Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	3166
Gene name	H6 family homeobox 1
Gene symbol	HMX1
Synonyms (NCBI Gene)	H6NKX5-3
Chromosome	4
Chromosome location	4p16.1
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 oculoauricula

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SNP ID	Visualize variation	Clinical significance	Consequence
rs876657398	T>G	Pathogenic	Coding sequence variant, intron variant, missense variant

Show/Hide all (54)

miRTarBase ID	miRNA	Experiments	Reference
MIRT438707	hsa-miR-211-5p	ImmunocytochemistryLuciferase reporter assayqRT-PCRWestern blot	24641951
MIRT438706	hsa-miR-204-5p	ImmunocytochemistryLuciferase reporter assayqRT-PCRWestern blot	24641951
MIRT438707	hsa-miR-211-5p	ImmunocytochemistryLuciferase reporter assayqRT-PCRWestern blot	24641951
MIRT438706	hsa-miR-204-5p	ImmunocytochemistryLuciferase reporter assayqRT-PCRWestern blot	24641951
MIRT487219	hsa-miR-4779	PAR-CLIP	23592263
MIRT487218	hsa-miR-6777-5p	PAR-CLIP	23592263
MIRT487216	hsa-miR-6889-5p	PAR-CLIP	23592263
MIRT487217	hsa-miR-3195	PAR-CLIP	23592263
MIRT487215	hsa-miR-3656	PAR-CLIP	23592263
MIRT487214	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT487213	hsa-miR-7154-3p	PAR-CLIP	23592263
MIRT487211	hsa-miR-765	PAR-CLIP	23592263
MIRT487212	hsa-miR-6894-5p	PAR-CLIP	23592263
MIRT487210	hsa-miR-6827-5p	PAR-CLIP	23592263
MIRT487209	hsa-miR-1343-5p	PAR-CLIP	23592263
MIRT487208	hsa-miR-939-5p	PAR-CLIP	23592263
MIRT487207	hsa-miR-363-5p	PAR-CLIP	23592263
MIRT487206	hsa-miR-6745	PAR-CLIP	23592263
MIRT487205	hsa-miR-6880-5p	PAR-CLIP	23592263
MIRT487203	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT487204	hsa-miR-3141	PAR-CLIP	23592263
MIRT487219	hsa-miR-4779	PAR-CLIP	23592263
MIRT487218	hsa-miR-6777-5p	PAR-CLIP	23592263
MIRT487216	hsa-miR-6889-5p	PAR-CLIP	23592263
MIRT487217	hsa-miR-3195	PAR-CLIP	23592263
MIRT487215	hsa-miR-3656	PAR-CLIP	23592263
MIRT487214	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT487213	hsa-miR-7154-3p	PAR-CLIP	23592263
MIRT487211	hsa-miR-765	PAR-CLIP	23592263
MIRT487212	hsa-miR-6894-5p	PAR-CLIP	23592263
MIRT487210	hsa-miR-6827-5p	PAR-CLIP	23592263
MIRT487209	hsa-miR-1343-5p	PAR-CLIP	23592263
MIRT487208	hsa-miR-939-5p	PAR-CLIP	23592263
MIRT487207	hsa-miR-363-5p	PAR-CLIP	23592263
MIRT487206	hsa-miR-6745	PAR-CLIP	23592263
MIRT487205	hsa-miR-6880-5p	PAR-CLIP	23592263
MIRT487203	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT487204	hsa-miR-3141	PAR-CLIP	23592263
MIRT1050180	hsa-miR-1184	CLIP-seq
MIRT1050181	hsa-miR-1205	CLIP-seq
MIRT1050182	hsa-miR-1225-3p	CLIP-seq
MIRT1050183	hsa-miR-1231	CLIP-seq
MIRT1050184	hsa-miR-1915	CLIP-seq
MIRT1050185	hsa-miR-2467-3p	CLIP-seq
MIRT1050186	hsa-miR-3120-5p	CLIP-seq
MIRT1050187	hsa-miR-3158-5p	CLIP-seq
MIRT1050188	hsa-miR-3678-3p	CLIP-seq
MIRT1050189	hsa-miR-4323	CLIP-seq
MIRT1050190	hsa-miR-4475	CLIP-seq
MIRT1050191	hsa-miR-4651	CLIP-seq
MIRT1050192	hsa-miR-4726-3p	CLIP-seq
MIRT1050193	hsa-miR-566	CLIP-seq
MIRT1050194	hsa-miR-604	CLIP-seq
MIRT1050195	hsa-miR-608	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	IMP	10206974
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IC	10206974
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IBA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IMP	10206974
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
142992	5017	ENSG00000215612

