HOXA2 homeobox A2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXA2provided by HGNC
Official Full Name: homeobox A2provided by HGNC
Primary source: HGNC:HGNC:5103
See related: Ensembl:ENSG00000105996 MIM:604685
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: HOX1K; MCOHI
Summary: In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. [provided by RefSeq, Jul 2008]
Expression: Broad expression in lung (RPKM 1.2), fat (RPKM 0.8) and 19 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 7p15.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	7	NC_000007.14 (27100354..27102683, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (27139973..27142394, complement)

Chromosome 7 - NC_000007.14 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?

our experiments support that PPP1CB and KPC2 together inhibit the activity of HOXA2 by activating its nuclear export, but favored HOXA2 de-ubiquitination and stabilization thereby establishing a store of HOXA2 in the cytoplasm.
Title: HOXA2 activity regulation by cytoplasmic relocation, protein stabilization and post-translational modification.
Performed mutational analysis of TCOF1, GSC, and HOXA2 to determine the mutational features of the 3 genes in Chinese patients with Treacher Collins syndrome.
Title: Mutational Analysis of TCOF1, GSC, and HOXA2 in Patients With Treacher Collins Syndrome.
The role of HOXA2 gene in dominant isolated microtia and the dysmorphogenetic effect of this gene on ear development
Title: Identification of a second HOXA2 nonsense mutation in a family with autosomal dominant non-syndromic microtia and distinctive ear morphology.
5 genomic variants in GSC, HOXA2 and PRKRA were identified through mutational analysis in Chinese patients with microtia.
Title: Mutational analysis of GSC, HOXA2 and PRKRA in 106 Chinese patients with microtia.
The Hoxa2-mediated decay of RCHY1 involves both the 19S and 20S proteasome complexes
Title: Molecular Analysis of the HOXA2-Dependent Degradation of RCHY1.
HOXA2 acts as a suppressor or TBP-antagonist to inhibit MMP-9 expression; while methylation-mediated inactivation of HOXA2 in NPC derepresses MMP-9 production and increases invasion of NPC cells.
Title: Aberrantly hypermethylated Homeobox A2 derepresses metalloproteinase-9 through TBP and promotes invasion in Nasopharyngeal carcinoma.
we have identified a nonsense mutation (Q235*) in HOXA2 that segregates with bilateral nonsyndromic microtia and hearing loss through three generations of a family in an autosomal dominant pattern.
Title: HOXA2 haploinsufficiency in dominant bilateral microtia and hearing loss.
Lack of mutations in the coding region of HOXA2 among the sporadic microtia patients.
Title: Mutational analysis of HOXA2 and SIX2 in a Bronx population with isolated microtia.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot.
Observational study of gene-disease association. (HuGE Navigator)
Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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
Microtia, hearing impairment, and cleft palate MedGen: C2676772 OMIM: 612290 GeneReviews: Not available	Compare labs

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

Hoxa2 (e-PCR), detects polymorphism
- UniSTS:143365

ECD23940 (e-PCR)
- UniSTS:304924

ECD00784 (e-PCR)
- UniSTS:281893

Hoxa2 (e-PCR), detects polymorphism
- UniSTS:536640

NoName (e-PCR)
- UniSTS:491328

ECD09630 (e-PCR)
- UniSTS:290671

ECD09887 (e-PCR)
- UniSTS:290928

stSG609312 (e-PCR)
- UniSTS:449411

stSG609313 (e-PCR)
- UniSTS:449412

SHGC-57559 (e-PCR)
- UniSTS:27278

ECD00644 (e-PCR)
- UniSTS:281753

REN100328 (e-PCR)
- UniSTS:425125

REN100329 (e-PCR)
- UniSTS:425126

REN100330 (e-PCR)
- UniSTS:425127

REN100331 (e-PCR)
- UniSTS:425128

REN100332 (e-PCR)
- UniSTS:425129

REN100333 (e-PCR)
- UniSTS:425130

REN100334 (e-PCR)
- UniSTS:425131

REN100335 (e-PCR)
- UniSTS:425132

REN100336 (e-PCR)
- UniSTS:425133

REN100337 (e-PCR)
- UniSTS:425134

MARC_12745-12746:1030738152:1 (e-PCR)
- UniSTS:267439

NoName (e-PCR)
- UniSTS:481967

REN100338 (e-PCR)
- UniSTS:425135

REN100339 (e-PCR)
- UniSTS:425136

REN100340 (e-PCR)
- UniSTS:425137

REN100341 (e-PCR)
- UniSTS:425138

REN100342 (e-PCR)
- UniSTS:425139

REN100343 (e-PCR)
- UniSTS:425140

REN100344 (e-PCR)
- UniSTS:425141

REN100345 (e-PCR)
- UniSTS:425142

REN100346 (e-PCR)
- UniSTS:425143

REN100347 (e-PCR)
- UniSTS:425144

NoName (e-PCR)
- UniSTS:494538

NoName (e-PCR)
- UniSTS:486643

Homology

Homologs of the HOXA2 gene: The HOXA2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 314 organisms have orthologs with human gene HOXA2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
RNA polymerase II proximal promoter sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
brain segmentation	IEA Inferred from Electronic Annotation more info
cell fate determination	IEA Inferred from Electronic Annotation more info
cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
dorsal/ventral pattern formation	IEA Inferred from Electronic Annotation more info
embryonic viscerocranium morphogenesis	IEA Inferred from Electronic Annotation more info
middle ear morphogenesis	IEA Inferred from Electronic Annotation more info
motor neuron axon guidance	IEA Inferred from Electronic Annotation more info
negative regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
negative regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
osteoblast development	IEA Inferred from Electronic Annotation more info
positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
rhombomere 2 development	IEA Inferred from Electronic Annotation more info
rhombomere 3 morphogenesis	IEA Inferred from Electronic Annotation more info
segment specification	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
nuclear chromatin	ISA Inferred from Sequence Alignment more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: homeobox protein Hox-A2

Names: homeobox protein Hox-1K

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.