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PITX1 Gene

protein-coding GIFtS: 65
GCID: GC05M134363

Paired-Like Homeodomain 1

(Previous name: paired-like homeodomain transcription factor 1)
(Previous symbol: BFT)

See PITX1-related diseases
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Paired-Like Homeodomain 1¹ ²		LBNBG² ⁵
BFT¹ ² ³ ⁵		POTX² ⁵
Paired-Like Homeodomain Transcription Factor 1¹ ² ³		Hindlimb Expressed Homeobox Protein Backfoot²
PTX1² ³ ⁵		Pituitary Homeo Box 1²
Hindlimb-Expressed Homeobox Protein Backfoot² ³		Pituitary Homeobox 1²
Homeobox Protein PITX1² ³		Pituitary Otx-Related Factor²
CCF² ⁵

External Ids:	HGNC: 9004¹	Entrez Gene: 5307²	Ensembl: ENSG00000069011⁷	OMIM: 602149⁵	UniProtKB: P78337³

Export aliases for PITX1 gene to outside databases

Previous GC identifers: GC05M134015 GC05M134930 GC05M134394 GC05M134439 GC05M134391 GC05M129551

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PITX1 Gene:

This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins.

Members of this family are involved in organ development and left-right asymmetry. This protein acts as a

transcriptional regulator involved in basal and hormone-regulated activity of prolactin. (provided by RefSeq, Jul

2008)

GeneCards Summary for PITX1 Gene:

PITX1 (paired-like homeodomain 1) is a protein-coding gene. Diseases associated with PITX1 include clubfoot, congenital, with or without deficiency of long bones and/or mirror-image polydactyly, and liebenberg syndrome. GO annotations related to this gene include protein binding transcription factor activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is GSC.

UniProtKB/Swiss-Prot: PITX1_HUMAN, P78337

Function: May play a role in the development of anterior structures, and in particular, the brain and facies and

in specifying the identity or structure of hindlimb

Gene Wiki entry for PITX1 Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:

NC_000005.9 NC_018916.2 NT_034772.7

Regulatory elements:

Regulatory transcription factor binding sites in the PITX1 gene promoter:
E2F-3a c-Fos E2F-5 AP-1 ATF-2 E2F-2 E2F-1 c-Jun
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PITX1 promoter sequence

Search Chromatin IP Primers for PITX1

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PITX1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31.1 Ensembl cytogenetic band: 5q31.1 HGNC cytogenetic band: 5q31.1

PITX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PITX1 gene location

GeneLoc information about chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05M134363: view genomic region (about GC identifiers)

Start:	134,363,424 bp from pter	End:	134,370,503 bp from pter
Size:	7,080 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PITX1_HUMAN, P78337 (See protein sequence)

Recommended Name: Pituitary homeobox 1

Size: 314 amino acids; 34128 Da

Secondary accessions: A8K3M0 D3DQB0 O14677 O60425 Q9BTI5

Explore the universe of human proteins at neXtProt for PITX1: NX_P78337

Explore proteomics data for PITX1 at MOPED

Post-translational modifications:

Modification sites at neXtProt

Modification sites at PhosphoSitePlus

See PITX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_002644.4

ENSEMBL proteins:

ENSP00000265340 ENSP00000427542 ENSP00000451199 ENSP00000422908 ENSP00000423624

PITX1 Human Recombinant Protein Products:

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	Novus Biologicals PITX1 Proteins Novus Biologicals PITX1 Lysate
	Browse Sino Biological Recombinant Proteins Browse Sino Biological Cell Lysates
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	Cloud-Clone Corp. Proteins for PITX1
	Search eBioscience for Proteins for PITX1
	antibodies-online proteins for PITX1 (9 products)
	antibodies-online peptides for PITX1

PITX1 Antibody Products:

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	antibodies-online antibodies for PITX1 (41 products)

PITX1 Assay Products:

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	antibodies-online kits for PITX1 (8 products)

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

PRD: Homeoboxes / PRD class

5 InterPro protein domains:

IPR003654 OAR_dom

IPR016233 Homeobox_Pitx/unc30

IPR017970 Homeobox_CS

IPR001356 Homeobox_dom

IPR009057 Homeodomain-like

Graphical View of Domain Structure for InterPro Entry P78337

ProtoNet protein and cluster: P78337

1 Blocks protein domain: IPB003654 Paired-like homeodomain protein

UniProtKB/Swiss-Prot: PITX1_HUMAN, P78337

Similarity: Belongs to the paired homeobox family. Bicoid subfamily

Similarity: Contains 1 homeobox DNA-binding domain

Find genes that share domains with PITX1 About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: PITX1_HUMAN, P78337

Function: May play a role in the development of anterior structures, and in particular, the brain and facies and

in specifying the identity or structure of hindlimb

Genatlas biochemistry entry for PITX1:

POU domain,class 1,transcription factor 3,mammalian homeo box backfoot,Drosophila bicoid related,mapping in TCOF1

region and possibly involved in the syndrome,expressed in Rathke pouch at an early stage of pituitary development

in a subset of adult anterior pituitary cells that express POMC,and in craniofacial development

Gene Ontology (GO): 5 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000988	protein binding transcription factor activity	--	--
GO:0001190	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription	IEA	--
GO:0003677	DNA binding	--	--
GO:0003700	sequence-specific DNA binding transcription factor activity	IEA	--
GO:0043565	sequence-specific DNA binding	IEA	--

Find genes that share ontologies with PITX1 About GenesLikeMe

Phenotypes:
3 GenomeRNAi human phenotypes for PITX1:

Decreased NANOG protein expres

Decreased OCT4 protein express

Decreased POU5F1-GFP protein e

13 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Pitx1):

adipose tissue	cardiovascular system	craniofacial	digestive/alimentary	embryogenesis
endocrine/exocrine gland	growth/size/body	hearing/vestibular/ear	limbs/digits/tail	mortality/aging
muscle	nervous system	skeleton

Find genes that share phenotypes with PITX1 About GenesLikeMe

Animal Models:
MGI mouse knock-out Pitx1^tm1Jdr for PITX1

genOway: Develop your customized and physiologically relevant rodent model for PITX1

Transcription Factor Targeting:

Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer

Consensus sequence: TAATCCCN

miRNA Products:		miRTarBase miRNAs that target PITX1: hsa-mir-92a-3p (MIRT049789), hsa-mir-149-5p (MIRT045636), hsa-mir-320a (MIRT044749), hsa-mir-331-3p (MIRT043542)

		Block miRNA regulation of human, mouse, rat PITX1 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate PITX1 (see all 18):
		hsa-miR-30c hsa-miR-3607-3p hsa-miR-218-2* hsa-miR-30d hsa-miR-759 hsa-miR-633 hsa-miR-30a hsa-miR-891b

		SwitchGear 3'UTR luciferase reporter plasmid: PITX1 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for PITX1
		Predesigned siRNA for gene silencing in human, mouse, rat PITX1

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for PITX1

Clone Products:		OriGene clones in human, mouse for PITX1 (see all 8) OriGene ORF clones in mouse, rat for PITX1 OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: PITX1 (NM_002653)
		Sino Biological Human cDNA Clone for PITX1
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for PITX1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PITX1

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for PITX1
		ESI BIO PureStem Progenitors for PITX1: PureStem MEL2, NCr-fac Progenitor, PureStem SK11, NCr-fac & Meso-prx Progenitor, PureStem SM30, NCr-fac & Meso-latp Progenitor

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PITX1

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

PITX1_HUMAN, P78337: Nucleus

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	5
cytoskeleton	1
extracellular	1

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Gene Ontology (GO): 4 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	--	--
GO:0005667	transcription factor complex	IEA	--
GO:0005730	nucleolus	IDA	--
GO:0005737	cytoplasm	IEA	--

Find genes that share ontologies with PITX1 About GenesLikeMe

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for PITX1 About

See pathways by source

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by

SuperPath

Contained pathways About

Ca-dependent events

Development Role of Activin A in cell differentiation and proliferation

0.32

Pathways by source See SuperPaths
Show all pathways

1 GeneGo (Thomson Reuters) Pathway for PITX1

Development Role of Activin A in cell differentiation and proliferation

Pathway & Disease-focused RT² Profiler PCR Array including PITX1:

Homeobox (HOX) Genes in human mouse rat

Interactions:

GeneGlobe Interaction Network for PITX1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for PITX1 (P78337^{2, 3} ENSP00000265340⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 41)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
RBPMS	Q93062²^,³, ENSP00000340176⁴	MINT-67242 I2D: score=5 STRING: ENSP00000340176
RHOXF2	Q9BQY4²^,³, ENSP00000360441⁴	MINT-67608 I2D: score=5 STRING: ENSP00000360441
EGR1	P18146³, ENSP00000239938⁴	I2D: score=3 STRING: ENSP00000239938
NR5A1	Q13285³, ENSP00000362690⁴	I2D: score=2 STRING: ENSP00000362690
POU1F1	P28069³, ENSP00000342931⁴	I2D: score=2 STRING: ENSP00000342931

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Gene Ontology (GO): Selected biological process terms (see all 11): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001501	skeletal system development	TAS	9070926
GO:0006351	transcription, DNA-templated	--	--
GO:0006355	regulation of transcription, DNA-templated	--	--
GO:0009653	anatomical structure morphogenesis	TAS	9070926
GO:0014707	branchiomeric skeletal muscle development	IEA	--

Find genes that share ontologies with PITX1 About GenesLikeMe

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for PITX1

3 Novoseek inferred chemical compound relationships for PITX1 gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
ptx1	97.1	77	9514159 (13), 10859489 (7), 8675014 (7), 11048804 (7) (see all 14)
enterotoxin	62.9	8	10832652 (2), 16701617 (1), 16128024 (1), 15273805 (1) (see all 5)
gnrh	23.4	5	10082522 (2), 11399488 (2), 17872365 (1)

Find genes that share compounds with PITX1 About GenesLikeMe

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for PITX1 gene:

NM_002653.4

Unigene Cluster for PITX1:

Paired-like homeodomain 1

Hs.84136 [show with all ESTs]

Unigene Representative Sequence: NM_002653

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000265340(uc010jea.3) ENST00000506438 ENST00000503586 ENST00000504936

ENST00000507253 ENST00000502676

miRNA Products:		Block miRNA regulation of human, mouse, rat PITX1 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate PITX1 (see all 18):
		hsa-miR-30c hsa-miR-3607-3p hsa-miR-218-2* hsa-miR-30d hsa-miR-759 hsa-miR-633 hsa-miR-30a hsa-miR-891b

		SwitchGear 3'UTR luciferase reporter plasmid: PITX1 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for PITX1
		Predesigned siRNA for gene silencing in human, mouse, rat PITX1

Clone Products:		OriGene clones in human, mouse for PITX1 (see all 8) OriGene ORF clones in mouse, rat for PITX1 OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: PITX1 (NM_002653)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for PITX1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PITX1

Primer Products:		OriGene qPCR primer pairs and template standards for PITX1 OriGene qSTAR qPCR primer pairs in human, mouse for PITX1
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat PITX1
		QuantiTect SYBR Green Assays in human, mouse, rat PITX1
		QuantiFast Probe-based Assays in human, mouse, rat PITX1

Additional mRNA sequence:

AK290635.1 BC003685.1 BC009412.1 U70370.1

9 DOTS entries:

DT.209362 DT.95158034 DT.75116760 DT.95158033 DT.97805157 DT.95342961 DT.100740270 DT.100833476

DT.92431026

Selected AceView cDNA sequences (see all 162):

BQ941107 BU633380 BX387202 BQ949996 CA313589 CB250464 CD106550 BC009412

BQ774469 BQ012307 CA313914 BU538150 BU726300 BM979671 AU117580 BU728971

AA480259 AI968981 BM823827 BU678820 BM969568 BM669565 BE900342 CR601326

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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PITX1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: TCGCCGGGCG

About this image

PITX1 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 18) fully expand


Neural Crest (Gastrulation Derivatives) fully expand to see all 5 entries
Mesencephalic Neural Crest Cells Prechordal Mesenchyme
PureStem SK11, NCr-fac & Meso-prx Progenitor

Head Mesenchyme (Muscoskeletal System) fully expand to see all 3 entries
Mesencephalic Neural Crest Cells Prechordal Mesenchyme

Esophagus (Gastrointestinal Tract) fully expand to see all 3 entries
esophagus ; squamous epithelial cells
esophageal epithelium

Epithelial Cells (Uncategorized) fully expand to see all 3 entries
esophagus ; squamous epithelial cells
esophageal epithelium

Bone (Muscoskeletal System) fully expand to see all 5 entries
Bone Marrow
HyStem+TGFbeta3+GDF5-induced SK11 cells

PITX1 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

PITX1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.84136

Pathway & Disease-focused RT² Profiler PCR Array including PITX1:

Homeobox (HOX) Genes in human mouse rat

Primer Products:		OriGene qPCR primer pairs and template standards for PITX1 OriGene qSTAR qPCR primer pairs in human, mouse for PITX1
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat PITX1
		QuantiTect SYBR Green Assays in human, mouse, rat PITX1
		QuantiFast Probe-based Assays in human, mouse, rat PITX1

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PITX1

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for PITX1 gene from Selected species (see all 16) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pitx1^{1 , 5}	paired-like homeodomain transcription factor 1^{1, 5}	91.3(n)¹ 96.5(a)¹		13 (30.06 cM)⁵ 18740¹ NM_011097.2¹ NP_035227.1¹ 55825051⁵
chicken (Gallus gallus)	Aves	PITX1¹	paired-like homeodomain 1	80.02(n) 84.11(a)		374201 NM_001167686.1 NP_001161158.1
lizard (Anolis carolinensis)	Reptilia	PITX1⁶	paired-like homeodomain 1	64(a)	1 ↔ 1	GL343223.1(498574-508364)
African clawed frog (Xenopus laevis)	Amphibia	pitx1²	Pitx1 protein	78.8(n)		AF217647.1
zebrafish (Danio rerio)	Actinopterygii	pitx1¹	paired-like homeodomain transcription factor 1	76.86(n) 77.7(a)		678598 NM_001040346.2 NP_001035436.3
fruit fly (Drosophila melanogaster)	Insecta	Ptx1³	specific RNA polymerase II transcription factor	44(a)		--
worm (Caenorhabditis elegans)	Secernentea	unc-30⁶	Protein UNC-30, isoform b	29(a)	1 → many	IV(13119096-13124387) WBGene00006766

ENSEMBL Gene Tree for PITX1 (if available)
TreeFam Gene Tree for PITX1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for PITX1 gene

GSC² OTX2² UNCX² VSX1² HESX1² PITX2² VSX2² PROP1²

PITX3² DMBX1² GSC2² CRX² OTX1² MIXL1²

14 SIMAP similar genes for PITX1 using alignment to 4 protein entries: PITX1_HUMAN (see all proteins):

PITX2 OTX2 PITX3 PHOX2B HOPX DUX2

RAX2 HOXB1 MNX1 NKX2-5 HOXA4 PRRX1

POU6F1 GSC2

Find genes that share paralogs with PITX1 About GenesLikeMe

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 5 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
VAR_058113⁴		Clubfoot, congenital, with or without deficiency of long bones and/or mirror-image polydactyly (CCF)⁴	--	see VAR_058113	2	E K	mis⁴		0	--	--	--	--
rs33940950^1,2	C	--	134363154(+)	`AGGGG-/GTTCTC`	1	--	ds500¹		0	--	--	--	--
rs70976561^1,2	C	--	134364157(-)	`GGGTGGT/-GTGTG`	1	--	ut3¹		2		NA CSA	4
rs371734693^1,2	C	--	134364158(+)	`GGGAA-/ACCACAC`	1	--	ut3¹		0	--	--	--	--
rs111319441^1,2	C	--	134364239(+)	`TTTTGC/TTTTTT`	1	--	ut3¹		0	--	--	--	--
rs70976562^1,2	C	--	134364256(-)	`AAAAAA/-AAAAA`	1	--	ut3¹		1		NA	2
rs71660434^1,2	C	--	134364407(+)	`GTCCT-/CCGCGC CCGCG`	1	--	cds¹		0	--	--	--	--
rs1131614^1,2	A	--	134364415(-)	`GGGCGC/TGGGCG`	1	--	ut3¹		0	--	--	--	--
rs10534528^1,2	C	--	134365709(+)	`CTTCCTATT/- TAATT`	1	--	int¹		1		CSA	2
rs3840350^1,2	C	--	134365711(+)	`TCCTA-/TTTA ATTTC`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for PITX1 (134363424 - 134370503 bp)

Structural Variations
Database of Genomic Variants (DGV) 7 variations for PITX1: About this table

Variant ID	Type	Subtype	PubMed ID
nsv882924	CNV	Loss	21882294
nsv830495	CNV	Loss	17160897
nsv462458	CNV	Loss	19166990
nsv823240	CNV	Gain	20364138
nsv823239	CNV	Gain	20364138
nsv823243	CNV	Gain	20364138
dgv969n67	CNV	Gain	20364138

