ONECUT1
Basic information
Region (hg38): 15:52755053-52791078
Previous symbols: [ "HNF6", "HNF6A" ]
Links
Phenotypes
GenCC
Source:
- neonatal diabetes mellitus (Strong), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- not_provided (2 variants)
- Autosomal_dominant_polycystic_liver_disease (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ONECUT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004498.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 54 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ONECUT1 | protein_coding | protein_coding | ENST00000305901 | 2 | 33637 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.523 | 0.473 | 125715 | 0 | 4 | 125719 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.524 | 237 | 261 | 0.909 | 0.0000123 | 3032 |
| Missense in Polyphen | 57 | 90.757 | 0.62805 | 1040 | ||
| Synonymous | -0.363 | 115 | 110 | 1.04 | 0.00000527 | 928 |
| Loss of Function | 2.45 | 2 | 10.6 | 0.188 | 5.24e-7 | 115 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.0000194 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator. Binds the consensus sequence 5'-DHWATTGAYTWWD-3' on a variety of gene promoters such as those of HNF3B and TTR. Important for liver genes transcription.;
- Pathway
- Maturity onset diabetes of the young - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Endoderm Differentiation;FOXM1 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.0302
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.6
Haploinsufficiency Scores
- pHI
- 0.423
- hipred
- Y
- hipred_score
- 0.751
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.583
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Onecut1
- Phenotype
- digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- onecut1
- Affected structure
- intrahepatic bile duct
- Phenotype tag
- abnormal
- Phenotype quality
- dilated
Gene ontology
- Biological process
- liver development;regulation of cell-matrix adhesion;epithelial cell development;glucose metabolic process;regulation of transcription, DNA-templated;Notch signaling pathway;endoderm development;anatomical structure morphogenesis;cell differentiation;B cell differentiation;positive regulation of cell migration;negative regulation of transforming growth factor beta receptor signaling pathway;endocrine pancreas development;cell fate commitment;positive regulation of transcription by RNA polymerase II;spleen development;cilium assembly
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding