Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3651
Gene name	Pancreatic and duodenal homeobox 1
Gene symbol	PDX1
Synonyms (NCBI Gene)	GSFIDX-1IPF1IUF1MODY4PAGEN1PDX-1STF-1
Chromosome	13
Chromosome location	13q12.2
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

Show/Hide all (17)

SNP ID	Visualize variation	Clinical significance	Consequence
rs75498935	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Downstream transcript variant, genic downstream transcript variant, synonymous variant, coding sequence variant
rs80356661	G>T	Risk-factor, pathogenic	Downstream transcript variant, missense variant, genic downstream transcript variant, coding sequence variant
rs80356662	G>A	Pathogenic	Downstream transcript variant, missense variant, genic downstream transcript variant, coding sequence variant
rs137852783	G>A,T	Uncertain-significance, likely-pathogenic, benign-likely-benign, likely-benign, benign, not-provided	Missense variant, non coding transcript variant, coding sequence variant
rs137852784	A>T	Risk-factor	Missense variant, non coding transcript variant, coding sequence variant
rs137852785	T>C	Likely-pathogenic, risk-factor	Missense variant, non coding transcript variant, coding sequence variant
rs137852786	G>A	Risk-factor	Downstream transcript variant, missense variant, genic downstream transcript variant, coding sequence variant
rs193922355	C>A,G	Likely-pathogenic	Coding sequence variant, non coding transcript variant, synonymous variant, missense variant
rs193922356	A>C	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, downstream transcript variant
rs193922358	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, genic downstream transcript variant, missense variant, downstream transcript variant
rs193922360	A>G	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, downstream transcript variant
rs193929377	C>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs387906777	A>G	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, downstream transcript variant
rs797045885	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs1445970498	C>-,CC	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1555241857	A>C	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, downstream transcript variant, missense variant
rs1566025668	CCGTGACCTCCGGCGAG>-	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant, downstream transcript variant

Show/Hide all (48)

miRTarBase ID	miRNA	Experiments
MIRT1223449	hsa-miR-1207-5p	CLIP-seq
MIRT1223450	hsa-miR-1253	CLIP-seq
MIRT1223451	hsa-miR-3154	CLIP-seq
MIRT1223452	hsa-miR-3179	CLIP-seq
MIRT1223453	hsa-miR-3185	CLIP-seq
MIRT1223454	hsa-miR-3616-3p	CLIP-seq
MIRT1223455	hsa-miR-4271	CLIP-seq
MIRT1223456	hsa-miR-4419a	CLIP-seq
MIRT1223457	hsa-miR-4434	CLIP-seq
MIRT1223458	hsa-miR-4436b-3p	CLIP-seq
MIRT1223459	hsa-miR-4510	CLIP-seq
MIRT1223460	hsa-miR-4516	CLIP-seq
MIRT1223461	hsa-miR-451b	CLIP-seq
MIRT1223462	hsa-miR-4668-5p	CLIP-seq
MIRT1223463	hsa-miR-4716-3p	CLIP-seq
MIRT1223464	hsa-miR-4723-5p	CLIP-seq
MIRT1223465	hsa-miR-4725-3p	CLIP-seq
MIRT1223466	hsa-miR-4763-3p	CLIP-seq
MIRT1223467	hsa-miR-4764-5p	CLIP-seq
MIRT1223468	hsa-miR-4779	CLIP-seq
MIRT1223469	hsa-miR-625	CLIP-seq
MIRT1223470	hsa-miR-765	CLIP-seq
MIRT1223471	hsa-miR-933	CLIP-seq
MIRT1223472	hsa-miR-939	CLIP-seq
MIRT2293006	hsa-miR-1236	CLIP-seq
MIRT2293007	hsa-miR-149	CLIP-seq
MIRT2293008	hsa-miR-193a-3p	CLIP-seq
MIRT2293009	hsa-miR-193b	CLIP-seq
MIRT2293010	hsa-miR-2117	CLIP-seq
MIRT2293011	hsa-miR-4273	CLIP-seq
MIRT2293012	hsa-miR-4753-3p	CLIP-seq
MIRT2293013	hsa-miR-511	CLIP-seq
MIRT2293014	hsa-miR-524-3p	CLIP-seq
MIRT2293015	hsa-miR-525-3p	CLIP-seq
MIRT2293016	hsa-miR-892b	CLIP-seq
MIRT1223450	hsa-miR-1253	CLIP-seq
MIRT2456186	hsa-miR-1301	CLIP-seq
MIRT2456187	hsa-miR-3123	CLIP-seq
MIRT2456188	hsa-miR-3125	CLIP-seq
MIRT2456189	hsa-miR-3916	CLIP-seq
MIRT2456190	hsa-miR-3925-5p	CLIP-seq
MIRT2456191	hsa-miR-4660	CLIP-seq
MIRT1223468	hsa-miR-4779	CLIP-seq
MIRT2456192	hsa-miR-5047	CLIP-seq
MIRT2465826	hsa-miR-4436b-5p	CLIP-seq
MIRT2465827	hsa-miR-4642	CLIP-seq
MIRT2465828	hsa-miR-4720-5p	CLIP-seq
MIRT2465829	hsa-miR-4799-3p	CLIP-seq

