URGCP
protein-codingupregulator of cell proliferation
Gene summary
URG4 is upregulated in the presence of hepatitis B virus (HBV)-encoded X antigen (HBxAg) and may contribute to the development of hepatocellular carcinoma by promoting hepatocellular growth and survival (Tufan et al., 2002 [PubMed 12082552]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to URGCP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001077663.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 7 | 9 | |||
| missense | 81 | 6 | 1 | 88 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 81 | 8 | 8 | 97 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001071131.1 | 6 | MANE Select | |
| Ensembl | ENSP00000396918.1 | 6 | MANE Select | |
| RefSeq | NP_001071132.1 | 3 | Standard | |
| RefSeq | NP_001277004.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell cycle
Molecular Function
- GTP binding
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000453200
- Coding exons
- 6
- Length
- 50518
- Individuals with no LoFs
- 124784
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 124797
- p
- 0.0000521
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 390 | 542 | 0.720 | 0.0000331 | 6080 |
| Missense (PolyPhen) | 108 | 193.62 | 0.55781 | 2303 | ||
| Synonymous | 0.953 | 212 | 230 | 0.920 | 0.0000153 | 1895 |
| Loss of Function | 4.22 | 7 | 33.3 | 0.210 | 0.00000184 | 364 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in cell cycle progression through the regulation of cyclin D1 expression. May participate in the development of hepatocellular carcinoma (HCC) by promoting hepatocellular growth and survival. May play an important role in development of gastric cancer. {ECO:0000269|PubMed:12082552, ECO:0000269|PubMed:17217616}.;
Intolerance Scores
- LoFtool
- 0.357
- RVIS EVS
- -0.51
- RVIS percentile EVS
- 21.8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |