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PITX2 paired like homeodomain 2 [ Homo sapiens (human) ]

Gene ID: 5308, updated on 5-Jul-2020

Summary

Official Symbol
PITX2provided by HGNC
Official Full Name
paired like homeodomain 2provided by HGNC
Primary source
HGNC:HGNC:9005
See related
Ensembl:ENSG00000164093 MIM:601542
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
RS; RGS; ARP1; Brx1; IDG2; IGDS; IHG2; PTX2; RIEG; ASGD4; IGDS2; IRID2; Otlx2; RIEG1
Summary
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. The encoded protein acts as a transcription factor and regulates procollagen lysyl hydroxylase gene expression. This protein plays a role in the terminal differentiation of somatotroph and lactotroph cell phenotypes, is involved in the development of the eye, tooth and abdominal organs, and acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. Mutations in this gene are associated with Axenfeld-Rieger syndrome, iridogoniodysgenesis syndrome, and sporadic cases of Peters anomaly. A similar protein in other vertebrates is involved in the determination of left-right asymmetry during development. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]
Expression
Biased expression in placenta (RPKM 15.1), urinary bladder (RPKM 3.5) and 6 other tissues See more
Orthologs

Genomic context

See PITX2 in Genome Data Viewer
Location:
4q25
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (110617423..110642123, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (111538579..111563279, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene glutamyl aminopeptidase Neighboring gene uncharacterized LOC105377363 Neighboring gene PITX2 adjacent non-coding RNA Neighboring gene VISTA enhancer hs930 Neighboring gene microRNA 297

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Anophthalmia-microphthalmia syndrome Compare labs
Anterior segment dysgenesis 4
MedGen: C1842031 OMIM: 137600 GeneReviews: Not available
Compare labs
Axenfeld-Rieger syndrome type 1
MedGen: C3714873 OMIM: 180500 GeneReviews: Not available
Compare labs
Ring dermoid of cornea
MedGen: C1867155 OMIM: 180550 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Common variants in KCNN3 are associated with lone atrial fibrillation.
NHGRI GWA Catalog
Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
Meta-analysis identifies six new susceptibility loci for atrial fibrillation.
NHGRI GWA Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
NHGRI GWA Catalog
Variants conferring risk of atrial fibrillation on chromosome 4q25.
NHGRI GWA Catalog
Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC20144, MGC111022

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
camera-type eye development IMP
Inferred from Mutant Phenotype
more info
PubMed 
cardiac neural crest cell migration involved in outflow tract morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation involved in outflow tract morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
deltoid tuberosity development IMP
Inferred from Mutant Phenotype
more info
PubMed 
determination of left/right symmetry ISS
Inferred from Sequence or Structural Similarity
more info
 
hair cell differentiation IC
Inferred by Curator
more info
PubMed 
iris morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
left/right axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
odontogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
prolactin secreting cell differentiation TAS
Traceable Author Statement
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
somatotropin secreting cell differentiation TAS
Traceable Author Statement
more info
PubMed 
spleen development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
pituitary homeobox 2
Names
ALL1-responsive protein ARP1
all1-responsive gene 1
homeobox protein PITX2
paired-like homeodomain transcription factor 2
rieg bicoid-related homeobox transcription factor 1
solurshin

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_007120.1 RefSeqGene

    Range
    230..24930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000325.6NP_000316.2  pituitary homeobox 2 isoform c

    See identical proteins and their annotated locations for NP_000316.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as ARP1c, lacks several exons at the 5' end and has an alternate 5' exon, as compared to variant 2. The resulting isoform (c) has a longer and distinct N-terminus, as compared to isoform b.
    Source sequence(s)
    AC017068, BC013998
    Consensus CDS
    CCDS3694.1
    UniProtKB/Swiss-Prot
    Q99697
    Related
    ENSP00000495061.1, ENST00000644743.1
    Conserved Domains (3) summary
    pfam00046
    Location:96148
    Homeobox; Homeobox domain
    pfam03826
    Location:282299
    OAR; OAR domain
    cl27820
    Location:40149
    Abdominal-A; Homeobox protein
  2. NM_001204397.1NP_001191326.1  pituitary homeobox 2 isoform b

