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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	285367
Gene name	RNA pseudouridine synthase D3
Gene symbol	RPUSD3
Synonyms (NCBI Gene)	-
Chromosome	3
Chromosome location	3p25.3
Summary	This gene encodes a protein that functions in the assembly of the mitochondrial ribosome by adding a pseudouridine group to 16S rRNA. Loss of this gene results in causes defects in mitochondrial protein production. Alternative splicing results in multiple

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SNP ID	Visualize variation	Clinical significance	Consequence
rs142932960	G>A	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs767103943	G>A,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant

Show/Hide all (89)

miRTarBase ID	miRNA	Experiments	Reference
MIRT038512	hsa-miR-296-3p	CLASH	23622248
MIRT1319251	hsa-miR-1225-3p	CLIP-seq
MIRT1319252	hsa-miR-1231	CLIP-seq
MIRT1319253	hsa-miR-1265	CLIP-seq
MIRT1319254	hsa-miR-198	CLIP-seq
MIRT1319255	hsa-miR-2467-3p	CLIP-seq
MIRT1319256	hsa-miR-3064-3p	CLIP-seq
MIRT1319257	hsa-miR-3120-3p	CLIP-seq
MIRT1319258	hsa-miR-3158-5p	CLIP-seq
MIRT1319259	hsa-miR-345	CLIP-seq
MIRT1319260	hsa-miR-3677-5p	CLIP-seq
MIRT1319261	hsa-miR-3678-3p	CLIP-seq
MIRT1319262	hsa-miR-3914	CLIP-seq
MIRT1319263	hsa-miR-3943	CLIP-seq
MIRT1319264	hsa-miR-4288	CLIP-seq
MIRT1319265	hsa-miR-4418	CLIP-seq
MIRT1319266	hsa-miR-4457	CLIP-seq
MIRT1319267	hsa-miR-4464	CLIP-seq
MIRT1319268	hsa-miR-4748	CLIP-seq
MIRT1319269	hsa-miR-4764-5p	CLIP-seq
MIRT1319270	hsa-miR-4795-3p	CLIP-seq
MIRT1319271	hsa-miR-509-3-5p	CLIP-seq
MIRT1319272	hsa-miR-509-5p	CLIP-seq
MIRT1319273	hsa-miR-513b	CLIP-seq
MIRT1319274	hsa-miR-520a-5p	CLIP-seq
MIRT1319275	hsa-miR-525-5p	CLIP-seq
MIRT1319276	hsa-miR-561	CLIP-seq
MIRT1319277	hsa-miR-632	CLIP-seq
MIRT1319278	hsa-miR-665	CLIP-seq
MIRT1319252	hsa-miR-1231	CLIP-seq
MIRT1319253	hsa-miR-1265	CLIP-seq
MIRT1319254	hsa-miR-198	CLIP-seq
MIRT1319260	hsa-miR-3677-5p	CLIP-seq
MIRT1319264	hsa-miR-4288	CLIP-seq
MIRT1319267	hsa-miR-4464	CLIP-seq
MIRT1319268	hsa-miR-4748	CLIP-seq
MIRT1319269	hsa-miR-4764-5p	CLIP-seq
MIRT1319274	hsa-miR-520a-5p	CLIP-seq
MIRT1319275	hsa-miR-525-5p	CLIP-seq
MIRT1319276	hsa-miR-561	CLIP-seq
MIRT1319277	hsa-miR-632	CLIP-seq
MIRT1319278	hsa-miR-665	CLIP-seq
MIRT1319251	hsa-miR-1225-3p	CLIP-seq
MIRT1319252	hsa-miR-1231	CLIP-seq
MIRT1319253	hsa-miR-1265	CLIP-seq
MIRT2319262	hsa-miR-1294	CLIP-seq
MIRT2319263	hsa-miR-145	CLIP-seq
MIRT2319264	hsa-miR-1825	CLIP-seq
MIRT1319254	hsa-miR-198	CLIP-seq
MIRT2319265	hsa-miR-199a-5p	CLIP-seq
MIRT2319266	hsa-miR-199b-5p	CLIP-seq
MIRT1319255	hsa-miR-2467-3p	CLIP-seq
MIRT1319256	hsa-miR-3064-3p	CLIP-seq
MIRT1319257	hsa-miR-3120-3p	CLIP-seq
MIRT1319258	hsa-miR-3158-5p	CLIP-seq
MIRT2319267	hsa-miR-3180-5p	CLIP-seq
MIRT2319268	hsa-miR-3184	CLIP-seq
MIRT1319259	hsa-miR-345	CLIP-seq
MIRT1319260	hsa-miR-3677-5p	CLIP-seq
MIRT1319261	hsa-miR-3678-3p	CLIP-seq
MIRT1319263	hsa-miR-3943	CLIP-seq
MIRT2319269	hsa-miR-423-5p	CLIP-seq
MIRT1319264	hsa-miR-4288	CLIP-seq
MIRT2319270	hsa-miR-4302	CLIP-seq
MIRT2319271	hsa-miR-4316	CLIP-seq
MIRT1319265	hsa-miR-4418	CLIP-seq
MIRT1319266	hsa-miR-4457	CLIP-seq
MIRT1319267	hsa-miR-4464	CLIP-seq
MIRT1319268	hsa-miR-4748	CLIP-seq
MIRT1319269	hsa-miR-4764-5p	CLIP-seq
MIRT1319270	hsa-miR-4795-3p	CLIP-seq
MIRT1319271	hsa-miR-509-3-5p	CLIP-seq
MIRT1319272	hsa-miR-509-5p	CLIP-seq
MIRT1319273	hsa-miR-513b	CLIP-seq
MIRT1319274	hsa-miR-520a-5p	CLIP-seq
MIRT1319275	hsa-miR-525-5p	CLIP-seq
MIRT1319276	hsa-miR-561	CLIP-seq
MIRT1319277	hsa-miR-632	CLIP-seq
MIRT1319278	hsa-miR-665	CLIP-seq
MIRT2319262	hsa-miR-1294	CLIP-seq
MIRT2458616	hsa-miR-1321	CLIP-seq
MIRT2319268	hsa-miR-3184	CLIP-seq
MIRT2319269	hsa-miR-423-5p	CLIP-seq
MIRT2319271	hsa-miR-4316	CLIP-seq
MIRT2458617	hsa-miR-4419a	CLIP-seq
MIRT2458618	hsa-miR-4510	CLIP-seq
MIRT2458619	hsa-miR-4739	CLIP-seq
MIRT2458620	hsa-miR-4756-5p	CLIP-seq
MIRT2458621	hsa-miR-873	CLIP-seq

