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	80324
Gene name	Pseudouridine synthase 1
Gene symbol	PUS1
Synonyms (NCBI Gene)	MLASA1
Chromosome	12
Chromosome location	12q24.33
Summary	This gene encodes a pseudouridine synthase that converts uridine to pseudouridine once it has been incorporated into an RNA molecule. The encoded enzyme may play an essential role in tRNA function and in stabilizing the secondary and tertiary structure of

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894371	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs104894372	G>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained, genic downstream transcript variant
rs149378338	C>A,T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs372753711	G>A	Likely-pathogenic	Missense variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs779193823	C>G,T	Pathogenic	Synonymous variant, non coding transcript variant, stop gained, genic downstream transcript variant, coding sequence variant
rs779651314	C>A	Likely-pathogenic	Stop gained, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs863224176	A>C	Likely-pathogenic	Genic downstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs869025309	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, missense variant
rs1555268564	->G	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs1566148136	C>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, non coding transcript variant

Show/Hide all (31)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022192	hsa-miR-124-3p	Microarray	18668037
MIRT027453	hsa-miR-98-5p	Microarray	19088304
MIRT032213	hsa-let-7b-5p	Proteomics	18668040
MIRT041439	hsa-miR-193b-3p	CLASH	23622248
MIRT1277969	hsa-miR-1184	CLIP-seq
MIRT1277970	hsa-miR-1200	CLIP-seq
MIRT1277971	hsa-miR-3160-3p	CLIP-seq
MIRT1277972	hsa-miR-335	CLIP-seq
MIRT1277973	hsa-miR-3622b-5p	CLIP-seq
MIRT1277974	hsa-miR-4304	CLIP-seq
MIRT1277975	hsa-miR-4324	CLIP-seq
MIRT1277976	hsa-miR-4663	CLIP-seq
MIRT1277977	hsa-miR-4666-5p	CLIP-seq
MIRT1277978	hsa-miR-4668-5p	CLIP-seq
MIRT1277979	hsa-miR-4696	CLIP-seq
MIRT1277980	hsa-miR-4728-3p	CLIP-seq
MIRT1277981	hsa-miR-4743	CLIP-seq
MIRT1277982	hsa-miR-4747-5p	CLIP-seq
MIRT1277983	hsa-miR-493	CLIP-seq
MIRT1277984	hsa-miR-544b	CLIP-seq
MIRT1277985	hsa-miR-570	CLIP-seq
MIRT1277986	hsa-miR-604	CLIP-seq
MIRT1277987	hsa-miR-647	CLIP-seq
MIRT1277988	hsa-miR-34b	CLIP-seq
MIRT1277976	hsa-miR-4663	CLIP-seq
MIRT1277977	hsa-miR-4666-5p	CLIP-seq
MIRT1277980	hsa-miR-4728-3p	CLIP-seq
MIRT1277971	hsa-miR-3160-3p	CLIP-seq
MIRT1277982	hsa-miR-4747-5p	CLIP-seq
MIRT1277983	hsa-miR-493	CLIP-seq
MIRT1277985	hsa-miR-570	CLIP-seq

Show/Hide all (39)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IDA	23707380
GO:0001522	Process	Pseudouridine synthesis	IEA
GO:0002153	Function	Steroid receptor RNA activator RNA binding	IDA	24722331
GO:0003682	Function	Chromatin binding	IEA
GO:0003713	Function	Transcription coactivator activity	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	15772074
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IDA	15772074
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	15772074, 28082677
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0009451	Process	RNA modification	IEA
GO:0009982	Function	Pseudouridine synthase activity	EXP	15772074, 22102571
GO:0009982	Function	Pseudouridine synthase activity	IBA
GO:0009982	Function	Pseudouridine synthase activity	IDA	31477916, 35051350
GO:0009982	Function	Pseudouridine synthase activity	IEA
GO:0009982	Function	Pseudouridine synthase activity	IMP	15772074, 24722331
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	15772074
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0070902	Process	Mitochondrial tRNA pseudouridine synthesis	TAS
GO:0106029	Function	TRNA pseudouridine synthase activity	IEA
GO:0160147	Function	TRNA pseudouridine(38-40) synthase activity	IEA
GO:1990481	Process	MRNA pseudouridine synthesis	IBA
GO:1990481	Process	MRNA pseudouridine synthesis	IDA	31477916, 35051350

MIM	HGNC	e!Ensembl
608109	15508	ENSG00000177192

Q9Y606

Protein name

Pseudouridylate synthase 1 homolog (EC 5.4.99.-) (tRNA pseudouridine synthase 1) (EC 5.4.99.12) (tRNA pseudouridine(38-40) synthase) (tRNA pseudouridylate synthase I) (tRNA-uridine isomerase I)

Protein function

Pseudouridylate synthase that catalyzes pseudouridylation of tRNAs and mRNAs (PubMed:15772074, PubMed:24722331). Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA (PubMed:247

PDB

4IQM , 4ITS , 4J37 , 4NZ6 , 4NZ7

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01416	PseudoU_synth_1	235 → 341	tRNA pseudouridine synthase	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed (PubMed:15108122). High levels of expression found in brain and skeletal muscle (PubMed:15108122). {ECO:0000269|PubMed:15108122}.

