ATOH7 (atonal bHLH transcription factor 7)

Gene

• Entrez ID: 220202
• Gene name: Atonal bHLH transcription factor 7
• Gene symbol: ATOH7
• Synonyms (NCBI Gene): Math5, NCRNA, PHPVAR, RNANC, bHLHa13
• Chromosome: 10
• Chromosome location: 10q21.3|10q21.3-q22.1
• Summary: This intronless gene encodes a member of the basic helix-loop-helix family of transcription factors, with similarity to Drosophila atonal gene that controls photoreceptor development. Studies in mice suggest that this gene plays a central role in retinal

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs138274069	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs587777664	T>A,C	Pathogenic	Coding sequence variant, missense variant
rs587777665	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs587777666	T>G	Pathogenic	Coding sequence variant, missense variant
rs754494518	G>A	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT806186	hsa-miR-1183	CLIP-seq
MIRT806187	hsa-miR-21	CLIP-seq
MIRT806188	hsa-miR-3177-5p	CLIP-seq
MIRT806189	hsa-miR-3646	CLIP-seq
MIRT806190	hsa-miR-3663-3p	CLIP-seq
MIRT806191	hsa-miR-412	CLIP-seq
MIRT806192	hsa-miR-4436a	CLIP-seq
MIRT806193	hsa-miR-4502	CLIP-seq
MIRT806194	hsa-miR-4672	CLIP-seq
MIRT806195	hsa-miR-4700-3p	CLIP-seq
MIRT806196	hsa-miR-4797-5p	CLIP-seq
MIRT806197	hsa-miR-500a	CLIP-seq
MIRT806198	hsa-miR-590-5p	CLIP-seq
MIRT1938052	hsa-miR-1224-5p	CLIP-seq
MIRT1938053	hsa-miR-3169	CLIP-seq
MIRT1938054	hsa-miR-3921	CLIP-seq
MIRT1938055	hsa-miR-4515	CLIP-seq
MIRT1938056	hsa-miR-4649-3p	CLIP-seq
MIRT1938057	hsa-miR-4653-5p	CLIP-seq
MIRT1938058	hsa-miR-4751	CLIP-seq
MIRT1938059	hsa-miR-4768-5p	CLIP-seq
MIRT1938052	hsa-miR-1224-5p	CLIP-seq
MIRT1938053	hsa-miR-3169	CLIP-seq
MIRT1938054	hsa-miR-3921	CLIP-seq
MIRT1938055	hsa-miR-4515	CLIP-seq
MIRT1938056	hsa-miR-4649-3p	CLIP-seq
MIRT1938057	hsa-miR-4653-5p	CLIP-seq
MIRT1938058	hsa-miR-4751	CLIP-seq
MIRT1938059	hsa-miR-4768-5p	CLIP-seq
MIRT1938052	hsa-miR-1224-5p	CLIP-seq
MIRT1938053	hsa-miR-3169	CLIP-seq
MIRT1938054	hsa-miR-3921	CLIP-seq
MIRT1938055	hsa-miR-4515	CLIP-seq
MIRT1938056	hsa-miR-4649-3p	CLIP-seq
MIRT1938057	hsa-miR-4653-5p	CLIP-seq
MIRT1938058	hsa-miR-4751	CLIP-seq
MIRT1938059	hsa-miR-4768-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	31696227
GO:0000976	Function	Transcription cis-regulatory region 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	ISA
GO:0003407	Process	Neural retina development	IEA
GO:0003407	Process	Neural retina development	IEA
GO:0003407	Process	Neural retina development	IMP	21441919
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	31696227, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	31696227
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005829	Component	Cytosol	IDA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	ISS
GO:0007399	Process	Nervous system development	IEA
GO:0007423	Process	Sensory organ development	IBA
GO:0007623	Process	Circadian rhythm	IEA
GO:0009649	Process	Entrainment of circadian clock	IEA
GO:0010996	Process	Response to auditory stimulus	IEA
GO:0010996	Process	Response to auditory stimulus	ISS
GO:0021554	Process	Optic nerve development	IMP	21441919
GO:0030154	Process	Cell differentiation	IEA
GO:0030424	Component	Axon	IEA
GO:0030424	Component	Axon	ISS
GO:0042995	Component	Cell projection	IEA
GO:0043153	Process	Entrainment of circadian clock by photoperiod	IEA
GO:0043153	Process	Entrainment of circadian clock by photoperiod	ISS
GO:0043204	Component	Perikaryon	IEA
GO:0043204	Component	Perikaryon	ISS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	31696227
GO:0046983	Function	Protein dimerization activity	IEA
GO:0048663	Process	Neuron fate commitment	IBA
GO:0048731	Process	System development	IEA
GO:0061564	Process	Axon development	IBA
GO:0070888	Function	E-box binding	IBA
GO:1902336	Process	Positive regulation of retinal ganglion cell axon guidance	IEA
GO:1902336	Process	Positive regulation of retinal ganglion cell axon guidance	ISS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

Other IDs

• MIM: 609875
• HGNC: 13907
• e!Ensembl: ENSG00000179774

Protein

• UniProt ID: Q8N100
• Protein name: Transcription factor ATOH7 (Atonal bHLH transcription factor 7) (Class A basic helix-loop-helix protein 13) (bHLHa13) (Protein atonal homolog 7)
• Protein function: Transcription factor that binds to DNA at the consensus sequence 5'-CAG[GC]TG-3' (PubMed:31696227). Dimerization with TCF3 isoform E47 may be required in certain situations (PubMed:31696227). Binds to gene promoters and enhancer elements, and th
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00010	HLH	41 → 93	Helix-loop-helix DNA-binding domain	Domain