Show/Hide all (16)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001522	Process	Pseudouridine synthesis	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	28082677
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	27974379
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0009451	Process	RNA modification	IEA
GO:0009982	Function	Pseudouridine synthase activity	IEA
GO:0016853	Function	Isomerase activity	IEA
GO:0035770	Component	Ribonucleoprotein granule	IDA	28082677
GO:0070131	Process	Positive regulation of mitochondrial translation	IMP	27667664
GO:1990481	Process	MRNA pseudouridine synthesis	IMP	27974379

MIM	HGNC	e!Ensembl
617759	28437	ENSG00000156990

Q6P087

Protein name

Mitochondrial mRNA pseudouridine synthase RPUSD3 (EC 5.4.99.-) (RNA pseudouridylate synthase domain-containing protein 3)

Protein function

Catalyzes uridine to pseudouridine isomerization (pseudouridylation) of specific mitochondrial mRNAs (mt-mRNAs), a post-transcriptional modification necessary for their translation. Acts at position 390 in COXI mt-mRNA and at position 697-699 in

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00849	PseudoU_synth_2	89 → 252	RNA pseudouridylate synthase	Family

Sequence

MRAVLAREMDGRRVLGRFWSGWRRGLGVRPVPEDAGFGTEARHQRQPRGSCQRSGPLGDQ
PFAGLLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQS
LGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPA
ASEGKIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVATGSGCALVQLQPL
TVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENNKPQRQVLDEALLRRLHL
TPSQAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTLQCLGLRLQ

Sequence length

351

Interactions

View interactions

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 Unknown Diseases (1)

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.
OCULAR HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

RPUSD3 (RNA pseudouridine synthase D3)