Show/Hide all (4)

Transcription factor	Regulation	Reference
ATF6	Repression	18450959
KLF11	Unknown	19843526
SREBF1	Repression	16091421
USF2	Activation	10393088

Show/Hide all (94)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	ISS
GO:0001889	Process	Liver development	IEA
GO:0003309	Process	Type B pancreatic cell differentiation	IBA
GO:0003309	Process	Type B pancreatic cell differentiation	IDA	12124776, 24567802
GO:0003309	Process	Type B pancreatic cell differentiation	IEA
GO:0003309	Process	Type B pancreatic cell differentiation	IEA
GO:0003309	Process	Type B pancreatic cell differentiation	ISS
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IDA	17941991
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0006006	Process	Glucose metabolic process	IEA
GO:0006091	Process	Generation of precursor metabolites and energy	TAS	8954967
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006366	Process	Transcription by RNA polymerase II	IEA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	8954967
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0008283	Process	Cell population proliferation	IEA
GO:0008284	Process	Positive regulation of cell population proliferation	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0009410	Process	Response to xenobiotic stimulus	IEA
GO:0009749	Process	Response to glucose	IEA
GO:0009887	Process	Animal organ morphogenesis	TAS	8988180
GO:0010040	Process	Response to iron(II) ion	IEA
GO:0010157	Process	Response to chlorate	IEA
GO:0010255	Process	Glucose mediated signaling pathway	IEA
GO:0010255	Process	Glucose mediated signaling pathway	ISS
GO:0010468	Process	Regulation of gene expression	IEA
GO:0016331	Process	Morphogenesis of embryonic epithelium	IEA
GO:0016607	Component	Nuclear speck	IEA
GO:0030073	Process	Insulin secretion	IDA	17941991
GO:0030154	Process	Cell differentiation	IEA
GO:0031016	Process	Pancreas development	IEA
GO:0031016	Process	Pancreas development	IEA
GO:0031017	Process	Exocrine pancreas development	IEA
GO:0031018	Process	Endocrine pancreas development	IEA
GO:0031100	Process	Animal organ regeneration	IEA
GO:0031667	Process	Response to nutrient levels	IEA
GO:0032024	Process	Positive regulation of insulin secretion	IEA
GO:0032024	Process	Positive regulation of insulin secretion	ISS
GO:0033273	Process	Response to vitamin	IEA
GO:0033993	Process	Response to lipid	IEA
GO:0034097	Process	Response to cytokine	IEA
GO:0035094	Process	Response to nicotine	IEA
GO:0035774	Process	Positive regulation of insulin secretion involved in cellular response to glucose stimulus	IEA
GO:0035883	Process	Enteroendocrine cell differentiation	IEA
GO:0042127	Process	Regulation of cell population proliferation	IEA
GO:0042593	Process	Glucose homeostasis	IEA
GO:0043201	Process	Response to L-leucine	IEA
GO:0043279	Process	Response to alkaloid	IEA
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0044342	Process	Type B pancreatic cell proliferation	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	17941991
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0048565	Process	Digestive tract development	IEA
GO:0048863	Process	Stem cell differentiation	IEA
GO:0050673	Process	Epithelial cell proliferation	IEA
GO:0050680	Process	Negative regulation of epithelial cell proliferation	IEA
GO:0051384	Process	Response to glucocorticoid	IEA
GO:0060290	Process	Transdifferentiation	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	ISS
GO:0070059	Process	Intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	IEA
GO:0070542	Process	Response to fatty acid	IEA
GO:0097050	Process	Type B pancreatic cell apoptotic process	IEA
GO:1902236	Process	Negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IEA
GO:1904102	Process	Cellular response to acadesine	IEA
GO:1904692	Process	Positive regulation of type B pancreatic cell proliferation	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990841	Function	Promoter-specific chromatin binding	IEA
GO:2000675	Process	Negative regulation of type B pancreatic cell apoptotic process	IEA

MIM	HGNC	e!Ensembl
600733	6107	ENSG00000139515

P52945

Protein name

Pancreas/duodenum homeobox protein 1 (PDX-1) (Glucose-sensitive factor) (GSF) (Insulin promoter factor 1) (IPF-1) (Insulin upstream factor 1) (IUF-1) (Islet/duodenum homeobox-1) (IDX-1) (Somatostatin-transactivating factor 1) (STF-1)

Protein function

Activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2 gene transcription. Particularly involved in glucose-dependent regulation of insulin gene transcription. As part of a PDX1:PBX1b:MEIS2b comple

PDB

6F8F , 7KPK

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	147 → 203	Homeodomain	Domain

Tissue specificity

TISSUE SPECIFICITY: Duodenum and pancreas (Langerhans islet beta cells and small subsets of endocrine non-beta-cells, at low levels in acinar cells).

Sequence

MNGEEQYYAATQLYKDPCAFQRGPAPEFSASPPACLYMGRQPPPPPPHPFPGALGALEQG
SPPDISPYEVPPLADDPAVAHLHHHLPAQLALPHPPAGPFPEGAEPGVLEEPNRVQLPFP
WMKSTKAHAWKGQWAGGAYAAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELA
VMLNLTERHIKIWFQNRRMKWKKEEDKKRGGGTAVGGGGVAEPEQDCAVTSGEELLALPP
PPPPGGAVPPAAPVAAREGRLPPGLSASPQPSSVAPRRPQEPR

Sequence length

283

Interactions

View interactions

	KEGG
	Insulin secretion Type II diabetes mellitus Maturity onset diabetes of the young

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Diabetes mellitus type 2, susceptibility to	Pathogenic	rs80356661	RCV001799505	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Maturity-onset diabetes of the young	Likely pathogenic	rs2500206807	RCV002367211	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Maturity-onset diabetes of the young type 4	Likely pathogenic; Pathogenic	rs2500206807, rs1566025744, rs387906777, rs1555241857, rs193922355, rs193922356	RCV005008559 RCV003444069 RCV000502995 RCV000501202 RCV000030079 RCV000030081 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pancreatic agenesis 1	Likely pathogenic; Pathogenic	rs2500206807, rs80356661, rs80356662, rs387906777, rs1555241857	RCV005008559 RCV000020215 RCV000020216 RCV000023034 RCV000501202	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PDX1-related disorder	Likely pathogenic	rs2500206217, rs2500206718	RCV004548508 RCV004552611	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Permanent neonatal diabetes mellitus	Pathogenic	rs387906777	RCV000239365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Type 2 diabetes mellitus	Likely pathogenic	rs2500206807	RCV005008559	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (20)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CEREBRAL INFARCTION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HYPOPLASIA OF PANCREAS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS, EXPERIMENTAL	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS, NON-INSULIN-DEPENDENT	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS, PERMANENT NEONATAL	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS, TYPE 2	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial Monogenic Diabetes (Maturity Onset Diabetes Of The Young 4)/Neonatal Diabetes Mellitus	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC ULCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERGLYCEMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED PERMANENT NEONATAL DIABETES MELLITUS	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MATURITY ONSET DIABETES MELLITUS IN YOUNG	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MATURITY-ONSET DIABETES OF THE YOUNG, TYPE 4	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MODY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Monogenic diabetes	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neonatal diabetes mellitus	Likely benign; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
PANCREATIC CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pancreatic hypoplasia	Conflicting classifications of pathogenicity; Uncertain significance; Uncertain risk allele; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARTIAL PANCREATIC AGENESIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PEPTIC ULCER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

PDX1 (pancreatic and duodenal homeobox 1)