• Sequence:

  MKSCKPSGPPAGARVAPPCAGGTECAGTCAGAGRLESAARRRLAANARERRRMQGLNTAF
  DRLRRVVPQWGQDKKLSKYETLQMALSYIMALTRILAEAERFGSERDWVGLHCEHFGRDH
  YLPFPGAKLPGESELYSQRLFGFQPEPFQMAT

• Sequence length: 152

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Foveal hypoplasia	Pathogenic	rs138274069	RCV001003479	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Optic nerve hypoplasia	Pathogenic	rs138274069	RCV001003479	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Persistent hyperplastic primary vitreous, autosomal recessive	Pathogenic; Likely pathogenic	rs587777664, rs587777666, rs774558993	RCV000133577 RCV000133579 RCV003232884	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANTERIOR SEGMENT DYSGENESIS 7	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOH7-related condition	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CATARACT MICROCORNEA WITH CORNEAL OPACITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Angle Closure Glaucoma	Angle Closure Glaucoma	BEFREE	25489222, 26497787		★☆☆☆☆ Found in Text Mining only
ANTERIOR SEGMENT DYSGENESIS 7	Segment dysgenesis	ORPHANET_DG	22068589		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	BEFREE	29936090		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract microcornea syndrome	Cataract-microcornea syndrome	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Congenital cataract microcornea with corneal opacity	Congenital Cataract Microcornea With Corneal Opacity	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	BEFREE	24859618		★☆☆☆☆ Found in Text Mining only
Corneal Opacity	Corneal opacity	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Eye Abnormalities	Eye abnormalities	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Eye Diseases	Eye disease	Pubtator	31696227	Associate	★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	BEFREE	21427129, 22222511, 24457358		★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	Pubtator	27293372	Associate	★☆☆☆☆ Found in Text Mining only
Glaucoma Open Angle	Open angle glaucoma	Pubtator	21398277, 22761751, 25414181, 25798827	Associate	★☆☆☆☆ Found in Text Mining only
Glaucoma, Primary Open Angle	Glaucoma	BEFREE	21398277, 22222511, 22761751, 25711633, 26690118, 27617586		★☆☆☆☆ Found in Text Mining only
Hydrophthalmos	Glaucoma, congenital	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperplasia	Hyperplasia	Pubtator	31696227	Associate	★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	29792847		★☆☆☆☆ Found in Text Mining only
Hypoplasia of the optic nerve	Hypoplasia Of The Optic Nerve	BEFREE	20395239, 23802135		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	39300613	Associate	★☆☆☆☆ Found in Text Mining only
Leukocoria	Leukocoria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Low Tension Glaucoma	Low Tension Glaucoma	BEFREE	22222511, 22584021, 25461262		★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus Pathologic	Nystagmus	Pubtator	22068589	Associate	★☆☆☆☆ Found in Text Mining only
Optic Nerve Aplasia, Bilateral	Optic nerve aplasia	BEFREE	22645276		★☆☆☆☆ Found in Text Mining only
Optic Nerve Hypoplasia, Bilateral	Optic nerve hypoplasia	BEFREE	31696227		★☆☆☆☆ Found in Text Mining only
Pendular Nystagmus	Pendular nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Persistent Hyperplastic Primary Vitreous	Persistent Hyperplastic Primary Vitreous	BEFREE	22645276		★☆☆☆☆ Found in Text Mining only
Persistent Hyperplastic Primary Vitreous	Persistent Hyperplastic Primary Vitreous	ORPHANET_DG	22645276		★☆☆☆☆ Found in Text Mining only
Persistent hyperplastic primary vitreous	Persistent Hyperplastic Primary Vitreous	Orphanet			★☆☆☆☆ Found in Text Mining only
Persistent Hyperplastic Primary Vitreous	Persistent Hyperplastic Primary Vitreous	HPO_DG			★☆☆☆☆ Found in Text Mining only
Persistent Hyperplastic Primary Vitreous, Autosomal Recessive	Persistent Hyperplastic Primary Vitreous	GENOMICS_ENGLAND_DG	11889557, 22068589		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Persistent Hyperplastic Primary Vitreous, Autosomal Recessive	Persistent Hyperplastic Primary Vitreous	UNIPROT_DG	21441919, 22068589, 22645276		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Persistent Hyperplastic Primary Vitreous, Autosomal Recessive	Persistent Hyperplastic Primary Vitreous	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Persistent pupillary membranes	Persistent Pupillary Membranes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Phthisis bulbi	Phthisis bulbi	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posterior synechiae	Synechiae	HPO_DG			★☆☆☆☆ Found in Text Mining only
Primary angle-closure glaucoma	Angle closure glaucoma	BEFREE	25489222, 26497787		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	22645276		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	27293372	Associate	★☆☆☆☆ Found in Text Mining only
Retinal nonattachment	Retinal nonattachment	HPO_DG			★☆☆☆☆ Found in Text Mining only
RETINAL NONATTACHMENT, NONSYNDROMIC CONGENITAL	PERSISTENT FETAL VASCULATURE	ORPHANET_DG	22645276		★☆☆☆☆ Found in Text Mining only
RETINAL NONATTACHMENT, NONSYNDROMIC CONGENITAL	PERSISTENT FETAL VASCULATURE	BEFREE	28192794, 31696227		★☆☆☆☆ Found in Text Mining only
RETINAL NONATTACHMENT, NONSYNDROMIC CONGENITAL	PERSISTENT FETAL VASCULATURE	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	PSYGENET_DG	24475125		★☆☆☆☆ Found in Text Mining only
Vascular Diseases	Vascular disease	Pubtator	31696227	Associate	★☆☆☆☆ Found in Text Mining only