PAX2 paired box 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAX2provided by HGNC
Official Full Name: paired box 2provided by HGNC
Primary source: HGNC:HGNC:8616
See related: Ensembl:ENSG00000075891 MIM:167409; AllianceGenome:HGNC:8616
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: FSGS7; PAPRS; PAX-2
Summary: 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]
Annotation information: Annotation category: suggests misassembly
Expression: Restricted expression toward kidney (RPKM 4.2) See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.31

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (100735396..100829944)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (101618753..101713301)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (102495153..102589701)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

PAX2 is regulated by estrogen/progesterone through promoter methylation in endometrioid adenocarcinoma and has an important role in carcinogenesis via the AKT/mTOR signaling pathway.
Title: PAX2 is regulated by estrogen/progesterone through promoter methylation in endometrioid adenocarcinoma and has an important role in carcinogenesis via the AKT/mTOR signaling pathway.
PAX2 Gene Mutation in Pediatric Renal Disorders-A Narrative Review.
Title: PAX2 Gene Mutation in Pediatric Renal Disorders-A Narrative Review.
PAX2/Renal Coloboma Syndrome Expresses Extreme Intrafamilial Phenotypic Variability.
Title: PAX2/Renal Coloboma Syndrome Expresses Extreme Intrafamilial Phenotypic Variability.
PAX2 and CAKUT Phenotypes: Report on Two New Variants and a Review of Mutations from the Leiden Open Variation Database.
Title: PAX2 and CAKUT Phenotypes: Report on Two New Variants and a Review of Mutations from the Leiden Open Variation Database.
PAX2, PAX8, and PR are correlated with ovarian seromucinous borderline tumor with endometriosis.
Title: PAX2, PAX8, and PR are correlated with ovarian seromucinous borderline tumor with endometriosis.
Reliable Identification of Endometrial Precancers Through Combined Pax2, beta-Catenin, and Pten Immunohistochemistry.
Title: Reliable Identification of Endometrial Precancers Through Combined Pax2, β-Catenin, and Pten Immunohistochemistry.
Phenotypic spectrum and genetics of PAX2-related disorder in the Chinese cohort.
Title: Phenotypic spectrum and genetics of PAX2-related disorder in the Chinese cohort.
PAX2 promoter methylation and AIB1 overexpression promote tamoxifen resistance in breast carcinoma patients.
Title: PAX2 promoter methylation and AIB1 overexpression promote tamoxifen resistance in breast carcinoma patients.
Identification of of a PAX2 mutation from maternal mosaicism causes recurrent renal disorder in siblings.
Title: Identification of of a PAX2 mutation from maternal mosaicism causes recurrent renal disorder in siblings.
Next-generation sequencing in patients with familial FSGS: first report of collagen gene mutations in Tunisian patients.
Title: Next-generation sequencing in patients with familial FSGS: first report of collagen gene mutations in Tunisian patients.

Submit: New GeneRIF Correction See all GeneRIFs (134)

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
Anophthalmia-microphthalmia syndrome MedGen: C5680330 GeneReviews: Not available	not available
Focal segmental glomerulosclerosis 7 MedGen: C4014925 OMIM: 616002 GeneReviews: Not available	not available
Renal coloboma syndrome MedGen: C1852759 OMIM: 120330 GeneReviews: PAX2-Related Disorder	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-02-26) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-02-26) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide scan of copy number variation in late-onset Alzheimer's disease. 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