Sequence

MGLQLRALLGAFGRWTLRLGPRPSCSPRMAGNAEPPPAGAACPQDRRSCSGRAGGDRVWE
DGEHPAKKLKSGGDEERREKPPKRKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSAL
VRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSLKVWLIDDILEKINSHLPSHIRI
LGLKRVTGGFNSKNRCDARTYCYLLPTFAFAHKDRDVQDETYRLSAETLQQVNRLLACYK
GTHNFHNFTSQKGPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGL
VVAIVKGYAPESVLERSWGTEKVDVPKAPGLGLVLERVHFEKYNQRFGNDGLHEPLDWAQ
EEGKVAAFKEEHIYPTIIGTERDERSMAQWLSTLPIHNFSATALTAGGTGAKVPSPLEGS
EGDGDTD

Sequence length

427

Interactions

View interactions

	Reactome
			tRNA modification in the mitochondrion

225

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Myopathy, lactic acidosis, and sideroblastic anemia	Likely pathogenic; Pathogenic	rs1555268564, rs1048018914	RCV001829384 RCV005606789
Myopathy, lactic acidosis, and sideroblastic anemia 1	Likely pathogenic; Pathogenic	rs754855677, rs895175332, rs104894371, rs104894372, rs1323139544, rs2540870188, rs2540862808, rs2541388871, rs1309276486, rs869025309, rs2540870135, rs2540872758, rs2540873492, rs751632633, rs2541389252 View all (11 more)	RCV004571708 RCV002283570 RCV000002645 RCV000002646 RCV002470133 RCV003459727 RCV003464621 RCV003464624 RCV003459711 RCV000207447 RCV003463403 RCV003463404 RCV003471753 RCV003463405 RCV003463406 RCV003463407 RCV003471754 RCV003463408 RCV003471755 RCV003471756 RCV005006338 RCV004573417 RCV003990582 RCV000454345 RCV004568212 RCV000714784 RCV000853196
PUS1-related disorder	Likely pathogenic; Pathogenic	rs895175332, rs2541388135, rs2540874019	RCV003401940 RCV003902236 RCV003899398
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B	Pathogenic	rs2540873599	RCV006444135

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	Likely benign; Benign	rs758753331, rs142954643, rs376656565	RCV005912811 RCV005886802 RCV005900027
Clear cell carcinoma of kidney	Benign; Likely benign	rs142954643	RCV005886803
Colon adenocarcinoma	Likely benign	rs751628847	RCV005870042
Familial cancer of breast	Benign; Likely benign	rs142954643, rs376656565	RCV005886800 RCV005900026
Gastric cancer	Benign; Likely benign	rs142954643	RCV005886804
Hepatocellular carcinoma	Benign; Likely benign	rs142954643	RCV005886801
Inborn mitochondrial myopathy	Benign; Likely benign	rs150359622, rs35461276, rs145798848, rs142954643, rs76655496, rs142044204, rs147555676, rs145061048	RCV001276804 RCV001276807 RCV001274800 RCV001274801 RCV001274802 RCV001274803 RCV001276806 RCV001276805
Mitochondrial disease	Uncertain significance	rs142624501	RCV005361775
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs142954643	RCV005886805
Sideroblastic anemia	Benign; Likely benign	rs150359622, rs35461276, rs145798848, rs142954643, rs76655496, rs142044204, rs147555676, rs145061048	RCV001276804 RCV001276807 RCV001274800 RCV001274801 RCV001274802 RCV001274803 RCV001276806 RCV001276805
Thymoma	Benign; Likely benign	rs142954643	RCV005886806
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs142954643	RCV005886807
Uterine corpus endometrial carcinoma	Likely benign	rs376656565	RCV005900028

Show/Hide Text Mining Associations (3)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Mitochondrial Diseases	Associate	15772074, 25227147
Myopathy with lactic acidosis and sideroblastic anemia	Associate	15108122, 15772074, 20598274, 25037980
Osteoarthritis	Associate	37006267

PUS1 (pseudouridine synthase 1)