PAX1 paired box 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAX1provided by HGNC
Official Full Name: paired box 1provided by HGNC
Primary source: HGNC:HGNC:8615
See related: Ensembl:ENSG00000125813 MIM:167411; AllianceGenome:HGNC:8615
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: OFC2; HUP48; OTFCS2
Summary: This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 20p11.22

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (21705664..21718481)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (21762357..21775174)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (21686302..21699119)

Chromosome 20 - NC_000020.11 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
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?

Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
Title: Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
PAX1 represses canonical Wnt signaling pathway and plays dual roles during endoderm differentiation.
Title: PAX1 represses canonical Wnt signaling pathway and plays dual roles during endoderm differentiation.
High-grade cervical lesions diagnosed by JAM3/PAX1 methylation in high-risk human papillomavirus-infected patients.
Title: High-grade cervical lesions diagnosed by JAM3/PAX1 methylation in high-risk human papillomavirus-infected patients.
PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
Title: PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
Title: Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
Real time quantitative methylation detection of PAX1 gene in cervical cancer screening.
Title: Real time quantitative methylation detection of PAX1 gene in cervical cancer screening.
The application value of PAX1 and ZNF582 gene methylation in high grade intraepithelial lesion and cervical cancer.
Title: The application value of PAX1 and ZNF582 gene methylation in high grade intraepithelial lesion and cervical cancer.
SOX1 and PAX1 Are Hypermethylated in Cervical Adenocarcinoma and Associated with Better Prognosis.
Title: SOX1 and PAX1 Are Hypermethylated in Cervical Adenocarcinoma and Associated with Better Prognosis.
Hypermethylated PAX1 and ZNF582 genes in the tissue sample are associated with aggressive progression of oral squamous cell carcinoma.
Title: Hypermethylated PAX1 and ZNF582 genes in the tissue sample are associated with aggressive progression of oral squamous cell carcinoma.
PAX1 is essential for development and function of the human thymus.
Title: PAX1 is essential for development and function of the human thymus.

Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Otofaciocervical syndrome 2 MedGen: C5442121 OMIM: 615560 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Male-pattern baldness susceptibility locus at 20p11. EBI GWAS Catalog EBI GWAS CatalogPubMed
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases. EBI GWAS Catalog EBI GWAS CatalogPubMed
Susceptibility variants for male-pattern baldness on chromosome 20p11. 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

NoName (e-PCR)
- UniSTS:481044

RH102861 (e-PCR)
- UniSTS:97195

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

NoName (e-PCR)
- UniSTS:483286

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in embryo development ending in birth or egg hatching	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: paired box protein Pax-1

Names: paired box gene 1; paired domain gene HuP48

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_047065.1 RefSeqGene

Range

5006..17823

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001257096.2 → NP_001244025.1 paired box protein Pax-1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AI167631, AL035562, BC143793

Consensus CDS

CCDS74709.1

UniProtKB/TrEMBL

A0A087WXV5

Related

ENSP00000481334.1, ENST00000613128.5

Conserved Domains (1) summary

cd00131
Location:98 → 225

PAX; Paired Box domain
NM_006192.5 → NP_006183.2 paired box protein Pax-1 isoform 1

See identical proteins and their annotated locations for NP_006183.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AI167631, AL035562, BC069134

Consensus CDS

CCDS13146.2

UniProtKB/Swiss-Prot

B4E0D6, P15863, Q642X9, Q6NTC0, Q9Y558

Related

ENSP00000381499.2, ENST00000398485.6

Conserved Domains (1) summary

cd00131
Location:98 → 225

PAX; Paired Box domain