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	84916
Gene name	UTP4 small subunit processome component
Gene symbol	UTP4
Synonyms (NCBI Gene)	CIRH1ACIRHINNAICTEX292
Chromosome	16
Chromosome location	16q22.1
Summary	This gene encodes a WD40-repeat-containing protein that is localized to the nucleolus. Mutation of this gene causes North American Indian childhood cirrhosis, a severe intrahepatic cholestasis that results in transient neonatal jaundice, and progresses to

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miRTarBase ID	miRNA	Experiments	Reference
MIRT723697	hsa-miR-495-3p	HITS-CLIP	19536157
MIRT723696	hsa-miR-5688	HITS-CLIP	19536157
MIRT723695	hsa-miR-4687-5p	HITS-CLIP	19536157
MIRT723694	hsa-miR-4690-3p	HITS-CLIP	19536157
MIRT723693	hsa-miR-5685	HITS-CLIP	19536157
MIRT723692	hsa-miR-6793-3p	HITS-CLIP	19536157
MIRT723691	hsa-miR-4290	HITS-CLIP	19536157
MIRT723690	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT723689	hsa-miR-6729-3p	HITS-CLIP	19536157
MIRT723688	hsa-miR-6887-3p	HITS-CLIP	19536157
MIRT723687	hsa-miR-6795-3p	HITS-CLIP	19536157
MIRT723686	hsa-miR-4667-3p	HITS-CLIP	19536157
MIRT723685	hsa-miR-5088-3p	HITS-CLIP	19536157
MIRT723684	hsa-miR-6734-3p	HITS-CLIP	19536157
MIRT723683	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT723682	hsa-miR-6826-3p	HITS-CLIP	19536157
MIRT723681	hsa-miR-623	HITS-CLIP	19536157
MIRT723680	hsa-miR-6868-3p	HITS-CLIP	19536157
MIRT723679	hsa-miR-4755-5p	HITS-CLIP	19536157
MIRT723678	hsa-miR-5006-3p	HITS-CLIP	19536157
MIRT530279	hsa-miR-1182	HITS-CLIP	21572407
MIRT499767	hsa-miR-4781-3p	HITS-CLIP	21572407
MIRT499766	hsa-miR-216b-3p	HITS-CLIP	21572407
MIRT499765	hsa-miR-1226-3p	HITS-CLIP	21572407
MIRT499764	hsa-miR-4733-3p	HITS-CLIP	21572407
MIRT499763	hsa-miR-5693	HITS-CLIP	21572407
MIRT530278	hsa-miR-342-3p	HITS-CLIP	21572407
MIRT499762	hsa-miR-6499-3p	HITS-CLIP	21572407
MIRT499761	hsa-miR-3135b	HITS-CLIP	21572407
MIRT499760	hsa-miR-504-3p	HITS-CLIP	21572407
MIRT499759	hsa-miR-122-5p	HITS-CLIP	21572407
MIRT499758	hsa-miR-3652	HITS-CLIP	21572407
MIRT499757	hsa-miR-4430	HITS-CLIP	21572407
MIRT499756	hsa-miR-143-5p	HITS-CLIP	21572407
MIRT499755	hsa-miR-6501-5p	HITS-CLIP	21572407
MIRT499754	hsa-miR-4423-5p	HITS-CLIP	21572407
MIRT499753	hsa-miR-197-3p	HITS-CLIP	21572407
MIRT499752	hsa-miR-744-3p	HITS-CLIP	21572407
MIRT499751	hsa-miR-5698	HITS-CLIP	21572407
MIRT647913	hsa-miR-1279	HITS-CLIP	23824327
MIRT647912	hsa-miR-4267	HITS-CLIP	23824327
MIRT647911	hsa-miR-486-5p	HITS-CLIP	23824327
MIRT647910	hsa-miR-5007-3p	HITS-CLIP	23824327
MIRT647909	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT647908	hsa-miR-508-5p	HITS-CLIP	23824327
MIRT647907	hsa-miR-451b	HITS-CLIP	23824327
MIRT647906	hsa-miR-6501-3p	HITS-CLIP	23824327
MIRT647905	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT647904	hsa-miR-766-3p	HITS-CLIP	23824327
MIRT647903	hsa-miR-4793-3p	HITS-CLIP	23824327
MIRT647902	hsa-miR-4299	HITS-CLIP	23824327
MIRT647901	hsa-miR-4696	HITS-CLIP	23824327
MIRT647900	hsa-miR-542-3p	HITS-CLIP	23824327
MIRT647899	hsa-miR-6512-3p	HITS-CLIP	23824327
MIRT647898	hsa-miR-6720-5p	HITS-CLIP	23824327
MIRT647897	hsa-miR-7703	HITS-CLIP	23824327
MIRT499765	hsa-miR-1226-3p	PAR-CLIP	20371350
MIRT499764	hsa-miR-4733-3p	PAR-CLIP	20371350
MIRT499763	hsa-miR-5693	PAR-CLIP	20371350
MIRT499762	hsa-miR-6499-3p	PAR-CLIP	20371350
MIRT499761	hsa-miR-3135b	PAR-CLIP	20371350
MIRT499760	hsa-miR-504-3p	PAR-CLIP	20371350
MIRT499759	hsa-miR-122-5p	PAR-CLIP	20371350
MIRT499758	hsa-miR-3652	PAR-CLIP	20371350
MIRT499757	hsa-miR-4430	PAR-CLIP	20371350
MIRT499756	hsa-miR-143-5p	PAR-CLIP	20371350
MIRT499753	hsa-miR-197-3p	PAR-CLIP	20371350
MIRT499751	hsa-miR-5698	PAR-CLIP	20371350
MIRT530279	hsa-miR-1182	PAR-CLIP	21572407
MIRT499767	hsa-miR-4781-3p	PAR-CLIP	21572407
MIRT499766	hsa-miR-216b-3p	PAR-CLIP	21572407
MIRT499765	hsa-miR-1226-3p	PAR-CLIP	21572407
MIRT499764	hsa-miR-4733-3p	PAR-CLIP	21572407
MIRT499763	hsa-miR-5693	PAR-CLIP	21572407
MIRT530278	hsa-miR-342-3p	PAR-CLIP	21572407
MIRT499762	hsa-miR-6499-3p	PAR-CLIP	21572407
MIRT499761	hsa-miR-3135b	PAR-CLIP	21572407
MIRT499760	hsa-miR-504-3p	PAR-CLIP	21572407
MIRT499759	hsa-miR-122-5p	PAR-CLIP	21572407
MIRT499758	hsa-miR-3652	PAR-CLIP	21572407
MIRT499757	hsa-miR-4430	PAR-CLIP	21572407
MIRT499756	hsa-miR-143-5p	PAR-CLIP	21572407
MIRT499755	hsa-miR-6501-5p	PAR-CLIP	21572407
MIRT499754	hsa-miR-4423-5p	PAR-CLIP	21572407
MIRT499753	hsa-miR-197-3p	PAR-CLIP	21572407
MIRT499752	hsa-miR-744-3p	PAR-CLIP	21572407
MIRT499751	hsa-miR-5698	PAR-CLIP	21572407
MIRT530279	hsa-miR-1182	PAR-CLIP	22012620
MIRT499767	hsa-miR-4781-3p	PAR-CLIP	22012620
MIRT499766	hsa-miR-216b-3p	PAR-CLIP	22012620
MIRT499765	hsa-miR-1226-3p	PAR-CLIP	22012620
MIRT499764	hsa-miR-4733-3p	PAR-CLIP	22012620
MIRT499763	hsa-miR-5693	PAR-CLIP	22012620
MIRT530278	hsa-miR-342-3p	PAR-CLIP	22012620
MIRT499762	hsa-miR-6499-3p	PAR-CLIP	22012620
MIRT499760	hsa-miR-504-3p	PAR-CLIP	22012620
MIRT499759	hsa-miR-122-5p	PAR-CLIP	22012620
MIRT499758	hsa-miR-3652	PAR-CLIP	22012620
MIRT499757	hsa-miR-4430	PAR-CLIP	22012620
MIRT499756	hsa-miR-143-5p	PAR-CLIP	22012620
MIRT499755	hsa-miR-6501-5p	PAR-CLIP	22012620
MIRT499754	hsa-miR-4423-5p	PAR-CLIP	22012620
MIRT499753	hsa-miR-197-3p	PAR-CLIP	22012620
MIRT499752	hsa-miR-744-3p	PAR-CLIP	22012620
MIRT499751	hsa-miR-5698	PAR-CLIP	22012620
MIRT499765	hsa-miR-1226-3p	PAR-CLIP	23446348
MIRT499764	hsa-miR-4733-3p	PAR-CLIP	23446348
MIRT499763	hsa-miR-5693	PAR-CLIP	23446348
MIRT499762	hsa-miR-6499-3p	PAR-CLIP	23446348
MIRT499761	hsa-miR-3135b	PAR-CLIP	23446348
MIRT499760	hsa-miR-504-3p	PAR-CLIP	23446348
MIRT499759	hsa-miR-122-5p	PAR-CLIP	23446348
MIRT499758	hsa-miR-3652	PAR-CLIP	23446348
MIRT499757	hsa-miR-4430	PAR-CLIP	23446348
MIRT499756	hsa-miR-143-5p	PAR-CLIP	23446348
MIRT499753	hsa-miR-197-3p	PAR-CLIP	23446348
MIRT499751	hsa-miR-5698	PAR-CLIP	23446348
MIRT499767	hsa-miR-4781-3p	PAR-CLIP	24398324
MIRT499766	hsa-miR-216b-3p	PAR-CLIP	24398324
MIRT499765	hsa-miR-1226-3p	PAR-CLIP	24398324
MIRT499764	hsa-miR-4733-3p	PAR-CLIP	24398324
MIRT499763	hsa-miR-5693	PAR-CLIP	24398324
MIRT499762	hsa-miR-6499-3p	PAR-CLIP	24398324
MIRT499761	hsa-miR-3135b	PAR-CLIP	24398324
MIRT499760	hsa-miR-504-3p	PAR-CLIP	24398324
MIRT499759	hsa-miR-122-5p	PAR-CLIP	24398324
MIRT499758	hsa-miR-3652	PAR-CLIP	24398324
MIRT499757	hsa-miR-4430	PAR-CLIP	24398324
MIRT499756	hsa-miR-143-5p	PAR-CLIP	24398324
MIRT499755	hsa-miR-6501-5p	PAR-CLIP	24398324
MIRT499754	hsa-miR-4423-5p	PAR-CLIP	24398324
MIRT499753	hsa-miR-197-3p	PAR-CLIP	24398324
MIRT499752	hsa-miR-744-3p	PAR-CLIP	24398324
MIRT499751	hsa-miR-5698	PAR-CLIP	24398324

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000462	Process	Maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA
GO:0000462	Process	Maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IEA
GO:0001650	Component	Fibrillar center	IDA	24219289
GO:0003723	Function	RNA binding	HDA	22658674
GO:0005515	Function	Protein binding	IPI	19732766, 22916032, 24219289, 28514442, 33961781, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IDA	20813266
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA	16225863, 17699751
GO:0005730	Component	Nucleolus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IDA	19732766
GO:0006364	Process	RRNA processing	IEA
GO:0030490	Process	Maturation of SSU-rRNA	IMP	22916032
GO:0030686	Component	90S preribosome	IEA
GO:0032040	Component	Small-subunit processome	IBA
GO:0032040	Component	Small-subunit processome	IDA	34516797
GO:0034455	Component	T-UTP complex	IBA
GO:0034455	Component	T-UTP complex	IDA	22916032
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042274	Process	Ribosomal small subunit biogenesis	IDA	34516797

MIM	HGNC	e!Ensembl
607456	1983	ENSG00000141076

Q969X6

Protein name

U3 small nucleolar RNA-associated protein 4 homolog (Cirhin) (UTP4 small subunit processome component)

Protein function

Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleo

PDB

7MQ8 , 7MQ9 , 7MQA

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00400	WD40	95 → 129	WD domain, G-beta repeat	Repeat

Sequence

MGEFKVHRVRFFNYVPSGIRCVAYNNQSNRLAVSRTDGTVEIYNLSANYFQEKFFPGHES
RATEALCWAEGQRLFSAGLNGEIMEYDLQALNIKYAMDAFGGPIWSMAASPSGSQLLVGC
EDGSVKLFQITPDKIQFERNFDRQKSRILSLSWHPSGTHIAAGSIDYISVFDVKSGSAVH
KMIVDRQYMGVSKRKCIVWGVAFLSDGTIISVDSAGKVQFWDSATGTLVKSHLIANADVQ
SIAVADQEDSFVVGTAEGTVFHFQLVPVTSNSSEKQWVRTKPFQHHTHDVRTVAHSPTAL
ISGGTDTHLVFRPLMEKVEVKNYDAALRKITFPHRCLISCSKKRQLLLFQFAHHLELWRL
GSTVATGKNGDTLPLSKNADHLLHLKTKGPENIICSCISPCGSWIAYSTVSRFFLYRLNY
EHDNISLKRVSKMPAFLRSALQILFSEDSTKLFVASNQGALHIVQLSGGSFKHLHAFQPQ
SGTVEAMCLLAVSPDGNWLAASGTSAGVHVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNN
LVIAHSDQQVFEYSIPDKQYTDWSRTVQKQGFHHLWLQRDTPITHISFHPKRPMHILLHD
AYMFCIIDKSLPLPNDKTLLYNPFPPTNESDVIRRRTAHAFKISKIYKPLLFMDLLDERT
LVAVERPLDDIIAQLPPPIKKKKFGT

