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Aliases for PAX2 Gene

Aliases for PAX2 Gene

  • Paired Box 2 2 3 5
  • Paired Box Homeotic Gene 2 3
  • Paired Box Protein Pax-2 3
  • Paired Box Gene 2 2
  • FSGS7 3
  • PAPRS 3

External Ids for PAX2 Gene

Previous GeneCards Identifiers for PAX2 Gene

  • GC10P101398
  • GC10P101739
  • GC10P102636
  • GC10P102170
  • GC10P102169
  • GC10P102495
  • GC10P096133

Summaries for PAX2 Gene

Entrez Gene Summary for PAX2 Gene

  • PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for PAX2 Gene

PAX2 (Paired Box 2) is a Protein Coding gene. Diseases associated with PAX2 include Papillorenal Syndrome and Focal Segmental Glomerulosclerosis 7. Among its related pathways are Wnt / Hedgehog / Notch and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include transcription factor binding and transcription regulatory region DNA binding. An important paralog of this gene is PAX5.

UniProtKB/Swiss-Prot for PAX2 Gene

  • Transcription factor that may have a role in kidney cell differentiation (PubMed:24676634). Has a critical role in the development of the urogenital tract, the eyes, and the CNS.

Gene Wiki entry for PAX2 Gene

Additional gene information for PAX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PAX2 Gene

Genomics for PAX2 Gene

GeneHancer (GH) Regulatory Elements for PAX2 Gene

Promoters and enhancers for PAX2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J100745 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 650.4 +10.2 10155 0.1 CTCF INSM2 ZNF335 ZFHX2 GLIS2 ZNF213 ZNF143 ZNF600 KLF8 EZH2 PAX2 GC10M100747
GH10J100735 Enhancer 0.6 ENCODE dbSUPER 650.7 +0.2 216 0.2 SUZ12 PRDM1 EZH2 PAX2 MRPL43 GC10M100747
GH10J100728 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 13.5 -5.6 -5587 2.9 SIN3A ZNF48 GLIS2 RUNX3 SP3 REST GLIS1 ZNF624 MYNN NBN PAX2 MRPL43 GC10M100721
GH10J100880 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.1 +147.2 147168 3.9 ELF3 FOXA2 ARID4B RARA EGR1 FOS CREM MIXL1 NFKBIZ EGR2 SLF2 PAX2 ENSG00000272572 SFXN3 GC10P100864 ENSG00000222072
GH10J100826 Enhancer 0.9 Ensembl ENCODE 11 +92.4 92418 3.8 CTCF SUZ12 RAD21 ZNF48 E2F1 ZFHX2 VEZF1 KLF8 EZH2 EGR2 PAX2 SCD GC10M100747
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PAX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PAX2 gene promoter:
  • AP-1
  • GATA-1

Genomic Locations for PAX2 Gene

Genomic Locations for PAX2 Gene
94,339 bases
Plus strand
94,339 bases
Plus strand

Genomic View for PAX2 Gene

Genes around PAX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX2 Gene

Proteins for PAX2 Gene

  • Protein details for PAX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Paired box protein Pax-2
    Protein Accession:
    Secondary Accessions:
    • Q15105
    • Q15110
    • Q15837
    • Q5SZP2
    • Q5SZP3

    Protein attributes for PAX2 Gene

    417 amino acids
    Molecular mass:
    44706 Da
    Quaternary structure:
    • Interacts with ELGN3; the interaction targets PAX2 for destruction. Interacts with TLE4.

    Alternative splice isoforms for PAX2 Gene


neXtProt entry for PAX2 Gene

Post-translational modifications for PAX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PAX2 Gene

Domains & Families for PAX2 Gene

Gene Families for PAX2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Transcription factors

Protein Domains for PAX2 Gene

Suggested Antigen Peptide Sequences for PAX2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PAX2: view

No data available for UniProtKB/Swiss-Prot for PAX2 Gene

Function for PAX2 Gene

Molecular function for PAX2 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that may have a role in kidney cell differentiation (PubMed:24676634). Has a critical role in the development of the urogenital tract, the eyes, and the CNS.
GENATLAS Biochemistry:
paired box (DNA binding) containing protein 2,with a truncated homeo domain and an alternatively spliced form PAX2D,leading to a shift in the reading frame and an extended conserved coding region at the C terminus,expressed in fetal kidney,throughout the branching ureteric bud Wolffian and Mullerian ducts,eye,CNS,ear,repressed by WT1 in podocyte during early stages of nephrogenesis,playing an essential role for the branching ureteric the development of renal epithelium,dysregulated and leading to diseases in cases of haploinsufficiency(see ONCRV) or persistent expression (see DDS)

