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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	65109
Gene name	UPF3B regulator of nonsense mediated mRNA decay
Gene symbol	UPF3B
Synonyms (NCBI Gene)	HUPF3BMRX62MRX82MRXS14RENT3BUPF3BP1UPF3BP2UPF3BP3UPF3XUpf3p-X
Chromosome	X
Chromosome location	Xq24
Summary	This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs wit

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs122468181	G>A,T	Pathogenic, likely-pathogenic	Coding sequence variant, synonymous variant, stop gained
rs122468182	A>C	Pathogenic	Coding sequence variant, missense variant
rs143538947	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, missense variant
rs794727881	TTCT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1064794254	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1131691699	CTTCTCTT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1556377028	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1569464167	->T	Likely-pathogenic	Frameshift variant, initiator codon variant
rs1603370185	CT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1603371016	AATT>-	Pathogenic	Coding sequence variant, stop gained

Show/Hide all (93)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029393	hsa-miR-26b-5p	Microarray	19088304
MIRT1476212	hsa-miR-1343	CLIP-seq
MIRT1476213	hsa-miR-185	CLIP-seq
MIRT1476214	hsa-miR-330-3p	CLIP-seq
MIRT1476215	hsa-miR-3667-3p	CLIP-seq
MIRT1476216	hsa-miR-3690	CLIP-seq
MIRT1476217	hsa-miR-4254	CLIP-seq
MIRT1476218	hsa-miR-4306	CLIP-seq
MIRT1476219	hsa-miR-4330	CLIP-seq
MIRT1476220	hsa-miR-4644	CLIP-seq
MIRT1476221	hsa-miR-501-3p	CLIP-seq
MIRT1476222	hsa-miR-502-3p	CLIP-seq
MIRT1476223	hsa-miR-548q	CLIP-seq
MIRT2143500	hsa-miR-3140-3p	CLIP-seq
MIRT2363692	hsa-miR-3074-5p	CLIP-seq
MIRT2363693	hsa-miR-3614-5p	CLIP-seq
MIRT2363694	hsa-miR-370	CLIP-seq
MIRT2363695	hsa-miR-4731-3p	CLIP-seq
MIRT2363696	hsa-miR-4801	CLIP-seq
MIRT2363697	hsa-miR-514	CLIP-seq
MIRT2363698	hsa-miR-514b-3p	CLIP-seq
MIRT2363699	hsa-miR-550b	CLIP-seq
MIRT2363700	hsa-miR-642b	CLIP-seq
MIRT2657382	hsa-miR-1184	CLIP-seq
MIRT2657383	hsa-miR-1205	CLIP-seq
MIRT2657384	hsa-miR-1226	CLIP-seq
MIRT2657385	hsa-miR-124	CLIP-seq
MIRT2657386	hsa-miR-146b-3p	CLIP-seq
MIRT2657387	hsa-miR-204	CLIP-seq
MIRT2657388	hsa-miR-211	CLIP-seq
MIRT2363692	hsa-miR-3074-5p	CLIP-seq
MIRT2657389	hsa-miR-3117-5p	CLIP-seq
MIRT2657390	hsa-miR-3157-3p	CLIP-seq
MIRT2657391	hsa-miR-3158-5p	CLIP-seq
MIRT2657392	hsa-miR-3173-5p	CLIP-seq
MIRT2657393	hsa-miR-3674	CLIP-seq
MIRT2363694	hsa-miR-370	CLIP-seq
MIRT2657394	hsa-miR-383	CLIP-seq
MIRT2657395	hsa-miR-3908	CLIP-seq
MIRT2657396	hsa-miR-4282	CLIP-seq
MIRT2657397	hsa-miR-4287	CLIP-seq
MIRT2657398	hsa-miR-4493	CLIP-seq
MIRT2657399	hsa-miR-4539	CLIP-seq
MIRT2657400	hsa-miR-4685-3p	CLIP-seq
MIRT2657401	hsa-miR-4720-3p	CLIP-seq
MIRT2363695	hsa-miR-4731-3p	CLIP-seq
MIRT2657402	hsa-miR-4768-5p	CLIP-seq
MIRT2657403	hsa-miR-4772-5p	CLIP-seq
MIRT2657404	hsa-miR-4775	CLIP-seq
MIRT2657405	hsa-miR-4782-5p	CLIP-seq
MIRT2363696	hsa-miR-4801	CLIP-seq
MIRT2657406	hsa-miR-4804-3p	CLIP-seq
MIRT2657407	hsa-miR-506	CLIP-seq
MIRT2363697	hsa-miR-514	CLIP-seq
MIRT2363698	hsa-miR-514b-3p	CLIP-seq
MIRT2657408	hsa-miR-518a-5p	CLIP-seq
MIRT2657409	hsa-miR-527	CLIP-seq
MIRT2363699	hsa-miR-550b	CLIP-seq
MIRT2657410	hsa-miR-634	CLIP-seq
MIRT2363700	hsa-miR-642b	CLIP-seq
MIRT2657411	hsa-miR-874	CLIP-seq
MIRT2657382	hsa-miR-1184	CLIP-seq
MIRT2657383	hsa-miR-1205	CLIP-seq
MIRT2657384	hsa-miR-1226	CLIP-seq
MIRT2657385	hsa-miR-124	CLIP-seq
MIRT2657386	hsa-miR-146b-3p	CLIP-seq
MIRT2657387	hsa-miR-204	CLIP-seq
MIRT2657388	hsa-miR-211	CLIP-seq
MIRT2657389	hsa-miR-3117-5p	CLIP-seq
MIRT2657390	hsa-miR-3157-3p	CLIP-seq
MIRT2657391	hsa-miR-3158-5p	CLIP-seq
MIRT2657392	hsa-miR-3173-5p	CLIP-seq
MIRT2657393	hsa-miR-3674	CLIP-seq
MIRT2657394	hsa-miR-383	CLIP-seq
MIRT2657395	hsa-miR-3908	CLIP-seq
MIRT2657396	hsa-miR-4282	CLIP-seq
MIRT2657397	hsa-miR-4287	CLIP-seq
MIRT2657398	hsa-miR-4493	CLIP-seq
MIRT2657399	hsa-miR-4539	CLIP-seq
MIRT2657400	hsa-miR-4685-3p	CLIP-seq
MIRT2363695	hsa-miR-4731-3p	CLIP-seq
MIRT2657402	hsa-miR-4768-5p	CLIP-seq
MIRT2657403	hsa-miR-4772-5p	CLIP-seq
MIRT2657404	hsa-miR-4775	CLIP-seq
MIRT2657405	hsa-miR-4782-5p	CLIP-seq
MIRT2363696	hsa-miR-4801	CLIP-seq
MIRT2657407	hsa-miR-506	CLIP-seq
MIRT2657408	hsa-miR-518a-5p	CLIP-seq
MIRT2657409	hsa-miR-527	CLIP-seq
MIRT2363699	hsa-miR-550b	CLIP-seq
MIRT2657410	hsa-miR-634	CLIP-seq
MIRT2363700	hsa-miR-642b	CLIP-seq
MIRT2657411	hsa-miR-874	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
SATB2	Activation	23925499

