OTX1

orthodenticle homeobox 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 2:63050056-63057836

Links

ENSG00000115507 ∙ NCBI:5013 ∙ OMIM:600036 ∙ HGNC:8521 ∙ Uniprot:P32242 ∙ 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 OTX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTX1 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			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	2

Variants in OTX1

This is a list of pathogenic ClinVar variants found in the OTX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-63053017-A-T		OTX1-related disorder	Benign/Likely benign (Jan 13, 2020)
2-63054086-C-A		not specified	Uncertain significance (Dec 13, 2023)
2-63055642-G-C		not specified	Uncertain significance (Mar 29, 2024)
2-63055732-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-63055754-T-G		not specified	Uncertain significance (Aug 02, 2021)
2-63055796-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-63055828-G-C		not specified	Uncertain significance (Feb 11, 2022)
2-63055927-G-A		OTX1-related disorder	Benign (Dec 31, 2019)
2-63056038-C-G		not specified	Uncertain significance (Sep 25, 2023)
2-63056043-C-G			Benign (Nov 05, 2018)
2-63056052-G-A		not specified	Uncertain significance (Mar 08, 2024)
2-63056092-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-63056146-C-A		not specified	Uncertain significance (Dec 20, 2021)
2-63056287-C-A		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTX1	protein_coding	protein_coding	ENST00000282549	3	7780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.855	0.144	125275	0	1	125276	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	156	213	0.733	0.0000104	2265
Missense in Polyphen		20	43.144	0.46356		463
Synonymous	0.937	88	99.9	0.881	0.00000549	758
Loss of Function	2.75	1	10.7	0.0933	4.60e-7	119

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)	0.00000884	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a role in the development of the brain and the sense organs. Can bind to the BCD target sequence (BTS): 5'-TCTAATCCC-3'.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.277

Intolerance Scores

• loftool: 0.0413
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.151
• hipred: Y
• hipred_score: 0.651
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.429

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otx1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; vision/eye phenotype; craniofacial phenotype; reproductive system phenotype; 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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

Zebrafish Information Network

• Gene name: otx1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: unbalanced

Gene ontology

• Biological process: anterior/posterior pattern specification;metencephalon development;midbrain development;inner ear morphogenesis;positive regulation of transcription by RNA polymerase II;diencephalon morphogenesis
• Cellular component: nucleus
• 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;protein binding