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... See more...

Aliases for PAX1 Gene

Aliases for PAX1 Gene

  • Paired Box 1 2 3 5
  • Paired Box Protein Pax-1 3 4
  • Paired Box Gene 1 2 3
  • HUP48 3 4
  • Paired Domain Gene HuP48 3
  • HuP48 4
  • OFC2 3

External Ids for PAX1 Gene

Previous GeneCards Identifiers for PAX1 Gene

  • GC20P021675
  • GC20P021682
  • GC20P021634

Summaries for PAX1 Gene

Entrez Gene Summary for PAX1 Gene

  • 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]

GeneCards Summary for PAX1 Gene

PAX1 (Paired Box 1) is a Protein Coding gene. Diseases associated with PAX1 include Otofaciocervical Syndrome 2 and Otofaciocervical Syndrome 1. An important paralog of this gene is PAX9.

UniProtKB/Swiss-Prot Summary for PAX1 Gene

  • This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity).

Gene Wiki entry for PAX1 Gene

Additional gene information for PAX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PAX1 Gene

Genomics for PAX1 Gene

GeneHancer (GH) Regulatory Elements for PAX1 Gene

Promoters and enhancers for PAX1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J021705 Promoter 0.7 EPDnew 500.7 +0.0 10 0.1 CTCF ZBTB26 ZNF335 ZNF398 RNF2 MAZ ZFX HNRNPK EZH2 SUZ12 LINC01726 PAX1 piR-59928-082
GH20J021706 Enhancer 0.4 ENCODE 500.7 +1.2 1179 0.1 EZH2 CREB1 CBX8 RNF2 SUZ12 LINC01726 PAX1 piR-59928-082
GH20J021681 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 12.4 -23.6 -23564 1.8 ZNF341 OSR2 ZBTB17 GATA3 PKNOX1 MAZ NFIB PRDM6 ZNF18 FEZF1 PAX1 LINC01726 ENSG00000278410
GH20J021521 Enhancer 0.9 FANTOM5 dbSUPER 12.1 -184.4 -184359 0.6 ZBTB10 ZNF423 ZBTB26 CTCF EZH2 ZFHX2 ZNF335 SUZ12 ZNF654 POLR2A NKX2-2 PAX1 NKX2-4 KIZ lnc-XRN2-9
GH20J021768 Enhancer 0.8 ENCODE 10.6 +62.5 62459 0.2 CTCF TCF7 SKI TEAD1 ZBTB26 TBX3 CTBP1 ESRRA BCL11A ZBTB17 PAX1 piR-31534-414 piR-34946-008
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PAX1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PAX1

Top Transcription factor binding sites by QIAGEN in the PAX1 gene promoter:
  • c-Myc
  • GATA-2
  • Max1
  • MAZR
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4

Genomic Locations for PAX1 Gene

Genomic Locations for PAX1 Gene
chr20:21,705,659-21,718,486
(GRCh38/hg38)
Size:
12,828 bases
Orientation:
Plus strand
chr20:21,686,297-21,696,620
(GRCh37/hg19)
Size:
10,324 bases
Orientation:
Plus strand

Genomic View for PAX1 Gene

Genes around PAX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX1 Gene

Proteins for PAX1 Gene

  • Protein details for PAX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P15863-PAX1_HUMAN
    Recommended name:
    Paired box protein Pax-1
    Protein Accession:
    P15863
    Secondary Accessions:
    • B4E0D6
    • Q642X9
    • Q6NTC0
    • Q9Y558

    Protein attributes for PAX1 Gene

    Size:
    534 amino acids
    Molecular mass:
    55499 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH69134.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAU21037.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for PAX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PAX1 Gene

Post-translational modifications for PAX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PAX1 Gene

No data available for DME Specific Peptides for PAX1 Gene

Domains & Families for PAX1 Gene

Gene Families for PAX1 Gene

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

Protein Domains for PAX1 Gene

Blocks:
  • Paired box protein, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PAX1 Gene

GenScript: Design optimal peptide antigens:
  • HuP48 (PAX1_HUMAN)
genes like me logo Genes that share domains with PAX1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PAX1 Gene

Function for PAX1 Gene

Molecular function for PAX1 Gene

UniProtKB/Swiss-Prot Function:
This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity).
GENATLAS Biochemistry:
paired box (DNA binding) containing protein 1,with homeo domain,expressed in the sclerotome,controlling chondrogenesis through SHH signaling,involved in the development of vertebral column,homologous to undulated

Phenotypes From GWAS Catalog for PAX1 Gene

Gene Ontology (GO) - Molecular Function for PAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with PAX1: view
genes like me logo Genes that share phenotypes with PAX1: view

Human Phenotype Ontology for PAX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PAX1 Gene

MGI Knock Outs for PAX1:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PAX1 Gene

Localization for PAX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX1 Gene

Subcellular locations from

COMPARTMENTS
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 PAX1 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with PAX1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PAX1 Gene

Pathways & Interactions for PAX1 Gene

PathCards logo

SuperPathways for PAX1 Gene

No Data Available

SIGNOR curated interactions for PAX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for PAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9671740
GO:0001756 somitogenesis IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 1358810
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with PAX1: view

No data available for Pathways by source for PAX1 Gene

Drugs & Compounds for PAX1 Gene

No Compound Related Data Available

Transcripts for PAX1 Gene

mRNA/cDNA for PAX1 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PAX1 Gene

No ASD Table

Relevant External Links for PAX1 Gene

GeneLoc Exon Structure for
PAX1

Expression for PAX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PAX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX1 Gene

This gene is overexpressed in Esophagus - Mucosa (x8.7), Muscle - Skeletal (x7.6), Thyroid (x7.2), Skin - Sun Exposed (Lower leg) (x5.6), and Minor Salivary Gland (x4.5).