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IDA	16601204
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP	18369367
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	NAS	11163187
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003729	Function	MRNA binding	IBA
GO:0003729	Function	MRNA binding	IDA	11163187, 11546873
GO:0005515	Function	Protein binding	IPI	11163187, 11546873, 11546874, 12417715, 15231747, 15361857, 15680326, 16209946, 16452507, 16601204, 18066079, 19410547, 19417104, 19478851, 19503078, 19864460, 20479275, 20930030, 22522823, 23084401, 23788676, 25220460, 26496610, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	11163187
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IBA
GO:0005730	Component	Nucleolus	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	11163187
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0007420	Process	Brain development	IEA
GO:0031175	Process	Neuron projection development	IEA
GO:0034451	Component	Centriolar satellite	IDA
GO:0035145	Component	Exon-exon junction complex	IDA	11546873, 12718880, 16601204
GO:0035145	Component	Exon-exon junction complex	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0045666	Process	Positive regulation of neuron differentiation	IEA
GO:0045727	Process	Positive regulation of translation	IBA
GO:0045727	Process	Positive regulation of translation	IDA	16601204
GO:0045727	Process	Positive regulation of translation	IEA
GO:0051028	Process	MRNA transport	IEA
GO:1905746	Process	Positive regulation of mRNA cis splicing, via spliceosome	IEA

MIM	HGNC	e!Ensembl
300298	20439	ENSG00000125351

Q9BZI7

Protein name

Regulator of nonsense transcripts 3B (Nonsense mRNA reducing factor 3B) (Up-frameshift suppressor 3 homolog B) (hUpf3B) (Up-frameshift suppressor 3 homolog on chromosome X) (hUpf3p-X)

Protein function

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of

PDB

1UW4 , 2XB2 , 7NWU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03467	Smg4_UPF3	48 → 209	Smg-4/UPF3 family	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta. {ECO:0000269|PubMed:11113196}.

Sequence

MKEEKEHRPKEKRVTLLTPAGATGSGGGTSGDSSKGEDKQDRNKEKKEALSKVVIRRLPP
TLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL
DNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLESYATDNEKMTSTPET
LLEEIEAKNRELIAKKTTPLLSFLKNKQRMREEKREERRRREIERKRQREEERRKWKEEE
KRKRKDIEKLKKIDRIPERDKLKDEPKIKVHRFLLQAVNQKNLLKKPEKGDEKELDKREK
AKKLDKENLSDERASGQSCTLPKRSDSELKDEKPKRPEDESGRDYREREREYERDQERIL
RERERLKRQEEERRRQKERYEKEKTFKRKEEEMKKEKDTLRDKGKKAESTESIGSSEKTE
KKEEVVKRDRIRNKDRPAMQLYQPGARSRNRLCPPDDSTKSGDSAAERKQESGISHRKEG
GEE

Sequence length

483

Interactions

View interactions

	KEGG		Reactome
	Nucleocytoplasmic transport mRNA surveillance pathway		Transport of Mature mRNA derived from an Intron-Containing Transcript mRNA Splicing - Major Pathway mRNA 3'-end processing RNA Polymerase II Transcription Termination Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

211

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Intellectual disability	Likely pathogenic	rs2056119926	RCV001260817
Syndromic X-linked intellectual disability 14	Pathogenic; Likely pathogenic	rs2147787295, rs2147787331, rs376175156, rs2147783395, rs2521574129, rs1480554912, rs794727881, rs2521577196, rs1603370185, rs122468181, rs122468182, rs2521576667, rs2521545000, rs1064794254, rs1556377028 View all (3 more)	RCV005094884 RCV001785117 RCV001784011 RCV002273274 RCV002294578 RCV002468879 RCV000012151 RCV003018402 RCV000012152 RCV000012153 RCV000012154 RCV003887831 RCV004595269 RCV000678370 RCV000578335 RCV000995676 RCV003485700 RCV001270413
UPF3B-associated intellectual disability	Pathogenic	rs794727881	RCV001787090
UPF3B-related disorder	Likely pathogenic	rs376175156	RCV004731180

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cataract	Conflicting classifications of pathogenicity	rs754982440	RCV000626987
Cervical cancer	-	rs752614151	RCV006175423
Familial cancer of breast	Benign; -	rs767518602, rs752614151	RCV005871244 RCV006175421
Germ cell tumor of testis	Benign	rs2428212	RCV005902297
Hepatocellular carcinoma	Benign	rs2428212	RCV005902296
Lung cancer	-	rs752614151	RCV006175425
Malignant tumor of esophagus	-	rs752614151	RCV006175422
Melanoma	Likely benign	rs749039837	RCV005931518
Microcephaly	Conflicting classifications of pathogenicity	rs754982440	RCV000626987
Neurodevelopmental disorder	Conflicting classifications of pathogenicity	rs2147802765, rs2056115071	RCV001375011 RCV002277648
Nonpapillary renal cell carcinoma	Uncertain significance; Conflicting classifications of pathogenicity	rs1007550463, rs2056116060	RCV005931127 RCV005932766
Ovarian serous cystadenocarcinoma	-	rs752614151	RCV006175424
Severe global developmental delay	Conflicting classifications of pathogenicity	rs754982440	RCV000626987
Thyroid cancer, nonmedullary, 1	Uncertain significance	rs1186494670	RCV005931065
Uterine corpus endometrial carcinoma	-	rs752614151	RCV006175426

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Apraxias	Associate	32667670
Autistic Disorder	Associate	26012578
Biliary Tract Diseases	Associate	26060332
Carcinoma Hepatocellular	Associate	36194583, 40621461
Cardiomyopathy Hypertrophic	Associate	37797718
Cholangiocarcinoma	Associate	26060332
Developmental Disabilities	Associate	26012578, 32667670, 35640974
Esophageal Neoplasms	Associate	34257547, 36194583
Genital Diseases Male	Associate	32667670
Intellectual Disability	Associate	22182939, 25649377, 26012578, 35640974
Kidney Diseases	Associate	36194583
Melanoma Cutaneous Malignant	Associate	36194583
Neoplasms	Associate	36194583
Neurologic Manifestations	Associate	22182939
Schizophrenia	Associate	26012578
Speech Disorders	Associate	32667670

UPF3B (UPF3B regulator of nonsense mediated mRNA decay)