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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	3651
Gene name Gene Name - the full gene name approved by the HGNC.	Pancreatic and duodenal homeobox 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PDX1
Synonyms (NCBI Gene) Gene synonyms aliases	GSF, IDX-1, IPF1, IUF1, MODY4, PAGEN1, PDX-1, STF-1
Chromosome Chromosome number	13
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	13q12.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

Transcription factors

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

Protein

UniProt ID

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

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital Pancreatic Agenesis	pancreatic agenesis 1	rs80356662, rs387906777	N/A
Diabetes Mellitus	permanent neonatal diabetes mellitus, Maturity-onset diabetes of the young type 4	rs387906777, rs193922355, rs193922356	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Gastric ulcer	Gastric ulcer	N/A	N/A	GWAS
Mason type diabetes	maturity onset diabetes mellitus in young	N/A	N/A	ClinVar
Monogenic Diabetes	monogenic diabetes	N/A	N/A	ClinVar, GenCC
pancreatic hypoplasia	Pancreatic hypoplasia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (60)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	36400857
Annular pancreas	Associate	29317564, 37635636
beta Thalassemia	Associate	19228875
Carcinogenesis	Associate	14960508, 30310259, 31261501
Carcinoma Acinar Cell	Associate	21297446
Carcinoma Lobular	Associate	21228366
Carcinoma Pancreatic Ductal	Associate	21297446, 26695692, 32580737
Colonic Neoplasms	Associate	18855980
Colorectal Neoplasms	Associate	18855980, 24023782, 30999858, 35169223, 35260172
Congenital Hyperinsulinism	Inhibit	9280302
Developmental Disabilities	Associate	22523087
Diabetes Gestational	Associate	36313769
Diabetes Mellitus	Associate	10545531, 16229747, 19496967, 20621032, 22570331, 25375650, 27879214, 28436541, 29107594, 29317564, 29396371, 30930126, 31366392, 33795639, 34732801 View all (4 more)
Diabetes Mellitus Permanent Neonatal	Associate	19496967, 23320570
Diabetes Mellitus Transient Neonatal 1	Associate	23320570, 28436541
Diabetes Mellitus Type 1	Associate	19228875, 23696946, 32882526, 34344789
Diabetes Mellitus Type 2	Associate	10545530, 10545531, 19843526, 20621032, 26287533, 27879211, 27879214, 28095440, 28436541, 28934129, 29185012, 30449689, 31322178, 32882526, 34135026 View all (6 more)
Diabetes Mellitus Type 2	Inhibit	22570331, 28041957
Diabetic Neuropathies	Associate	10545531
Early Onset Glaucoma	Associate	34135026
Endocrine Gland Neoplasms	Associate	21297446
Exocrine Pancreatic Insufficiency	Associate	28436541, 29317564
Familial duodenal atresia	Associate	29317564
Fetal Growth Retardation	Associate	20962579
Gallbladder Diseases	Associate	29317564
Gallbladder Neoplasms	Associate	29317564
Gastritis Atrophic	Associate	14631368
Glucose Intolerance	Inhibit	28041957
Glucose Intolerance	Associate	30930126
Hereditary renal agenesis	Associate	23320570
HIV Infections	Associate	33013899
Hyperglycemia	Associate	10545530, 31366392
Hyperglycemia	Inhibit	22570331
Hyperglycemic Hyperosmolar Nonketotic Coma	Inhibit	34639069
Hyperinsulinism	Associate	20621032
Hyperplasia	Associate	14631368
Hypertension	Associate	25813534
Idiopathic Pulmonary Fibrosis	Associate	35563422
Infections	Inhibit	23775130
Insulin Resistance	Associate	30930126
Intestinal Diseases	Associate	14960508
Kimura Disease	Associate	14631368
Lymphatic Metastasis	Associate	17552012, 28951630
Mason Type Diabetes	Associate	19843526, 37652665
Maturity Onset Diabetes of the Young Type 4	Associate	22570331, 27879211, 27879214, 28436541, 29396371, 31322178
Maturity Onset Diabetes of the Young Type 8 with Exocrine Dysfunction	Associate	28436541
Neoplasm Metastasis	Stimulate	18855980
Neoplasms	Associate	14960508, 18855980, 21297446, 25287138, 28951630, 30999858, 31263286, 33906633
Neuroendocrine Tumors	Associate	21739268, 29985747, 30315258, 31263286, 31846235, 32103422, 35739266
Obesity	Associate	20621032, 32456644, 36714595
Osteoporosis	Associate	35183219
Pancreas agenesis dorsal	Associate	38408297
Pancreatic Agenesis Congenital	Associate	10545530, 10545531, 19496967, 20621032, 22158542, 23320570, 27879211, 27879214, 28436541, 29396371
Pancreatic Diseases	Associate	21297446
Pancreatic Neoplasms	Associate	10545531, 17552012, 21099298, 21297446, 29107594, 31261501, 31917448, 32456644, 32907841, 33849943, 35227293
Pancreatitis	Associate	14631368, 22136171, 28436541, 30359326, 32456644, 33198821
Prostatic Neoplasms	Associate	29985747
Pyruvate Dehydrogenase Complex Deficiency Disease	Associate	16904023
Pyruvate Dehydrogenase E3 Binding Protein Deficiency	Associate	16904023
Stomach Neoplasms	Associate	14960508, 20622005, 30310259

PDX1 (pancreatic and duodenal homeobox 1)