ONECUT1

one cut homeobox 1, the group of CUT class homeoboxes and pseudogenes

Basic information

Region (hg38): 15:52755052-52791078

Previous symbols: [ "HNF6", "HNF6A" ]

Links

ENSG00000169856 ∙ NCBI:3175 ∙ OMIM:604164 ∙ HGNC:8138 ∙ Uniprot:Q9UBC0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ONECUT1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 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.

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				1		1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in ONECUT1

This is a list of pathogenic ClinVar variants found in the ONECUT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-52757607-C-A		not specified	Uncertain significance (May 18, 2023)
15-52757684-C-T			Likely benign (Jul 16, 2018)
15-52757734-T-G		not specified	Uncertain significance (Jun 06, 2023)
15-52788858-C-A		not specified	Uncertain significance (Jan 03, 2024)
15-52788932-C-T		not specified	Uncertain significance (Jan 06, 2023)
15-52788959-C-G		not specified	Uncertain significance (Aug 04, 2022)
15-52788962-T-C		not specified	Uncertain significance (Jul 28, 2021)
15-52789056-C-T		not specified	Uncertain significance (Dec 14, 2023)
15-52789079-C-T		not specified	Uncertain significance (Sep 13, 2023)
15-52789080-G-C		Autosomal dominant polycystic liver disease	Uncertain significance (Sep 01, 2021)
15-52789088-C-A		not specified	Uncertain significance (Dec 17, 2023)
15-52789155-T-C		not specified	Uncertain significance (Jan 03, 2024)
15-52789157-G-T		not specified	Uncertain significance (Jul 09, 2021)
15-52789161-C-T		not specified	Uncertain significance (Jan 29, 2024)
15-52789236-C-T		not specified	Uncertain significance (Nov 09, 2022)
15-52789238-T-C		not specified	Uncertain significance (Mar 07, 2024)
15-52789322-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-52789365-C-T		not specified	Uncertain significance (Dec 14, 2022)
15-52789404-T-G		not specified	Uncertain significance (Mar 31, 2023)
15-52789438-G-C		not specified	Uncertain significance (Apr 12, 2023)
15-52789496-T-C		not specified	Uncertain significance (Jan 10, 2022)
15-52789511-T-C		not specified	Uncertain significance (Jun 18, 2021)
15-52789554-G-A		not specified	Uncertain significance (Jun 01, 2023)
15-52789643-C-T		Autosomal dominant polycystic liver disease	Uncertain significance (Sep 01, 2021)
15-52789740-G-T		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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