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

134

Show/Hide all (134)

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

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 (27)

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.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BILIARY CIRRHOSIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHOLESTASIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CIRRHOSIS, FAMILIAL	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIGESTIVE SYSTEM DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary North American Indian childhood cirrhosis	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY BILIARY CHOLANGITIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTP4-related disorder	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (9)

Disease Name	Disease (Merged)	Source	PMID	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Cholestasis	Cholestasis	BEFREE	10820129, 11045837	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Carcinoma	Colorectal Cancer	BEFREE	28350096	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary North American Indian childhood cirrhosis	Cirrhosis	Orphanet		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ICHTHYOSIS, LEUKOCYTE VACUOLES, ALOPECIA, AND SCLEROSING CHOLANGITIS	Ichthyosis-Sclerosing Cholangitis Syndrome	BEFREE	15768832	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholestasis	Intrahepatic Cholestasis	BEFREE	16225863	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28350096	★★★★★ ★☆☆☆☆ Found in Text Mining only
NORTH AMERICAN INDIAN CHILDHOOD CIRRHOSIS	Cirrhosis	BEFREE	10820129, 11045837, 12417987, 15768832, 16225863, 20385600, 24147052	★★★★★ ★☆☆☆☆ Found in Text Mining only
NORTH AMERICAN INDIAN CHILDHOOD CIRRHOSIS	Cirrhosis	ORPHANET_DG	12417987	★★★★★ ★☆☆☆☆ Found in Text Mining only
NORTH AMERICAN INDIAN CHILDHOOD CIRRHOSIS	Cirrhosis	GENOMICS_ENGLAND_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only

UTP4 (UTP4 small subunit processome component)