Protein differential expression in normal tissues from HIPED for PAX1 Gene

This gene is overexpressed in Platelet (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PAX1 Gene



Protein tissue co-expression partners for PAX1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PAX1

SOURCE GeneReport for Unigene cluster for PAX1 Gene:

Hs.122310

Phenotype-based relationships between genes and organs from Gene ORGANizer for PAX1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • face
  • head
  • inner ear
  • jaw
  • lacrimal apparatus
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with PAX1: view

No data available for mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for PAX1 Gene

Orthologs for PAX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PAX1 31
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PAX1 31 30
  • 89.96 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PAX1 31 30
  • 88.54 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pax1 17 31 30
  • 86.92 (n)
oppossum
(Monodelphis domestica)
Mammalia PAX1 31
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PAX1 31
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves PAX1 31 30
  • 79.39 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PAX1 31
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pax1 30
  • 70.69 (n)
zebrafish
(Danio rerio)
Actinopterygii pax1a 31 30
  • 68.56 (n)
OneToMany
pax1b 31
  • 66 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta sv 32
  • 69 (a)
Poxn 32
  • 66 (a)
Poxm 31 32
  • 41 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea K07C11.1 32
  • 72 (a)
egl-38 32
  • 67 (a)
K06B9.5 32
  • 63 (a)
pax-1 31
  • 42 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 41 (a)
OneToMany
Species where no ortholog for PAX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rat (Rattus norvegicus)
  • 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 PAX1 Gene

ENSEMBL:
Gene Tree for PAX1 (if available)
TreeFam:
Gene Tree for PAX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PAX1: view image

Paralogs for PAX1 Gene

(8) SIMAP similar genes for PAX1 Gene using alignment to 1 proteins:

  • PAX1_HUMAN
genes like me logo Genes that share paralogs with PAX1: view

Variants for PAX1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PAX1 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
715199 Benign: not provided 21,714,576(+) C/A SYNONYMOUS_VARIANT,THREE_PRIME_UTR_VARIANT
721776 Likely Benign: not provided 21,705,775(+) G/T SYNONYMOUS_VARIANT
725902 Benign: not provided 21,714,689(+) C/G SYNONYMOUS_VARIANT,THREE_PRIME_UTR_VARIANT
726728 Likely Benign: not provided 21,705,796(+) G/T SYNONYMOUS_VARIANT
728185 Likely Benign: not provided 21,706,836(+) G/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for PAX1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PAX1 Gene

Variant ID Type Subtype PubMed ID
nsv1058137 CNV loss 25217958
nsv828703 CNV gain 20364138
nsv952999 CNV deletion 24416366

Variation tolerance for PAX1 Gene

Residual Variation Intolerance Score: 34.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.24; 52.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PAX1 Gene

Human Gene Mutation Database (HGMD)
PAX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PAX1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX1 Gene

Disorders for PAX1 Gene

MalaCards: The human disease database

(19) MalaCards diseases for PAX1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
otofaciocervical syndrome 2
  • orofacial cleft 2
otofaciocervical syndrome 1
  • orofacial cleft 1
klippel-feil syndrome
  • kfs
spondylocostal dysostosis 1, autosomal recessive
  • spondylothoracic dysostosis
idiopathic scoliosis
  • scoliosis idiopathic
- elite association - COSMIC cancer census association via MalaCards
Search PAX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PAX1_HUMAN
  • Otofaciocervical syndrome 2 (OTFCS2) [MIM:615560]: A disorder characterized by facial dysmorphism, cup-shaped low-set ears, preauricular fistulas, hearing loss, branchial defects, skeletal anomalies including vertebral defects, low-set clavicles, winged scapulae, sloping shoulders, and mild intellectual disability. {ECO:0000269 PubMed:23851939}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PAX1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PAX1: view

No data available for Genatlas for PAX1 Gene

Publications for PAX1 Gene

  1. Pax1, a member of the paired box-containing class of developmental control genes, is mapped to human chromosome 20p11.2 by in situ hybridization (ISH and FISH). (PMID: 1358810) Schnittger S … Hansmann I (Genomics 1992) 2 3 23 54
  2. A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome. (PMID: 23851939) Pohl E … Wollnik B (Human genetics 2013) 3 4 54
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 41 54
  4. Male-pattern baldness susceptibility locus at 20p11. (PMID: 18849991) Richards JB … Mooser V (Nature genetics 2008) 3 41 54
  5. Susceptibility variants for male-pattern baldness on chromosome 20p11. (PMID: 18849994) Hillmer AM … Nöthen MM (Nature genetics 2008) 3 41 54

Products for PAX1 Gene

Sources for PAX1 Gene