20371350
MIRT564497	hsa-miR-1286	PAR-CLIP	20371350
MIRT564496	hsa-miR-4722-5p	PAR-CLIP	20371350
MIRT564495	hsa-miR-5585-3p	PAR-CLIP	20371350
MIRT564494	hsa-miR-6511b-5p	PAR-CLIP	20371350
MIRT564493	hsa-miR-6811-5p	PAR-CLIP	20371350
MIRT665105	hsa-miR-6512-5p	HITS-CLIP	23824327
MIRT665104	hsa-miR-6815-5p	HITS-CLIP	23824327
MIRT665103	hsa-miR-6865-5p	HITS-CLIP	23824327
MIRT665102	hsa-miR-6800-5p	HITS-CLIP	23824327
MIRT665101	hsa-miR-6802-5p	HITS-CLIP	23824327
MIRT635980	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT635979	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT635978	hsa-miR-4652-3p	HITS-CLIP	23824327
MIRT635984	hsa-miR-3606-3p	HITS-CLIP	23824327
MIRT635983	hsa-miR-513a-3p	HITS-CLIP	23824327
MIRT635982	hsa-miR-513c-3p	HITS-CLIP	23824327
MIRT635981	hsa-miR-627-3p	HITS-CLIP	23824327
MIRT635980	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT635979	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT635978	hsa-miR-4652-3p	HITS-CLIP	23824327
MIRT564502	hsa-miR-624-3p	PAR-CLIP	20371350
MIRT564501	hsa-miR-3159	PAR-CLIP	20371350
MIRT564500	hsa-miR-300	PAR-CLIP	20371350
MIRT564499	hsa-miR-381-3p	PAR-CLIP	20371350
MIRT564498	hsa-miR-873-5p	PAR-CLIP	20371350
MIRT564497	hsa-miR-1286	PAR-CLIP	20371350
MIRT564496	hsa-miR-4722-5p	PAR-CLIP	20371350
MIRT564495	hsa-miR-5585-3p	PAR-CLIP	20371350
MIRT564494	hsa-miR-6511b-5p	PAR-CLIP	20371350
MIRT564493	hsa-miR-6811-5p	PAR-CLIP	20371350
MIRT2432354	hsa-miR-124	CLIP-seq
MIRT2432355	hsa-miR-3180-5p	CLIP-seq
MIRT2432356	hsa-miR-381	CLIP-seq
MIRT2432357	hsa-miR-506	CLIP-seq
MIRT2432358	hsa-miR-624	CLIP-seq

Show/Hide all (20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001522	Process	Pseudouridine synthesis	IEA
GO:0003723	Function	RNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006400	Process	TRNA modification	TAS
GO:0008033	Process	TRNA processing	IEA
GO:0009451	Process	RNA modification	IEA
GO:0009982	Function	Pseudouridine synthase activity	EXP	27055666
GO:0009982	Function	Pseudouridine synthase activity	IBA
GO:0009982	Function	Pseudouridine synthase activity	IEA
GO:0016853	Function	Isomerase activity	IEA
GO:0031119	Process	TRNA pseudouridine synthesis	IBA
GO:0031119	Process	TRNA pseudouridine synthesis	IEA
GO:0031119	Process	TRNA pseudouridine synthesis	IEA
GO:0031119	Process	TRNA pseudouridine synthesis	IMP	27055666
GO:0160154	Function	TRNA pseudouridine(38/39) synthase activity	IEA
GO:0160154	Function	TRNA pseudouridine(38/39) synthase activity	IMP	27055666
GO:1990481	Process	MRNA pseudouridine synthesis	IBA

MIM	HGNC	e!Ensembl
616283	25461	ENSG00000110060

Q9BZE2

Protein name

tRNA pseudouridine(38/39) synthase (EC 5.4.99.45) (tRNA pseudouridine synthase 3) (tRNA pseudouridylate synthase 3) (tRNA-uridine isomerase 3)

Protein function

Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs.

PDB

8OKD , 9ENB , 9ENC , 9ENE , 9ENF , 9F9Q

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01416	PseudoU_synth_1	212 → 330	tRNA pseudouridine synthase	Domain

Sequence

MAYNDTDRNQTEKLLKRVRELEQEVQRLKKEQAKNKEDSNIRENSAGAGKTKRAFDFSAH
GRRHVALRIAYMGWGYQGFASQENTNNTIEEKLFEALTKTRLVESRQTSNYHRCGRTDKG
VSAFGQVISLDLRSQFPRGRDSEDFNVKEEANAAAEEIRYTHILNRVLPPDIRILAWAPV
EPSFSARFSCLERTYRYFFPRADLDIVTMDYAAQKYVGTHDFRNLCKMDVANGVINFQRT
ILSAQVQLVGQSPGEGRWQEPFQLCQFEVTGQAFLYHQVRCMMAILFLIGQGMEKPEIID
ELLNIEKNPQKPQYSMAVEFPLVLYDCKFENVKWIYDQEAQEFNITHLQQLWANHAVKTH
MLYSMLQGLDTVPVPCGIGPKMDGMTEWGNVKPSVIKQTSAFVEGVKMRTYKPLMDRPKC
QGLESRIQHFVRRGRIEHPHLFHEEETKAKRDCNDTLEEENTNLETPTKRVCVDTEIKSI
I

Sequence length

481

Interactions

View interactions

	Reactome
			tRNA modification in the nucleus 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 (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Anencephaly	Likely pathogenic; Pathogenic	rs374443634, rs752052349	RCV001257392 RCV001257393	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ankle flexion contracture	Likely pathogenic; Pathogenic	rs374443634, rs752052349	RCV001257392 RCV001257393	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Aplasia/Hypoplasia of the cerebellum	Likely pathogenic; Pathogenic	rs374443634, rs752052349	RCV001257392 RCV001257393	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Heart, malformation of	Likely pathogenic; Pathogenic	rs374443634, rs752052349	RCV001257392 RCV001257393	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Polyhydramnios	Likely pathogenic; Pathogenic	rs374443634, rs752052349	RCV001257392 RCV001257393	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PUS3-related disorder	Likely pathogenic; Pathogenic	rs374443634	RCV003399034	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe growth deficiency-strabismus-extensive dermal melanocytosis-intellectual disability syndrome	Likely pathogenic; Pathogenic	rs1208593429, rs761792490, rs774005569, rs758320488, rs753229591, rs1023270270, rs1944570170	RCV001783650 RCV002471197 RCV000239585 RCV003479632 RCV000758220 RCV001195995 RCV001198632 View all (2 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (6)

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.
ATROPHY/DEGENERATION AFFECTING THE CEREBELLUM	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HEART DEFECTS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DANDY-WALKER SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYDROLETHALUS SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYDROLETHALUS SYNDROME 1	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY AND GRAY SCLERAE	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Arachnoid Cysts	Arachnoid cyst	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	27055666		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydrolethalus syndrome	Hydrolethalus Syndrome	CLINVAR_DG	15843405, 18648327, 19400947, 2074561		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYDROLETHALUS SYNDROME 1	Hydrolethalus Syndrome	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	BEFREE	27055666, 28134782		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	27055666		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	27055666	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 55	Mental retardation	GENOMICS_ENGLAND_DG	27055666		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 55	Mental retardation	ORPHANET_DG	27055666		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 55	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 55	Mental retardation	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	27055666		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe growth deficiency-strabismus-extensive dermal melanocytosis-intellectual disability syndrome	Growth Deficiency-Strabismus-Extensive Dermal Melanocytosis-Intellectual Disability Syndrome	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

PUS3 (pseudouridine synthase 3)