HMX1 H6 family homeobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HMX1provided by HGNC
Official Full Name: H6 family homeobox 1provided by HGNC
Primary source: HGNC:HGNC:5017
See related: Ensembl:ENSG00000215612 MIM:142992; AllianceGenome:HGNC:5017
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: H6; NKX5-3
Summary: This gene encodes a transcription factor that belongs to the H6 family of homeobox proteins. This protein can bind a 5'-CAAG-3' core DNA sequence, and it is involved in the development of craniofacial structures. Mutations in this gene cause oculoauricular syndrome, a disorder of the eye and external ear. [provided by RefSeq, Oct 2009]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 4p16.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (8846076..8871839, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (8812981..8838746, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (8847802..8873565, complement)

Chromosome 4 - NC_000004.12 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?

Duplications involving the long range HMX1 enhancer are associated with human isolated bilateral concha-type microtia.
Title: Duplications involving the long range HMX1 enhancer are associated with human isolated bilateral concha-type microtia.
Mutation analysis revealed a novel homozygous nonsense mutation c.487G>T in the second exon of the HMX1 that predicted to introduce a premature stop codon at position 163 (p.E163*).
Title: Further delineation of the oculoauricular syndrome phenotype: A new family with a novel truncating HMX1 mutation.
The retinal degeneration in the recessively inherited oculo-auricular syndrome is a progressive rod-cone dystrophy.
Title: Retinal dystrophy in the oculo-auricular syndrome due to HMX1 mutation.
Linkage analysis and mutation screening revealed in the first exon of the NKX5-3 gene a homozygous 26 nucleotide deletion, generating a truncating protein that lacked the complete homeodomain.
Title: Mutation in the human homeobox gene NKX5-3 causes an oculo-auricular syndrome.

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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
Oculoauricular syndrome MedGen: C2677500 OMIM: 612109 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of H6 family homeobox 1 (HMX1) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	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 DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription 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 negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	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

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: homeobox protein HMX1

Names: H6 homeodomain protein; NK5 homeobox 3; homeobox protein H6

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_013062.2 RefSeqGene

Range

4979..9770

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001306142.2 → NP_001293071.1 homeobox protein HMX1 isoform 2

See identical proteins and their annotated locations for NP_001293071.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and uses an alternate exon in the 3' coding region that results in a frameshift compared to variant 1. It encodes isoform 2, which is shorter than and has a novel C-terminus compared to isoform 1.

Source sequence(s)

AB593128, AC116612, BM701514, CK299519, M99587

Consensus CDS

CCDS77900.1

UniProtKB/TrEMBL

F1T0J4, F8W1B1

Related

ENSP00000446997.2, ENST00000506970.2
NM_018942.3 → NP_061815.2 homeobox protein HMX1 isoform 1

See identical proteins and their annotated locations for NP_061815.2

Status: REVIEWED

Description

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

Source sequence(s)

AC116612

Consensus CDS

CCDS47018.1

UniProtKB/Swiss-Prot

Q9NP08

Related

ENSP00000383516.3, ENST00000400677.5

Conserved Domains (1) summary

pfam00046
Location:206 → 259

Homeobox; Homeobox domain