ONECUT3

one cut homeobox 3, the group of CUT class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:1753505-1780988

Links

ENSG00000205922 ∙ NCBI:390874 ∙ OMIM:611294 ∙ HGNC:13399 ∙ Uniprot:O60422 ∙ 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 ONECUT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ONECUT3 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						0
missense			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	3	0

Variants in ONECUT3

This is a list of pathogenic ClinVar variants found in the ONECUT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1753681-A-G		not specified	Uncertain significance (May 14, 2024)
19-1753690-G-A		not specified	Uncertain significance (May 23, 2024)
19-1753699-A-G		not specified	Likely benign (Apr 07, 2023)
19-1753734-C-G		not specified	Uncertain significance (Aug 16, 2022)
19-1753736-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-1753738-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-1753744-G-T		not specified	Uncertain significance (Dec 21, 2022)
19-1753747-C-A		not specified	Uncertain significance (May 09, 2023)
19-1753748-G-A		not specified	Uncertain significance (May 27, 2022)
19-1753762-C-A		not specified	Uncertain significance (Jun 23, 2023)
19-1753768-C-A		not specified	Uncertain significance (Apr 13, 2022)
19-1753834-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-1753850-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-1753862-G-C		not specified	Uncertain significance (Feb 16, 2023)
19-1753903-C-T		not specified	Uncertain significance (Mar 11, 2022)
19-1754068-G-A		not specified	Uncertain significance (Dec 02, 2022)
19-1754105-C-G		not specified	Uncertain significance (May 27, 2022)
19-1754111-C-G		not specified	Uncertain significance (Feb 28, 2023)
19-1754114-C-A		not specified	Uncertain significance (Jun 27, 2023)
19-1754116-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-1754128-C-G		not specified	Uncertain significance (Jan 24, 2024)
19-1754158-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-1754192-C-T		not specified	Uncertain significance (Feb 03, 2022)
19-1754194-C-G		not specified	Uncertain significance (Feb 27, 2023)
19-1754197-G-T		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ONECUT3	protein_coding	protein_coding	ENST00000382349	2	28616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00292	0.598	115981	0	2	115983	0.00000862

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	50	83.6	0.598	0.00000392	3056
Missense in Polyphen		8	38.824	0.20606		517
Synonymous	0.531	32	36.1	0.887	0.00000170	1139
Loss of Function	0.399	4	4.96	0.807	2.13e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000301	0.0000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000963	0.00000963
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 DNA sequence 5'-DHWATTGAYTWWD-3' on a variety of gene promoters such as those of HNF3B and TTR (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.0809
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Onecut3
• Phenotype: endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: onecut3a
• Affected structure: hepatic duct
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding