UTP4

UTP4 small subunit processome component, the group of WD repeat domain containing|UTPa subcomplex

Basic information

Region (hg38): 16:69131291-69231130

Previous symbols: [ "CIRH1A" ]

Links

ENSG00000141076NCBI:84916OMIM:607456HGNC:1983Uniprot:Q969X6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hereditary North American Indian childhood cirrhosis (Supportive), mode of inheritance: AR
  • cirrhosis, familial (Disputed Evidence), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
North American Indian childhood cirrhosisARGastrointestinalIndividuals may initially present with neonatal cholestatic jaundice, and the condition may progress to end-stage, severe liver failure; Liver transplantation has been described as effective, and individuals have been described as dying before liver transplantation was availableGastrointestinal6894906; 10820129; 11045837

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UTP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
6
clinvar
28
clinvar
7
clinvar
41
missense
38
clinvar
4
clinvar
2
clinvar
44
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
5
7
non coding
2
clinvar
4
clinvar
2
clinvar
8
Total 0 0 47 36 11

Variants in UTP4

This is a list of pathogenic ClinVar variants found in the UTP4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
16-69133455-T-C Hereditary North American Indian childhood cirrhosis Uncertain significance (Jan 12, 2018)886048
16-69133495-T-C UTP4-related disorder Likely benign (Jun 03, 2022)3032640
16-69133516-C-A Hereditary North American Indian childhood cirrhosis Uncertain significance (Jan 13, 2018)887041
16-69133533-A-G UTP4-related disorder • not specified Uncertain significance (Apr 06, 2023)2636139
16-69133557-T-C Uncertain significance (Jul 17, 2023)2779242
16-69133574-A-G UTP4-related disorder Uncertain significance (Oct 19, 2023)3045663
16-69136751-A-G Uncertain significance (May 23, 2023)2969613
16-69136774-A-C UTP4-related disorder Uncertain significance (Jun 23, 2023)2629050
16-69136780-G-A Uncertain significance (Jul 03, 2022)2421536
16-69136806-G-A Hereditary North American Indian childhood cirrhosis Benign (Jan 16, 2024)887042
16-69136838-G-T Hereditary North American Indian childhood cirrhosis • UTP4-related disorder Conflicting classifications of pathogenicity (Dec 21, 2023)710240
16-69136881-A-G UTP4-related disorder Likely benign (Apr 12, 2023)3050466
16-69137867-A-G Hereditary North American Indian childhood cirrhosis Uncertain significance (Jan 12, 2018)887043
16-69137876-C-T not specified Uncertain significance (Oct 26, 2021)2374366
16-69139852-C-A UTP4-related disorder Likely benign (Jan 25, 2024)2890657
16-69139853-C-T Likely benign (May 31, 2023)2712960
16-69139866-A-G UTP4-related disorder Uncertain significance (Dec 07, 2023)3033774
16-69143182-C-T Hereditary North American Indian childhood cirrhosis Uncertain significance (Jan 13, 2018)887044
16-69143185-T-C UTP4-related disorder Likely benign (May 10, 2022)3029319
16-69143186-G-T UTP4-related disorder Likely benign (May 23, 2023)2712345
16-69143221-C-T Likely benign (Jun 27, 2023)2886969
16-69143222-G-A Uncertain significance (Apr 24, 2023)2898888
16-69143242-C-T UTP4-related disorder Benign/Likely benign (Mar 16, 2023)2724483
16-69143266-C-T Hereditary North American Indian childhood cirrhosis Benign/Likely benign (Dec 28, 2023)887045
16-69143283-G-A Hereditary North American Indian childhood cirrhosis Uncertain significance (Mar 30, 2018)887046

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UTP4protein_codingprotein_codingENST00000314423 1699840
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.71e-71.001257160321257480.000127
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1603673760.9770.00002194526
Missense in Polyphen7196.3530.736881166
Synonymous-1.391541341.150.000007851315
Loss of Function3.251738.90.4370.00000235414

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001810.000181
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001630.000163
Finnish0.0001850.000185
European (Non-Finnish)0.00009680.0000967
Middle Eastern0.0001630.000163
South Asian0.0002950.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Involved in small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b. Required for optimal pre-ribosomal RNA transcription by RNA polymerase (PubMed:17699751, PubMed:19732766). May be a transcriptional regulator. Acts as a positive regulator of HIVEP1 which specifically binds to the DNA sequence 5'-GGGACTTTCC-3' found in enhancer elements of numerous viral promoters such as those of HIV-1, SV40, or CMV (PubMed:19732766). {ECO:0000269|PubMed:17699751, ECO:0000269|PubMed:19732766, ECO:0000269|PubMed:22916032}.;
Pathway
Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

pRec
0.152

Intolerance Scores

loftool
rvis_EVS
-0.13
rvis_percentile_EVS
43.98

Haploinsufficiency Scores

pHI
0.443
hipred
Y
hipred_score
0.694
ghis
0.559

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Utp4
Phenotype

Zebrafish Information Network

Gene name
utp4
Affected structure
hepatocyte
Phenotype tag
abnormal
Phenotype quality
increased amount

Gene ontology

Biological process
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);regulation of transcription, DNA-templated;rRNA processing;maturation of SSU-rRNA
Cellular component
fibrillar center;nucleoplasm;chromosome;nucleolus;90S preribosome;small-subunit processome;t-UTP complex
Molecular function
RNA binding;protein binding