    See identical proteins and their annotated locations for NP_001191326.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional exon in the 5' UTR, as compared to variant 2. Variants 2, 4 and 5 encode the same isoform b.
    Source sequence(s)
    AK127829, BC106010, BP372081, BX380370, U69961
    Consensus CDS
    CCDS3692.1
    UniProtKB/Swiss-Prot
    Q99697
    Related
    ENSP00000347004.2, ENST00000354925.6
    Conserved Domains (2) summary
    pfam00046
    Location:89141
    Homeobox; Homeobox domain
    pfam03826
    Location:275292
    OAR; OAR domain
  3. NM_001204398.1NP_001191327.1  pituitary homeobox 2 isoform b

    See identical proteins and their annotated locations for NP_001191327.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' UTR, as compared to variant 2. Variants 2, 4 and 5 encode the same isoform b.
    Source sequence(s)
    BC106010, BP372081
    Consensus CDS
    CCDS3692.1
    UniProtKB/Swiss-Prot
    Q99697
    Related
    ENSP00000481951.1, ENST00000614423.4
    Conserved Domains (2) summary
    pfam00046
    Location:89141
    Homeobox; Homeobox domain
    pfam03826
    Location:275292
    OAR; OAR domain
  4. NM_001204399.1NP_001191328.1  pituitary homeobox 2 isoform a

    See identical proteins and their annotated locations for NP_001191328.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an exon in the 5' UTR and an in-frame exon in the 5' CDS, as compared to variant 2. The resulting isoform (a) lacks an internal segment, as compared to isoform b. Variants 1 and 6 encode the same isoform a.
    Source sequence(s)
    BC106010, BP372081
    Consensus CDS
    CCDS3693.1
    UniProtKB/Swiss-Prot
    Q99697
    Conserved Domains (2) summary
    pfam03826
    Location:229246
    OAR; OAR domain
    pfam00046
    Location:4396
    Homeobox; Homeobox domain
  5. NM_153426.2NP_700475.1  pituitary homeobox 2 isoform b

    See identical proteins and their annotated locations for NP_700475.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as ARP1b, encodes the predominant isoform (b).
    Source sequence(s)
    AK127829, BC013998, BC106010, BP372081, BX380370, U69961
    Consensus CDS
    CCDS3692.1
    UniProtKB/Swiss-Prot
    Q99697
    Related
    ENSP00000484763.1, ENST00000613094.4
    Conserved Domains (2) summary
    pfam00046
    Location:89141
    Homeobox; Homeobox domain
    pfam03826
    Location:275292
    OAR; OAR domain
  6. NM_153427.2NP_700476.1  pituitary homeobox 2 isoform a

    See identical proteins and their annotated locations for NP_700476.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as ARP1a, lacks an in-frame exon in the 5' region, as compared to variant 2. The resulting isoform (a) lacks an internal segment, as compared to isoform b. Variants 1 and 6 encode the same isoform a.
    Source sequence(s)
    AK127829, BC106010, BP372081, BX380370, U69961
    Consensus CDS
    CCDS3693.1
    UniProtKB/Swiss-Prot
    Q99697
    Related
    ENSP00000484909.1, ENST00000616641.4
    Conserved Domains (2) summary
    pfam03826
    Location:229246
    OAR; OAR domain
    pfam00046
    Location:4396
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    110617423..110642123 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454090.1XP_024309858.1  pituitary homeobox 2 isoform X1

    Conserved Domains (2) summary
    pfam00046
    Location:330
    Homeobox; Homeobox domain
    pfam03826
    Location:164181
    OAR; OAR domain
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