Sequence length

686

Interactions

View interactions

	KEGG		Reactome
	Ribosome biogenesis in eukaryotes		Major pathway of rRNA processing in the nucleolus and cytosol

133

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs138645239, rs112053857, rs61185783	RCV005904657 RCV005905955 RCV005913755
Adrenocortical carcinoma, hereditary	Benign	rs61185783	RCV005913758
Cervical cancer	Conflicting classifications of pathogenicity; Benign	rs144369314, rs138645239	RCV005902641 RCV005904658
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity; Benign; Likely benign	rs144369314, rs112053857	RCV005902642 RCV005905956
Colon adenocarcinoma	Benign	rs61185783	RCV005913754
Colorectal cancer	Benign	rs61185783	RCV005913761
Familial cancer of breast	Conflicting classifications of pathogenicity	rs144369314	RCV005902639
Gastric cancer	Benign	rs138645239	RCV005904659
Hepatocellular carcinoma	Benign	rs61185783	RCV005913756
Hereditary North American Indian childhood cirrhosis	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	rs119465999, rs144369314, rs8056684, rs112053857, rs75998507, rs141243868, rs16958656, rs1962851495, rs370682701, rs144266389, rs1963017242, rs538321215, rs2288036, rs375128162, rs150182351 View all (24 more)	RCV000003345 RCV001119544 RCV001118104 RCV001116661 RCV001119646 RCV001119542 RCV001119543 RCV001119545 RCV001119546 RCV001119547 RCV001119548 RCV001119549 RCV001121543 RCV001121545 RCV001121546 RCV001121547 RCV001121548 RCV001121550 RCV001116663 RCV001116664 RCV001116665 RCV001116668 RCV001118105 RCV001118107 RCV001118108 RCV001118109 RCV001118110 RCV001118111 RCV001119647 RCV001119648 RCV001119649 RCV001119650 RCV001118011 RCV001121544 RCV001121549 RCV001116662 RCV001116666 RCV001116667 RCV001118106
Lung cancer	Conflicting classifications of pathogenicity; Benign; Likely benign	rs144369314, rs112053857	RCV005902646 RCV005905960
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	rs112053857, rs61185783	RCV005905957 RCV005913760
Melanoma	Conflicting classifications of pathogenicity; Benign; Likely benign	rs144369314, rs201384904	RCV005902645 RCV005913744
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity; Benign	rs144369314, rs61185783	RCV005902640 RCV005913757
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity; Benign; Likely benign	rs144369314, rs138645239, rs112053857, rs201384904	RCV005902644 RCV005904660 RCV005905958 RCV005913743
Sarcoma	Conflicting classifications of pathogenicity; Benign	rs144369314, rs61185783	RCV005902643 RCV005913762
Thymoma	Benign; Likely benign	rs112053857, rs61185783	RCV005905959 RCV005913764
Uterine carcinosarcoma	Benign	rs61185783	RCV005913763
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs112053857, rs61185783	RCV005905961 RCV005913765
UTP4-related disorder	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance; Benign	rs119465999, rs34057086, rs200047779, rs139624123, rs776624025, rs750196540, rs758406726, rs146966335, rs142116140, rs149282985, rs201153482, rs147819992, rs766637431, rs1417609006, rs766781882 View all (31 more)	RCV004751196 RCV003943659 RCV004750855 RCV004750860 RCV003399814 RCV003392767 RCV003392788 RCV003393091 RCV003946653 RCV003901168 RCV003901310 RCV004750925 RCV003896471 RCV003893651 RCV003896425 RCV003902262 RCV003902324 RCV003894495 RCV003901507 RCV003901542 RCV003911757 RCV003984597 RCV003899605 RCV003943887 RCV003927263 RCV003949747 RCV003951392 RCV003954525 RCV003982098 RCV003983552 RCV003954815 RCV003954842 RCV003969804 RCV003967016 RCV003967188 RCV003910396 RCV003930772 RCV003973090 RCV003928722 RCV003953490 RCV003945824 RCV004751887 RCV003405326 RCV003953489 RCV003945823 RCV003953492
Uveal melanoma	Benign	rs61185783	RCV005913759

Show/Hide Text Mining Associations (2)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Fibrosis	Associate	22916032
North American Indian Childhood Cirrhosis	Associate	22916032

UTP4 (UTP4 small subunit processome component)