PITX3 paired like homeodomain 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PITX3provided by HGNC
Official Full Name: paired like homeodomain 3provided by HGNC
Primary source: HGNC:HGNC:9006
See related: Ensembl:ENSG00000107859 MIM:602669; AllianceGenome:HGNC:9006
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ASMD; ASOD; PTX3; ASGD1; CTPP4; CTRCT11
Summary: This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors. This protein is involved in lens formation during eye development. Mutations of this gene have been associated with anterior segment mesenchymal dysgenesis and congenital cataracts. [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.32

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (102230189..102241512, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (103115176..103126499, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (103989946..104001269, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts.
Title: Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts.
Complementation of dopaminergic signaling by Pitx3-GDNF synergy induces dopamine secretion by multipotent Ntera2 cells.
Title: Complementation of dopaminergic signaling by Pitx3-GDNF synergy induces dopamine secretion by multipotent Ntera2 cells.
The mutation c.797_814del, p.Ser266_Ala271del is a novel mutation in the conserved DNA-binding OAR domain of PITX3 that causes congenital cataract.
Title: A novel mutation in the OAR domain of PITX3 associated with congenital posterior subcapsular cataract.
The functional analysis of these 2 PITX3 mutations in the in vitro functional studies is an important complement and extension, which provides a potential interpretation for the pathogenesis and molecular mechanism of PITX3 mutations associated with CC.
Title: PITX3 mutations associated with autosomal dominant congenital cataract in the Chinese population.
Heterozygous mutation in the PITX3 gene is associated with ocular developmental defects.
Title: Identification of PITX3 mutations in individuals with various ocular developmental defects.
Results show that a common polymorphism in the PITX3 gene affects the risk of developing Parkinson's disease (PD) dementia and visuospatial dysfunction in idiopathic PD. If validated, these findings can provide new insights into the neurobiology and genetics of non-motor symptoms in PD.
Title: PITX3 genotype and risk of dementia in Parkinson's disease: A population-based study.
Study showed that PITX3 methylation was significantly methylated in head and neck squamous cell carcinoma (HNSCC) tumor compared to normal adjacent tissue and correlated with lymph node status. These results provide evidence that PITX3 DNA methylation is an independent prognostic biomarker for overall survival in patients with HNSCC and might aid in the process of risk stratification for individualized treatment.
Title: PITX3 DNA methylation is an independent predictor of overall survival in patients with head and neck squamous cell carcinoma.
Study showed that PITX3 and PITX2 were hypermethylated in prostate carcinomas (PCa) and significantly associated with established clinicopathologic parameters characteristic of PCa.
Title: PITX3 promoter methylation is a prognostic biomarker for biochemical recurrence-free survival in prostate cancer patients after radical prostatectomy.
These findings suggest that p.A203fs in PITX3 is the cause of cataracts in the recruited family.
Title: Whole Exome Sequencing Identifies a Novel Mutation in the PITX3 Gene, Causing Autosomal Dominant Congenital Cataracts in a Chinese Family.
PITX3 variants rs3758549 and rs4919621 are not associated with ET in Chinese Han population.
Title: Genetic analysis of PITX3 variants in patients with essential tremor.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Anophthalmia-microphthalmia syndrome MedGen: C5680330 GeneReviews: Not available	Compare labs
Anterior segment dysgenesis 1 MedGen: C4551992 OMIM: 107250 GeneReviews: Not available	Compare labs
Cataract 11 multiple types MedGen: C1864567 OMIM: 610623 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2013-11-06) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2013-11-06) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-147498 (e-PCR)
- UniSTS:172818

Pitx3 (e-PCR), detects polymorphism
- UniSTS:144186

UniSTS:144187 (e-PCR)
- UniSTS:144187

Pitx3 (e-PCR), detects polymorphism
- UniSTS:144187

D1Bda64 (e-PCR)
- UniSTS:239817

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to glial cell derived neurotrophic factor	IEA Inferred from Electronic Annotation more info
involved_in dopaminergic neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in dopaminergic neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in dopaminergic neuron differentiation	TAS Traceable Author Statement more info	PubMed
involved_in lens development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in lens development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in lens fiber cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in lens morphogenesis in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in lens morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within locomotory behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within midbrain development	IEA Inferred from Electronic Annotation more info
involved_in midbrain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of gliogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neurogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell proliferation in midbrain	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to cocaine	IEA Inferred from Electronic Annotation more info
involved_in response to immobilization stress	IEA Inferred from Electronic Annotation more info
involved_in response to methamphetamine hydrochloride	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: pituitary homeobox 3

Names: homeobox protein PITX3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.