PDX1 pancreatic and duodenal homeobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDX1provided by HGNC
Official Full Name: pancreatic and duodenal homeobox 1provided by HGNC
Primary source: HGNC:HGNC:6107
See related: Ensembl:ENSG00000139515 MIM:600733
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: GSF; IPF1; IUF1; IDX-1; MODY4; PDX-1; STF-1; PAGEN1
Summary: The protein encoded by this gene is a transcriptional activator of several genes, including insulin, somatostatin, glucokinase, islet amyloid polypeptide, and glucose transporter type 2. The encoded nuclear protein is involved in the early development of the pancreas and plays a major role in glucose-dependent regulation of insulin gene expression. Defects in this gene are a cause of pancreatic agenesis, which can lead to early-onset insulin-dependent diabetes mellitus (IDDM), as well as maturity onset diabetes of the young type 4 (MODY4). [provided by RefSeq, Aug 2017]
Expression: Biased expression in duodenum (RPKM 9.6), stomach (RPKM 1.5) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q12.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
109.20201120	current	GRCh38.p13 (GCF_000001405.39)	13	NC_000013.11 (27919982..27926313)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (28494168..28500451)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Annexin A10 is involved in the induction of pancreatic duodenal homeobox1 in gastric cancer tissue, cells and organoids.
Title: Annexin A10 is involved in the induction of pancreatic duodenal homeobox‑1 in gastric cancer tissue, cells and organoids.
A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion.
Title: A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion.
Point mutations in PDX1 transactivation domain disrupt beta-cell differentiation and insulin secretion.
Title: Point mutations in the PDX1 transactivation domain impair human β-cell development and function.
Study presents the crystal structure of the SPOP-Pdx1 complex. Pdx1 residues 223-233 bind to SPOP MATH domain with low micromolar affinity. Pdx1 phosphorylation lowers its affinity to SPOP. A reduction of Pdx1 levels in beta cells is linked to apoptosis and considered a hallmark of type 2 diabetes.
Title: The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation.
Pancreatic ductal and acinar cell tumors and gastric signet ring cell carcinomas are most commonly PDX-1-positive. Most tumors that do not originate from the digestive tract have a PDX-1 negative immunophenotype.
Title: [Differential diagnostic value of the expression of the transcription factor PDX-1 in neuroendocrine and non-neuroendocrine tumors of the pancreas and other organs].
PDX can suppress cervical cancer HeLa cell proliferation, cell invasion and migration, improve general status of tumor-bearing nude mice and reduce tumor weight and volume. These data highlight the clinical benefits of PDX in inhibiting cervical cancer proliferation, invasion, and metastasis.
Title: The mechanism of PDX in regulating cervical cancer HeLa cell proliferation and tumor formation.
The unusual presentation in this Brazilian family enabled expansion upon a rare disease phenotype, demonstrating the possibility of detecting pancreatic malformation even in cases of PDX1 -related diabetes diagnosed after the first year of life. This finding can improve the management of MODY4 patients, leading to precocious investigation of pancreatic dysgenesis and exocrine dysfunction.
Title: PDX1 -MODY and dorsal pancreatic agenesis: New phenotype of a rare disease.
heat shock proteins are involved in PDX1-mediated effects on the genesis of gastric cancer
Title: Potential involvement of heat shock proteins in pancreatic-duodenal homeobox-1-mediated effects on the genesis of gastric cancer: A 2D gel-based proteomic study.
Investigated the effect of gestational diabetes mellitus (GDM) on the expression and methylation of PGC-1alpha and PDX1 in placenta and their effects on fetal glucose metabolism. Blood glucose was negatively correlated with the expression of PGC-1alpha and PDX1 mRNA in the placenta.
Title: Altered expression of PGC-1α and PDX1 and their methylation status are associated with fetal glucose metabolism in gestational diabetes mellitus.
PDX1, Neurogenin-3, and MAFA are critical transcription regulators for beta cell development and regeneration. (Review)
Title: PDX1, Neurogenin-3, and MAFA: critical transcription regulators for beta cell development and regeneration.

Submit: New GeneRIF Correction See all GeneRIFs (125)

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
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. GeneReviews: Not available
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. GeneReviews: Not available
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. GeneReviews: Not available
Maturity-onset diabetes of the young type 4 MedGen: C1833382 OMIM: 606392 GeneReviews: Maturity-Onset Diabetes of the Young Overview	Compare labs
Pancreatic agenesis 1 MedGen: C3891828 OMIM: 260370 GeneReviews: Not available	Compare labs
Permanent neonatal diabetes mellitus MedGen: C1833104 GeneReviews: Permanent Neonatal Diabetes Mellitus	Compare labs
Type 2 diabetes mellitus MedGen: C0011860 OMIM: 125853 GeneReviews: Not available	Compare labs

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

G05158 (e-PCR)
- UniSTS:3169

Pdx1 (e-PCR), detects polymorphism
- UniSTS:464793

Pdx1 (e-PCR), detects polymorphism
- UniSTS:224153

NoName (e-PCR)
- UniSTS:483240

RH79140 (e-PCR)
- UniSTS:37111

Homology

Homologs of the PDX1 gene: The PDX1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 320 organisms have orthologs with human gene PDX1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
protein-containing complex binding	IEA Inferred from Electronic Annotation more info
sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
transcription factor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
animal organ regeneration	IEA Inferred from Electronic Annotation more info
animal organ senescence	IEA Inferred from Electronic Annotation more info
central nervous system development	IEA Inferred from Electronic Annotation more info
detection of glucose	ISS Inferred from Sequence or Structural Similarity more info
digestive tract development	IEA Inferred from Electronic Annotation more info
exocrine pancreas development	IEA Inferred from Electronic Annotation more info
generation of precursor metabolites and energy	TAS Traceable Author Statement more info	PubMed
glucose homeostasis	IEA Inferred from Electronic Annotation more info
glucose metabolic process	IEA Inferred from Electronic Annotation more info
insulin secretion	IDA Inferred from Direct Assay more info	PubMed
liver development	IEA Inferred from Electronic Annotation more info
morphogenesis of embryonic epithelium	IEA Inferred from Electronic Annotation more info
negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
negative regulation of type B pancreatic cell apoptotic process	IEA Inferred from Electronic Annotation more info
nitric oxide mediated signal transduction	IDA Inferred from Direct Assay more info	PubMed
positive regulation of DNA binding	IEA Inferred from Electronic Annotation more info
positive regulation of cell death	IEA Inferred from Electronic Annotation more info
positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
positive regulation of insulin secretion involved in cellular response to glucose stimulus	IEA Inferred from Electronic Annotation more info
positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
response to alkaloid	IEA Inferred from Electronic Annotation more info
response to chlorate	IEA Inferred from Electronic Annotation more info
response to cytokine	IEA Inferred from Electronic Annotation more info
response to drug	IEA Inferred from Electronic Annotation more info
response to fatty acid	IEA Inferred from Electronic Annotation more info
response to glucocorticoid	IEA Inferred from Electronic Annotation more info
response to iron(II) ion	IEA Inferred from Electronic Annotation more info
response to leucine	IEA Inferred from Electronic Annotation more info
response to nicotine	IEA Inferred from Electronic Annotation more info
response to vitamin	IEA Inferred from Electronic Annotation more info
response to wounding	IEA Inferred from Electronic Annotation more info
smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
stem cell differentiation	IEA Inferred from Electronic Annotation more info
transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
transdifferentiation	IEA Inferred from Electronic Annotation more info
type B pancreatic cell differentiation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
type B pancreatic cell differentiation	IDA Inferred from Direct Assay more info	PubMed
type B pancreatic cell differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
chromatin	ISA Inferred from Sequence Alignment more info
cytosol	IEA Inferred from Electronic Annotation more info
nuclear speck	IEA Inferred from Electronic Annotation more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: pancreas/duodenum homeobox protein 1

Names: IPF-1; IUF-1; glucose-sensitive factor; insulin promoter factor 1, homeodomain transcription factor; insulin upstream factor 1; islet/duodenum homeobox-1; pancreatic-duodenal homeobox factor 1; somatostatin transcription factor 1; somatostatin-transactivating factor 1

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.