Human Gene Mutation Database (HGMD): PITX1

Site Specific Mutation Identification with PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 602149
OMIM disorders: 119800 186550
UniProtKB/Swiss-Prot: PITX1_HUMAN, P78337

Clubfoot, congenital, with or without deficiency of long bones and/or mirror-image polydactyly (CCF)

[MIM:119800]: A congenital limb deformity defined as fixation of the foot in cavus, adductus, varus, and equinus

(i.e., inclined inwards, axially rotated outwards, and pointing downwards) with concomitant soft tissue

abnormalities. Clubfoot may occur in isolation or as part of a syndrome. Some patients present tibial hemimelia,

bilateral patellar hypoplasia, and preaxial mirror-image polydactyly. Note=The disease is caused by mutations

affecting the gene represented in this entry

Liebenberg syndrome (LBNBG) [MIM:186550]: An upper limb-malformation syndrome characterized by the

combination of dysplastic elbow joints and the fusion of wrist bones with consequent radial deviation. Note=The

gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration involving the PITX1

locus results in LBNBG. Translocation t(5;18)(q31.1;q12.3). Additionally, two chromosome 5 deletions located 5'of

PITX1 have been found in LBNBG patients. These structural variations cause altered expression of PITX1 in the

forelimb via the activation of ectopic enhancers (PubMed:23022097)

11 diseases for PITX1:
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clubfoot, congenital, with or without deficiency of long bones and/or mirror-image polydactyly liebenberg syndrome acute diarrhea exophthalmos

familial clubfoot due to 5q31 microdeletion pitx1-related congenital clubfoot clubfoot isolated acth deficiency

acth deficiency diarrhea treacher collins syndrome

3 inferred disease relationships from the University of Copenhagen DISEASES database for PITX1:

Clubfoot Exophthalmos Ophthalmoplegia

Find genes that share disorders with PITX1 About GenesLikeMe

3 Novoseek inferred disease relationships for PITX1 gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
pituitary adenoma	26.5	9	11048804 (4), 10372733 (1)
adenoma	3.94	6	11048804 (1)
virus infection	0	1	16166650 (1)

Genetic Association Database (GAD): PITX1
Human Genome Epidemiology (HuGE) Navigator: PITX1 (3 documents)

Export disorders for PITX1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for PITX1 gene, integrated from 10 sources (see all 101):
(articles sorted by number of sources associating them with PITX1)

Utopia: connect your pdf to the dynamic
world of online information

Human and murine PTX1/Ptx1 gene maps to the region for Treacher Collins syndrome. (PubMed id 9337397)^{1, 2, 3, 9} Crawford M.J.... Drouin J. (Mamm. Genome 1997)
Backfoot, a novel homeobox gene, maps to human chromosome 5 (BFT) and mouse chromosome 13 (Bft). (PubMed id 9070926)^{1, 2, 3} Shang J.... Francke U. (Genomics 1997)
Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. (PubMed id 23022097)^{1, 2} Spielmann M....Mundlos S. (Am. J. Hum. Genet. 2012)
Deletions in PITX1 cause a spectrum of lower-limb malformations including mirror-image polydactyly. (PubMed id 22258522)^{1, 2} Klopocki E.... Kurth I. (Eur. J. Hum. Genet. 2012)
Genetic polymorphism of PITX1 in susceptibility to knee osteoarthritis in a Chinese Han population: a case-control study. (PubMed id 20054692)^{1, 4} Fan J....Jiang Q. (Rheumatol. Int. 2011)
Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)^{1, 4} Jugessur A....Murray J.C. (PLoS ONE 2010)
Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)^{1, 4} Gudbjartsson D.F....Stefansson K. (Nat. Genet. 2008)
Asymmetric lower-limb malformations in individuals with homeobox PITX1 gene mutation. (PubMed id 18950742)^{1, 2} Gurnett C.A.... Dobbs M.B. (Am. J. Hum. Genet. 2008)
Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis. (PubMed id 18053270)^{1, 4} Philippi A....Hager J. (BMC Med. Genet. 2007)
The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)^{1, 2} Schmutz J.... Rubin E.M. (Nature 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 5307	HGNC: 9004	AceView: PITX1	Ensembl:ENSG00000069011	euGenes: HUgn5307
ECgene: PITX1	H-InvDB: PITX1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for PITX1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PITX1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for PITX1 gene:
Search GeneIP for patents involving PITX1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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