PAX9 paired box 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAX9provided by HGNC
Official Full Name: paired box 9provided by HGNC
Primary source: HGNC:HGNC:8623
See related: Ensembl:ENSG00000198807 MIM:167416; AllianceGenome:HGNC:8623
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: STHAG3
Summary: This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]
Expression: Biased expression in esophagus (RPKM 29.7), salivary gland (RPKM 11.4) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 14q13.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (36657568..36679362)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (30846888..30868704)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (37126773..37148567)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

The phenotype and genotype of PAX9 mutations causing tooth agenesis.
Title: The phenotype and genotype of PAX9 mutations causing tooth agenesis.
PAX9 mutations and genetic synergism in familial tooth agenesis.
Title: PAX9 mutations and genetic synergism in familial tooth agenesis.
Detection of novel variant and functional study in a Chinese family with nonsyndromic oligodontia.
Title: Detection of novel variant and functional study in a Chinese family with nonsyndromic oligodontia.
Novel PAX9 compound heterozygous variants in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants.
Title: Novel PAX9 compound heterozygous variants in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants.
An inclusive study of deleterious missense PAX9 variants using user-friendly tools reveals structural, functional alterations, as well as potential therapeutic targets.
Title: An inclusive study of deleterious missense PAX9 variants using user-friendly tools reveals structural, functional alterations, as well as potential therapeutic targets.
An in vitro and computational validation of a novel loss-of-functional mutation in PAX9 associated with non-syndromic tooth agenesis.
Title: An in vitro and computational validation of a novel loss-of-functional mutation in PAX9 associated with non-syndromic tooth agenesis.
Four Novel PAX9 Variants and the PAX9-Related Non-Syndromic Tooth Agenesis Patterns.
Title: Four Novel PAX9 Variants and the PAX9-Related Non-Syndromic Tooth Agenesis Patterns.
PAX9 functions as a tumor suppressor gene for cervical cancer via modulating cell proliferation and apoptosis.
Title: PAX9 functions as a tumor suppressor gene for cervical cancer via modulating cell proliferation and apoptosis.
Mutation Detection and Functional Analysis of MSX1, PAX9, AXIN2, and BMP in Nonsyndromic Congenital Missing Teeth Based on Intelligent Image Detection.
Title: Mutation Detection and Functional Analysis of MSX1, PAX9, AXIN2, and BMP in Nonsyndromic Congenital Missing Teeth Based on Intelligent Image Detection.
Patterns of molar agenesis associated with p.P20L and p.R77Q variants in PAX9.
Title: Patterns of molar agenesis associated with p.P20L and p.R77Q variants in PAX9.

Submit: New GeneRIF Correction See all GeneRIFs (90)

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
Tooth agenesis, selective, 3 MedGen: C1970291 OMIM: 604625 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-07-08) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-08) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. 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

D10Bir5 (e-PCR), detects polymorphism
- UniSTS:141485

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	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

Process	Evidence Code	Pubs
involved_in anatomical structure development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cellular response to growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in endoderm development	IEA Inferred from Electronic Annotation more info
involved_in face morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in odontogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of odontogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: paired box protein Pax-9

Names: paired domain gene 9

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.