UTP4
Basic information
Region (hg38): 16:69131291-69231130
Previous symbols: [ "CIRH1A" ]
Links
Phenotypes
GenCC
Source:
- hereditary North American Indian childhood cirrhosis (Supportive), mode of inheritance: AR
- cirrhosis, familial (Disputed Evidence), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
North American Indian childhood cirrhosis | AR | Gastrointestinal | Individuals 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 available | Gastrointestinal | 6894906; 10820129; 11045837 |
ClinVar
This is a list of variants' phenotypes submitted to
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 | 28 | 41 | ||||
missense | 38 | 44 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 5 | 7 | |||
non coding | 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) | ||
16-69133495-T-C | UTP4-related disorder | Likely benign (Jun 03, 2022) | ||
16-69133516-C-A | Hereditary North American Indian childhood cirrhosis | Uncertain significance (Jan 13, 2018) | ||
16-69133533-A-G | UTP4-related disorder • not specified | Uncertain significance (Apr 06, 2023) | ||
16-69133552-G-A | UTP4-related disorder | Likely benign (Mar 24, 2024) | ||
16-69133557-T-C | Uncertain significance (Jul 17, 2023) | |||
16-69133574-A-G | UTP4-related disorder | Uncertain significance (Oct 19, 2023) | ||
16-69136751-A-G | Uncertain significance (May 23, 2023) | |||
16-69136774-A-C | UTP4-related disorder | Uncertain significance (Jun 23, 2023) | ||
16-69136780-G-A | Uncertain significance (Jul 03, 2022) | |||
16-69136806-G-A | Hereditary North American Indian childhood cirrhosis | Benign (Jan 16, 2024) | ||
16-69136838-G-T | Hereditary North American Indian childhood cirrhosis • UTP4-related disorder | Conflicting classifications of pathogenicity (Dec 21, 2023) | ||
16-69136881-A-G | UTP4-related disorder | Likely benign (Apr 12, 2023) | ||
16-69137867-A-G | Hereditary North American Indian childhood cirrhosis | Uncertain significance (Jan 12, 2018) | ||
16-69137876-C-T | not specified • UTP4-related disorder | Uncertain significance (Oct 26, 2021) | ||
16-69137892-G-A | UTP4-related disorder | Likely benign (May 03, 2024) | ||
16-69139852-C-A | UTP4-related disorder | Likely benign (Jan 25, 2024) | ||
16-69139853-C-T | Likely benign (May 31, 2023) | |||
16-69139866-A-G | UTP4-related disorder | Uncertain significance (Dec 07, 2023) | ||
16-69143182-C-T | Hereditary North American Indian childhood cirrhosis | Uncertain significance (Jan 13, 2018) | ||
16-69143185-T-C | UTP4-related disorder | Likely benign (May 10, 2022) | ||
16-69143186-G-T | UTP4-related disorder | Likely benign (May 23, 2023) | ||
16-69143221-C-T | Likely benign (Jun 27, 2023) | |||
16-69143222-G-A | Uncertain significance (Apr 24, 2023) | |||
16-69143226-C-G | UTP4-related disorder | Uncertain significance (Mar 27, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UTP4 | protein_coding | protein_coding | ENST00000314423 | 16 | 99840 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.71e-7 | 1.00 | 125716 | 0 | 32 | 125748 | 0.000127 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.160 | 367 | 376 | 0.977 | 0.0000219 | 4526 |
Missense in Polyphen | 71 | 96.353 | 0.73688 | 1166 | ||
Synonymous | -1.39 | 154 | 134 | 1.15 | 0.00000785 | 1315 |
Loss of Function | 3.25 | 17 | 38.9 | 0.437 | 0.00000235 | 414 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000181 | 0.000181 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000185 | 0.000185 |
European (Non-Finnish) | 0.0000968 | 0.0000967 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000295 | 0.000294 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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