Phenotypes From GWAS Catalog for PAX2 Gene

Gene Ontology (GO) - Molecular Function for PAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0000987 proximal promoter sequence-specific DNA binding IDA 19118900
GO:0003677 DNA binding TAS,ISS --
GO:0005515 protein binding IPI 9178767
GO:0008134 transcription factor binding IPI 24676634
genes like me logo Genes that share ontologies with PAX2: view
genes like me logo Genes that share phenotypes with PAX2: view

Human Phenotype Ontology for PAX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PAX2 Gene

MGI Knock Outs for PAX2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PAX2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PAX2 Gene

Localization for PAX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX2 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PAX2 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
golgi apparatus 4
extracellular 2
lysosome 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 19048125
GO:0005730 nucleolus IDA --
GO:0005764 lysosome IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005815 microtubule organizing center IDA 18000879
genes like me logo Genes that share ontologies with PAX2: view

Pathways & Interactions for PAX2 Gene

genes like me logo Genes that share pathways with PAX2: view

Gene Ontology (GO) - Biological Process for PAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001655 urogenital system development ISS --
GO:0001658 branching involved in ureteric bud morphogenesis ISS --
GO:0001709 cell fate determination ISS --
GO:0001823 mesonephros development ISS --
GO:0001843 neural tube closure ISS --
genes like me logo Genes that share ontologies with PAX2: view

No data available for SIGNOR curated interactions for PAX2 Gene

Drugs & Compounds for PAX2 Gene

(3) Drugs for PAX2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for PAX2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PAX2: view

Transcripts for PAX2 Gene

Unigene Clusters for PAX2 Gene

Paired box 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PAX2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PAX2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12
SP2: -
SP3: -
SP4: - - - -

Relevant External Links for PAX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PAX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PAX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX2 Gene

This gene is overexpressed in Kidney - Cortex (x41.7) and Cervix - Endocervix (x4.6).

Protein differential expression in normal tissues from HIPED for PAX2 Gene

This gene is overexpressed in Heart (67.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PAX2 Gene

Protein tissue co-expression partners for PAX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PAX2 Gene:


SOURCE GeneReport for Unigene cluster for PAX2 Gene:


mRNA Expression by UniProt/SwissProt for PAX2 Gene:

Tissue specificity: Expressed in primitive cells of the kidney, ureter, eye, ear and central nervous system.

Evidence on tissue expression from TISSUES for PAX2 Gene

  • Kidney(4.7)
  • Nervous system(2.3)
  • Eye(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PAX2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • outer ear
  • pituitary gland
  • skull
  • breast
  • heart
  • lung
  • kidney
  • ovary
  • placenta
  • ureter
  • urinary bladder
  • uterus
  • vagina
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • blood vessel
  • coagulation system
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with PAX2: view

Orthologs for PAX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PAX2 34 33
  • 99.32 (n)
(Canis familiaris)
Mammalia PAX2 34 33
  • 96.66 (n)
(Bos Taurus)
Mammalia PAX2 34 33
  • 96.1 (n)
(Rattus norvegicus)
Mammalia Pax2 33
  • 94.64 (n)
(Mus musculus)
Mammalia Pax2 16 34 33
  • 94.57 (n)
(Monodelphis domestica)
Mammalia PAX2 34
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 79 (a)
-- 34
  • 67 (a)
(Gallus gallus)
Aves PAX2 34 33
  • 85.67 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 100 (a)
-- 34
  • 94 (a)
African clawed frog
(Xenopus laevis)
Amphibia pax2-A 33
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10259 33
(Danio rerio)
Actinopterygii pax2b 34
  • 88 (a)
pax2a 34 33 33
  • 79.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Poxn 35
  • 71 (a)
Poxm 35
  • 70 (a)
sv 34 35
  • 23 (a)
(Caenorhabditis elegans)
Secernentea K07C11.1 35
  • 67 (a)
K06B9.5 35
  • 64 (a)
egl-38 34 35
  • 43 (a)
pax-2 34
  • 36 (a)
npax-2 34
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
-- 34
  • 16 (a)
Cin.1461 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1461 33
Species where no ortholog for PAX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PAX2 Gene

Gene Tree for PAX2 (if available)
Gene Tree for PAX2 (if available)
Evolutionary constrained regions (ECRs) for PAX2: view image