RH80285 (e-PCR)
- UniSTS:88437

D10S2478 (e-PCR)
- UniSTS:74159

D10S278 (e-PCR)
- UniSTS:147948

NoName (e-PCR)
- UniSTS:482033

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
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
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axonogenesis	TAS Traceable Author Statement more info	PubMed
involved_in brain morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in branching involved in ureteric bud morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell fate determination	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to retinoic acid	ISS Inferred from Sequence or Structural Similarity more info
involved_in cochlea development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cochlea morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesenchymal to epithelial transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesodermal cell fate specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesonephros development	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric collecting duct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric distal convoluted tubule development	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric epithelium development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric mesenchymal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric mesenchyme development	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric nephron tubule formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process involved in metanephric collecting duct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process involved in metanephric nephron tubule development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephros development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of programmed cell death	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of reactive oxygen species metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in nephric duct formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neural tube closure	ISS Inferred from Sequence or Structural Similarity more info
involved_in optic chiasma development	ISS Inferred from Sequence or Structural Similarity more info
involved_in optic cup morphogenesis involved in camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
involved_in optic nerve development	ISS Inferred from Sequence or Structural Similarity more info
involved_in optic nerve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in optic nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of epithelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of metanephric DCT cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of metanephric glomerulus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of optic nerve formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in pronephric field specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in pronephros development	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of metanephric nephron tubule epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of metanephros size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to nutrient levels	IEA Inferred from Electronic Annotation more info
involved_in retinal pigment epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in sensory organ development	IBA Inferred from Biological aspect of Ancestor more info
involved_in stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureter development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureter maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in urogenital system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in vestibulocochlear nerve formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual perception	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in centriolar satellite	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in microtubule organizing center	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-DNA complex	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: paired box protein Pax-2

Names: paired box homeotic gene 2

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.

Genomic

NG_008680.2 RefSeqGene

Range

14874..99236

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000278.5 → NP_000269.3 paired box protein Pax-2 isoform b

Status: REVIEWED

Source sequence(s)

AL138762, AL589862, M89470

Consensus CDS

CCDS41561.1

UniProtKB/TrEMBL

A0A7P0TAC9

Related

ENSP00000347385.3, ENST00000355243.8

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 392

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_001304569.2 → NP_001291498.1 paired box protein Pax-2 isoform f precursor

See identical proteins and their annotated locations for NP_001291498.1

Status: REVIEWED

Source sequence(s)

AL138762, AL589862, BJ989901, DB077633, M89470

UniProtKB/TrEMBL

A0A7P0TAC9, A0A9L9PYK3

Related

ENSP00000516729.1, ENST00000707078.1

Conserved Domains (3) summary

smart00351
Location:47 → 171

PAX; Paired Box domain

pfam12403
Location:313 → 423

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:263 → 286

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_001374303.1 → NP_001361232.1 paired box protein Pax-2 isoform g

Status: REVIEWED

Source sequence(s)

AL589862
NM_003987.5 → NP_003978.3 paired box protein Pax-2 isoform a

Status: REVIEWED

Source sequence(s)

AL138762, AL589862

Consensus CDS

CCDS53569.1

UniProtKB/Swiss-Prot

Q02962, Q15105, Q15110, Q15837, Q5SZP2, Q5SZP3

UniProtKB/TrEMBL

A0A7P0TAC9

Related

ENSP00000396259.1, ENST00000428433.5

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:305 → 415

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:255 → 278

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003988.5 → NP_003979.2 paired box protein Pax-2 isoform c

See identical proteins and their annotated locations for NP_003979.2

Status: REVIEWED

Source sequence(s)

AL138762, AL589862, M89470

Consensus CDS

CCDS7499.1

UniProtKB/TrEMBL

A0A7P0TAC9

Related

ENSP00000359319.3, ENST00000370296.6

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 340

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003989.5 → NP_003980.3 paired box protein Pax-2 isoform d

Status: REVIEWED

Source sequence(s)

AL138762, AL589862, M89470

Consensus CDS

CCDS91319.1

UniProtKB/TrEMBL

A0A7P0TAC9, Q5SZP1

Related

ENSP00000398652.2, ENST00000427256.6

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 367

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003990.5 → NP_003981.3 paired box protein Pax-2 isoform e

Status: REVIEWED

Source sequence(s)

AL138762, AL589862, M89470

UniProtKB/TrEMBL

A0A7P0TAC9, A0A9L9PXU6

Related

ENSP00000516730.1, ENST00000707079.1

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:305 → 390

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:255 → 278

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.