OTP

orthopedia homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 5:77628712-77638713

Links

ENSG00000171540 ∙ NCBI:23440 ∙ OMIM:604529 ∙ HGNC:8518 ∙ Uniprot:Q5XKR4 ∙ 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 OTP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTP 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in OTP

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

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

Position	Type	Phenotype	Significance	ClinVar
5-77630273-G-T		not specified	Uncertain significance (Sep 26, 2023)
5-77630385-T-C		not specified	Uncertain significance (Aug 17, 2022)
5-77630477-G-T		not specified	Uncertain significance (Jan 24, 2023)
5-77630544-G-C		not specified	Uncertain significance (Apr 16, 2024)
5-77630546-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-77630548-T-C		not specified	Uncertain significance (Jan 08, 2024)
5-77630593-C-T		not specified	Uncertain significance (May 11, 2022)
5-77630607-G-A		not specified	Uncertain significance (May 10, 2022)
5-77630648-G-T		not specified	Uncertain significance (Jul 20, 2021)
5-77630722-T-G		not specified	Uncertain significance (May 14, 2024)
5-77630740-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-77630748-G-A		not specified	Uncertain significance (Nov 02, 2023)
5-77636847-T-C		not specified	Uncertain significance (Jan 29, 2024)
5-77636975-T-A		not specified	Uncertain significance (Aug 11, 2022)
5-77636981-C-T		not specified	Uncertain significance (May 04, 2023)
5-77636984-G-A			Likely benign (Mar 01, 2023)
5-77637012-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-77637015-C-G		not specified	Uncertain significance (Feb 23, 2023)
5-77637031-G-C		not specified	Uncertain significance (Jun 24, 2022)
5-77637047-G-T		not specified	Uncertain significance (Dec 01, 2022)
5-77637126-T-C		not specified	Uncertain significance (Apr 15, 2024)
5-77637131-G-T		not specified	Uncertain significance (Jul 13, 2021)
5-77637153-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-77637164-C-A		not specified	Uncertain significance (Jan 09, 2023)
5-77637171-C-A		not specified	Uncertain significance (Mar 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTP	protein_coding	protein_coding	ENST00000306422	3	10976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.740	0.257	125223	0	1	125224	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	134	172	0.781	0.00000784	2038
Missense in Polyphen		29	60.797	0.47699		742
Synonymous	0.646	71	78.3	0.907	0.00000380	710
Loss of Function	2.43	1	8.78	0.114	3.87e-7	91

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)	0.00000887	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in the differentiation of hypothalamic neuroendocrine cells.

Haploinsufficiency Scores

• pHI: 0.230
• hipred: Y
• hipred_score: 0.789

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.749

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otp
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region 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); 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)

Zebrafish Information Network

• Gene name: otpb
• Affected structure: dopaminergic neuron
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: positive regulation of neuroblast proliferation;regulation of transcription by RNA polymerase II;forebrain neuron differentiation;hypothalamus cell differentiation;neurohypophysis development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding