OVOL2

ovo like zinc finger 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 20:17956978-18059188

Previous symbols: [ "ZNF339", "CHED1" ]

Links

ENSG00000125850 ∙ NCBI:58495 ∙ OMIM:616441 ∙ HGNC:15804 ∙ Uniprot:Q9BRP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• posterior polymorphous corneal dystrophy 1 (Limited), mode of inheritance: AD
• posterior polymorphous corneal dystrophy (Supportive), mode of inheritance: AD
• congenital hereditary endothelial dystrophy type I (Supportive), mode of inheritance: AD
• posterior polymorphous corneal dystrophy 1 (Strong), mode of inheritance: AD
• posterior polymorphous corneal dystrophy 1 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corneal dystrophy, posterior polymorphous, 1	AD	Ophthalmologic	Individuals are at risk of glaucoma prior to or following corneal transplantation, and surveillance and early treatment may be beneficial	Ophthalmologic	4900143; 26749309
A variant in the OVOL2 promoter have been described in Corneal dystrophy, posterior polymorphous, 1

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OVOL2 gene.

• Inborn genetic diseases (10 variants)
• not provided (9 variants)
• Posterior polymorphous corneal dystrophy 1 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OVOL2 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	2
missense			11		2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding				1		1
Total	0	0	11	2	3

Variants in OVOL2

This is a list of pathogenic ClinVar variants found in the OVOL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-17957006-T-C		not specified	Uncertain significance (May 10, 2023)
20-17957016-G-C		not specified	Uncertain significance (Sep 01, 2021)
20-17968383-G-C		not specified	Uncertain significance (Jan 04, 2024)
20-17969103-C-T			Likely benign (Jun 24, 2021)
20-17969679-C-T			Likely benign (Jun 28, 2018)
20-17969694-T-G			Likely benign (Jul 07, 2018)
20-17969860-A-G			Uncertain significance (Aug 04, 2023)
20-17969866-A-G		Inborn genetic diseases	Uncertain significance (Feb 08, 2023)
20-17969868-G-A			Uncertain significance (Dec 28, 2021)
20-17969871-G-C		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
20-17969882-C-G			Uncertain significance (Feb 06, 2023)
20-17969882-C-T			Uncertain significance (Dec 30, 2021)
20-17969893-CA-C			Pathogenic (Jun 27, 2022)
20-17969902-A-T		not specified • Mitochondrial DNA depletion syndrome 11	Benign (Jan 31, 2024)
20-17969903-G-A			Uncertain significance (Sep 12, 2022)
20-17969906-CAAA-C			Uncertain significance (Aug 15, 2022)
20-17969908-A-G			Uncertain significance (May 08, 2023)
20-17969911-T-C		Inborn genetic diseases	Uncertain significance (May 18, 2023)
20-17969912-TTTC-T		Mitochondrial DNA depletion syndrome 11	Uncertain significance (Aug 10, 2022)
20-17969924-C-A			Pathogenic (Feb 06, 2023)
20-17969930-C-T		Inborn genetic diseases	Uncertain significance (Aug 31, 2023)
20-17969938-G-A		Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
20-17969940-T-G			Likely benign (Jul 06, 2022)
20-17969945-C-G		not specified • MGME1-related disorder	Benign/Likely benign (Jan 19, 2024)
20-17969958-C-T			Likely benign (Mar 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OVOL2	protein_coding	protein_coding	ENST00000278780	4	102210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.709	0.288	125185	0	9	125194	0.0000359

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	114	152	0.751	0.00000936	1779
Missense in Polyphen		55	79.347	0.69315		764
Synonymous	0.769	59	67.0	0.880	0.00000449	522
Loss of Function	2.36	1	8.37	0.119	3.55e-7	113

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	0.0000463	0.0000463
European (Non-Finnish)	0.0000708	0.0000708
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Zinc-finger transcription repressor factor (PubMed:19700410). Plays a critical role in maintaining the identity of epithelial lineages by suppressing epithelial-to mesenchymal transition (EMT) mainly through the repression of ZEB1, an EMT inducer (By similarity). Positively regulates neuronal differentiation (By similarity). Suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing MYC and NOTCH1 (PubMed:19700410). Important for the correct development of primordial germ cells in embryos (By similarity). {ECO:0000250|UniProtKB:Q8CIV7, ECO:0000269|PubMed:19700410}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.251
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.826
• hipred: N
• hipred_score: 0.369
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ovol2
• Phenotype: vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear 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); embryo phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;neural crest cell migration;neural fold formation;heart looping;epidermal cell differentiation;dorsal/ventral pattern formation;positive regulation of gene expression;negative regulation of gene expression;negative regulation of epithelial to mesenchymal transition;regulation of keratinocyte proliferation;positive regulation of keratinocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic digestive tract morphogenesis;endocardium formation;heart trabecula formation;regulation of SMAD protein signal transduction;labyrinthine layer blood vessel development;cellular response to transforming growth factor beta stimulus;negative regulation of stem cell proliferation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;sequence-specific DNA binding;metal ion binding