Paralogs for PAX2 Gene

Paralogs for PAX2 Gene

(9) SIMAP similar genes for PAX2 Gene using alignment to 7 proteins:

  • G3V5M8_HUMAN
  • G3V5S4_HUMAN
  • G3V5U4_HUMAN
genes like me logo Genes that share paralogs with PAX2: view

Variants for PAX2 Gene

Sequence variations from dbSNP and Humsavar for PAX2 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs104894170 pathogenic, Papillorenal syndrome with macular abnormalities, Papillorenal syndrome (PAPRS) [MIM:120330] 100,749,914(+) G/C coding_sequence_variant, missense_variant
rs1057518761 likely-pathogenic, Renal cyst 100,750,693(+) GGTACTACGAGACCGG/GG coding_sequence_variant, splice_acceptor_variant
rs138490772 uncertain-significance, Renal coloboma syndrome 100,827,078(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1800897 not-provided, benign, not provided, not specified 100,809,115(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs1800898 not-provided, benign, not provided, not specified 100,809,226(+) A/C/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for PAX2 Gene

Variant ID Type Subtype PubMed ID
esv2669276 CNV deletion 23128226
esv2740128 CNV deletion 23290073
esv2740140 CNV deletion 23290073
esv2759779 CNV gain+loss 17122850
nsv1069960 CNV deletion 25765185
nsv1126266 CNV deletion 24896259
nsv7524 CNV insertion 18451855
nsv825545 CNV gain 20364138
nsv831964 CNV loss 17160897
nsv951002 CNV deletion 24416366

Variation tolerance for PAX2 Gene

Residual Variation Intolerance Score: 15.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.93; 19.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PAX2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX2 Gene

Disorders for PAX2 Gene

MalaCards: The human disease database

(54) MalaCards diseases for PAX2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PAX2 in MalaCards View complete list of genes associated with diseases


  • Papillorenal syndrome (PAPRS) [MIM:120330]: An autosomal dominant disorder characterized by both ocular and renal anomalies, but may also include vesicoureteral reflux, high frequency hearing loss, central nervous system anomalies, and/or genital anomalies. Eye anomalies in this disorder consist of a wide and sometimes excavated dysplastic optic disk with the emergence of the retinal vessels from the periphery of the disk, designated optic nerve coloboma or morning glory anomaly. Associated findings may include a small corneal diameter, retinal coloboma, scleral staphyloma, optic nerve cyst, microphthalmia, and pigmentary macular dysplasia. The kidneys are small and abnormally formed (renal hypodysplasia), and have fewer than the normal number of glomeruli, which are enlarged (oligomeganephronia). These ocular and renal anomalies result in decreased visual acuity and retinal detachment, as well as hypertension, proteinuria, and renal insufficiency that frequently progresses to end-stage renal disease. {ECO:0000269 PubMed:11168927, ECO:0000269 PubMed:15652857, ECO:0000269 PubMed:19954729, ECO:0000269 PubMed:22213154, ECO:0000269 PubMed:24676634, ECO:0000269 PubMed:9760197}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Focal segmental glomerulosclerosis 7 (FSGS7) [MIM:616002]: A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and progressive decline in renal function. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation. {ECO:0000269 PubMed:24676634}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PAX2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PAX2: view

No data available for Genatlas for PAX2 Gene

Publications for PAX2 Gene

  1. A common variant of the PAX2 gene is associated with reduced newborn kidney size. (PMID: 17513325) Quinlan J … Goodyer P (Journal of the American Society of Nephrology : JASN 2007) 3 22 44 58
  2. Role of PAX2 gene polymorphisms in Henoch-Schonlein purpura nephritis. (PMID: 16509931) Yi ZW … Mo SH (Nephrology (Carlton, Vic.) 2006) 3 22 44 58
  3. Macular abnormalities and optic disk anomaly associated with a new PAX2 missense mutation. (PMID: 15652857) Higashide T … Sugiyama K (American journal of ophthalmology 2005) 3 4 22 58
  4. PAX2 mutations in oligomeganephronia. (PMID: 11168927) Salomon R … Broyer M (Kidney international 2001) 3 4 22 58
  5. Missense mutation and hexanucleotide duplication in the PAX2 gene in two unrelated families with renal-coloboma syndrome (MIM 120330). (PMID: 9760197) Devriendt K … Leys A (Human genetics 1998) 3 4 22 58

Products for PAX2 Gene

Sources for PAX2 Gene

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