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; AllianceGenome:HGNC:6107
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
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (27920000..27926313)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (27141129..27147442)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (28494137..28500450)

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?

Significance of pancreatic duodenal homeobox-1 (PDX-1) genetic polymorphism in insulin secretion in Japanese patients with type 2 diabetes.
Title: Significance of pancreatic duodenal homeobox-1 (PDX-1) genetic polymorphism in insulin secretion in Japanese patients with type 2 diabetes.
Biophysical insights into glucose-dependent transcriptional regulation by PDX1.
Title: Biophysical insights into glucose-dependent transcriptional regulation by PDX1.
STAT3 suppression and beta-cell ablation enhance alpha-to-beta reprogramming mediated by Pdx1.
Title: STAT3 suppression and β-cell ablation enhance α-to-β reprogramming mediated by Pdx1.
Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer.
Title: Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer.
TAZ promotes PDX1-mediated insulinogenesis.
Title: TAZ promotes PDX1-mediated insulinogenesis.
Dysregulation of the Pdx1/Ovol2/Zeb2 axis in dedifferentiated beta-cells triggers the induction of genes associated with epithelial-mesenchymal transition in diabetes.
Title: Dysregulation of the Pdx1/Ovol2/Zeb2 axis in dedifferentiated β-cells triggers the induction of genes associated with epithelial-mesenchymal transition in diabetes.
Knockdown of PDX1 enhances the osteogenic differentiation of ADSCs partly via activation of the PI3K/Akt signaling pathway.
Title: Knockdown of PDX1 enhances the osteogenic differentiation of ADSCs partly via activation of the PI3K/Akt signaling pathway.
PDX1 and MC4R genetic polymorphisms are associated with type 2 diabetes mellitus risk in the Chinese Han population.
Title: PDX1 and MC4R genetic polymorphisms are associated with type 2 diabetes mellitus risk in the Chinese Han population.
Saturated fatty acids entrap PDX1 in stress granules and impede islet beta cell function.
Title: Saturated fatty acids entrap PDX1 in stress granules and impede islet beta cell function.
Oxidative Stress Leads to beta-Cell Dysfunction Through Loss of beta-Cell Identity.
Title: Oxidative Stress Leads to β-Cell Dysfunction Through Loss of β-Cell Identity.

Submit: New GeneRIF Correction See all GeneRIFs (142)

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
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: WFS1 Spectrum Disorder	Compare labs

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed

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: 480 organisms have orthologs with human gene PDX1
Orthologs

Gene Ontology Provided by GOA

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

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in 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.