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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 Glomerulosclerosis, Focal Segmental, 7. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. 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

Regulatory Elements for PAX2 Gene

Enhancers for PAX2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H100728 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13.5 -5.6 -5588 2.9 SIN3A GLIS2 RUNX3 SP3 REST GLIS1 ZNF624 MYNN NBN HNF4A PAX2 MRPL43 SEC31B GC10M100721
GH10H100880 1.4 Ensembl ENCODE dbSUPER 10.1 +147.2 147169 3.9 ELF3 FOXA2 ARID4B RARA EGR1 FOS CREM MIXL1 EGR2 PPARG SLF2 PAX2 ENSG00000272572 SFXN3 GC10P100864 ENSG00000222072
GH10H100826 1 Ensembl ENCODE 11 +92.4 92419 3.8 CTCF HINFP SUZ12 RAD21 E2F1 ZFHX2 BCL11A ZNF512 IKZF1 ZBTB33 PAX2 SCD GC10M100747
GH10H100697 0.8 ENCODE 11.4 -38.3 -38285 0.2 ZNF146 ZSCAN18 ZBTB21 JUN ZEB1 ZNF121 ZNF366 ZSCAN5C ZNF600 KLF8 PAX2 GC10M100694 GC10P100685
GH10H100696 0.8 ENCODE 11.4 -38.9 -38865 0.2 ZSCAN4 BMI1 BATF RELA ZNF366 EED ATF7 RUNX3 IKZF2 CBFB EBAG9P1 MRPL43 LZTS2 PAX2 GC10M100694 GC10P100685
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PAX2 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the PAX2 gene promoter:

Genomic Locations for PAX2 Gene

Genomic Locations for PAX2 Gene
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

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)
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.

Phenotypes From GWAS Catalog for PAX2 Gene

Gene Ontology (GO) - Molecular Function for PAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000987 core promoter proximal region 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
GO:0016175 superoxide-generating NADPH oxidase activity ISS --
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

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

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, PaxDb, 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 33 34
  • 99.32 (n)
(Canis familiaris)
Mammalia PAX2 33 34
  • 96.66 (n)
(Bos Taurus)
Mammalia PAX2 33 34
  • 96.1 (n)
(Rattus norvegicus)
Mammalia Pax2 33
  • 94.64 (n)
(Mus musculus)
Mammalia Pax2 33 16 34
  • 94.57 (n)
(Monodelphis domestica)
Mammalia PAX2 34
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 79 (a)
-- 34
  • 67 (a)
(Gallus gallus)
Aves PAX2 33 34
  • 85.67 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 100 (a)
-- 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10259 33
African clawed frog
(Xenopus laevis)
Amphibia pax2-A 33
(Danio rerio)
Actinopterygii pax2b 34
  • 88 (a)
pax2a 33 34
  • 79.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Poxn 35
  • 71 (a)
Poxm 35
  • 70 (a)
sv 34 35
  • 23 (a)
(Caenorhabditis elegans)
Secernentea egl-38 35 34
  • 75 (a)
K07C11.1 35
  • 67 (a)
K06B9.5 35
  • 64 (a)
pax-2 34
  • 36 (a)
npax-2 34
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
-- 34
  • 16 (a)
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)

Paralogs for PAX2 Gene

Paralogs for PAX2 Gene

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

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 Sequence Context AA Info Type
rs104894170 Pathogenic, Papillorenal syndrome (PAPRS) [MIM:120330] 100,749,914(+) GGGCA(C/G)GTGAG reference, missense
rs370214925 Focal segmental glomerulosclerosis 7 (FSGS7) [MIM:616002] 100,779,578(+) CCACA(A/C/G)CATTG reference, missense
rs587777708 Pathogenic, Focal segmental glomerulosclerosis 7 (FSGS7) [MIM:616002] 100,749,869(+) CTCCC(A/G)GCAGC reference, missense
rs79555199 Pathogenic, Papillorenal syndrome (PAPRS) [MIM:120330] 100,750,707(+) AGACC(A/G)GCAGC reference, missense
VAR_068080 Papillorenal syndrome (PAPRS) [MIM:120330]

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

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

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)

Relevant External Links for PAX2 Gene

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

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

Disorders for PAX2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
papillorenal syndrome
  • renal coloboma syndrome
glomerulosclerosis, focal segmental, 7
  • focal segmental glomerulosclerosis 7
glomerulosclerosis, focal segmental, 1
  • focal segmental glomerulosclerosis 1
renal hypodysplasia
  • renal hypoplasia, isolated
renal hypoplasia
- elite association - COSMIC cancer census association via MalaCards
Search PAX2 in MalaCards View complete list of genes associated with diseases


  • 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.
  • 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.

Relevant External Links for PAX2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 45 60
  2. Role of PAX2 gene polymorphisms in Henoch-Schonlein purpura nephritis. (PMID: 16509931) Yi ZW … Mo SH (Nephrology (Carlton, Vic.) 2006) 3 22 45 60
  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 60
  4. PAX2 mutations in oligomeganephronia. (PMID: 11168927) Salomon R … Broyer M (Kidney international 2001) 3 4 22 60
  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 60

Products for PAX2 Gene

Sources for PAX2 Gene

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