Q9NP08

Protein name

Homeobox protein HMX1 (Homeobox protein H6)

Protein function

DNA-binding protein that binds to the 5'-CAAG-3' core sequence. May function as a transcriptional repressor. Seems to act as a transcriptional antagonist of NKX2-5. May play an important role in the development of craniofacial structures such as

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	204 → 260	Homeodomain	Domain

Sequence

MPDELTEPGRATPARASSFLIENLLAAEAKGAGRATQGDGSREDEEEDDDDPEDEDAEQA
RRRRLQRRRQLLAGTGPGGEARARALLGPGALGLGPRPPPGPGPPFALGCGGAARWYPRA
HGGYGGGLSPDTSDRDSPETGEEMGRAEGAWPRGPGPGAVQREAAELAARGPAAGTEEAS
ELAEVPAAAGETRGGVGVGGGRKKKTRTVFSRSQVFQLESTFDLKRYLSSAERAGLAASL
QLTETQVKIWFQNRRNKWKRQLAAELEAASLSPPGAQRLVRVPVLYHESPPAAAAAGPPA
TLPFPLAPAAPAPPPPLLGFSGALAYPLAAFPAAASVPFLRAQMPGLV

Sequence length

348

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Isolated microphthalmia 6	Pathogenic	rs2474393026	RCV003389574	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular syndrome	Pathogenic	rs876657398, rs63751898	RCV000172907 RCV000015991	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CATARACT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIFFUSE GASTRIC ADENOCARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HMX1-related disorder	Likely benign; Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROPHTHALMIA, ISOLATED 6	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROPHTHALMOS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULOAURICULAR SYNDROME SCHORDERET TYPE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULOAURICULAR SYNDROME, SCHORDERET TYPE	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (25)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Cataract	Cataract	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Microtia	Congenital microtia	Pubtator	24983964, 34087987	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	BEFREE	24983964, 31691317		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	GENOMICS_ENGLAND_DG	9337406		★★★★★ ★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	29140751		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ear Diseases	Ear disease	Pubtator	34087987	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphakia	Microphakia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	BEFREE	18423520		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microphthalmos	Microphthalmos	CTD_human_DG	19379485		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microphthalmos	Microphthalmos	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ocular Hypertension	Ocular Hypertension	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Oculoauricular Syndrome	Oculoauricular Syndrome	GENOMICS_ENGLAND_DG	18423520, 19379485, 29140751, 9337406		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular Syndrome	Oculoauricular Syndrome	ORPHANET_DG	18423520, 25574057		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular Syndrome	Oculoauricular Syndrome	BEFREE	29140751		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular Syndrome	Oculoauricular Syndrome	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular Syndrome	Oculoauricular Syndrome	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculoauricular syndrome, Schorderet type	Oculoauricular Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal Dystrophies	Retinal Dystrophy	BEFREE	21417677		★★★★★ ★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sclerocornea	Sclerocornea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sjogren's Syndrome	Sjogren syndrome	Pubtator	34594326	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Waardenburg Anophthalmia Syndrome	Microphthalmia with limb anomalies	BEFREE	29140751		★★★★★ ★☆☆☆☆ Found in Text Mining only

HMX1 (H6 family homeobox 1)