OTP

protein-coding

orthopedia homeobox, the group of PRD class homeoboxes and pseudogenes

Gene summary

This gene encodes a member of the homeodomain (HD) family. HD family proteins are helix-turn-helix transcription factors that play key roles in the specification of cell fates. This protein may function during brain development. [provided by RefSeq, Jul 2008]

MANE transcript

NM_032109.3

Inheritance

—

ClinVar variants

U:44B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr5:77,628,712-77,638,713

External References & Databases

Ensembl (ENSG00000171540)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OTP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032109.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			44 clinvar	1 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	1	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032109.3	RefSeq	NP_115485.1	3	MANE Select
ENST00000306422.5	Ensembl	ENSP00000302814.3	3	MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
otpb	Danio rerio	Structure: dopaminergic neuron Quality: disorganized abnormal

Gene / Model

Organism

Observed Phenotype

otpb

Danio rerio

Structure: dopaminergic neuron

Quality: disorganized

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of neuroblast proliferation
regulation of transcription by RNA polymerase II
forebrain neuron differentiation
hypothalamus cell differentiation
neurohypophysis development

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306422
Coding exons: 3
Length: 10976
Individuals with no LoFs: 125223
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125224
p: 0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.02	134	172	0.781	0.00000784	2038
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000089	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.749

Gene Damage Prediction

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