ONECUT2

one cut homeobox 2, the group of CUT class homeoboxes and pseudogenes

Basic information

Region (hg38): 18:57435373-57491298

Links

ENSG00000119547 ∙ NCBI:9480 ∙ OMIM:604894 ∙ HGNC:8139 ∙ Uniprot:O95948 ∙ 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 ONECUT2 gene.

• Inborn genetic diseases (19 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ONECUT2 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	2	3
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	2

Variants in ONECUT2

This is a list of pathogenic ClinVar variants found in the ONECUT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-57435735-G-A		not specified	Uncertain significance (Jun 24, 2022)
18-57435774-A-G		not specified	Uncertain significance (Oct 22, 2021)
18-57435775-T-C		not specified	Uncertain significance (Mar 30, 2022)
18-57435781-C-G		not specified	Uncertain significance (Nov 21, 2022)
18-57435816-G-T		not specified	Uncertain significance (May 16, 2022)
18-57435831-G-T		not specified	Uncertain significance (Nov 13, 2023)
18-57435832-G-A		not specified	Uncertain significance (Nov 09, 2023)
18-57435846-G-A		not specified	Likely benign (Aug 17, 2022)
18-57435860-C-G			Likely benign (Feb 01, 2023)
18-57435877-G-T		not specified	Uncertain significance (Oct 05, 2023)
18-57435886-A-G		not specified	Uncertain significance (Feb 27, 2024)
18-57435890-G-T		not specified	Uncertain significance (Apr 07, 2023)
18-57435894-G-A		not specified	Uncertain significance (May 27, 2022)
18-57435934-G-T		not specified	Uncertain significance (May 23, 2023)
18-57435951-C-T		not specified	Uncertain significance (Dec 06, 2023)
18-57436076-G-A			Benign (Apr 20, 2018)
18-57436207-C-G		Autosomal dominant polycystic liver disease	Uncertain significance (Sep 01, 2021)
18-57436268-C-G		not specified	Uncertain significance (Nov 08, 2022)
18-57436287-G-A		not specified	Uncertain significance (Nov 28, 2023)
18-57436293-G-A		not specified	Uncertain significance (Nov 12, 2021)
18-57436319-G-T		not specified	Uncertain significance (Oct 26, 2022)
18-57436354-C-T		not specified	Uncertain significance (Jun 24, 2022)
18-57436392-C-G		Autosomal dominant polycystic liver disease	Uncertain significance (Sep 01, 2021)
18-57436398-G-A		not specified	Uncertain significance (Apr 07, 2023)
18-57436420-G-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ONECUT2	protein_coding	protein_coding	ENST00000491143	2	55613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.907	0.0929	124347	0	1	124348	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	219	281	0.779	0.0000147	3248
Missense in Polyphen		87	111.01	0.7837		1150
Synonymous	-1.02	133	119	1.12	0.00000608	1058
Loss of Function	2.95	1	12.1	0.0830	6.06e-7	127

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	0.00	0.00
European (Non-Finnish)	0.00000888	0.00000888
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator. Activates the transcription of a number of liver genes such as HNF3B.

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.0369
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.800
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Onecut2
• Phenotype: liver/biliary system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: liver development;regulation of cell-matrix adhesion;epithelial cell development;animal organ morphogenesis;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;peripheral nervous system neuron development;cilium assembly
• Cellular component: nucleus;nucleoplasm;actin cytoskeleton
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding