GeneBe

ATOH7

protein-coding

atonal bHLH transcription factor 7, the group of Basic helix-loop-helix proteins

Gene 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 ganglion cell and optic nerve formation. Mutations in this gene are associated with nonsyndromic congenital retinal nonattachment. [provided by RefSeq, Dec 2011]

MANE transcript

NM_145178.4

Inheritance

AR, AD

ClinVar variants

P:4U:100B:30

Top phenotype

Persistent hyperplastic primary vitreous, autosomal recessive

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr10:68,230,595-68,232,113

External References & Databases

Ensembl (ENSG00000179774)NCBI Gene (220202)OMIM (609875)HGNC:13907GenCCUniProt (Q8N100)AlphaFoldClinVar (ATOH7)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~1.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

persistent hyperplastic primary vitreous, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009097

Submitter: PanelApp Australia

persistent hyperplastic primary vitreous, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009097

Submitter: Labcorp Genetics (formerly Invitae)

persistent hyperplastic primary vitreous, autosomal recessiveLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0009097

Submitter: Labcorp Genetics (formerly Invitae)

anterior segment dysgenesis 7SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010015

Submitter: Orphanet

persistent hyperplastic primary vitreous, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009097

Submitter: G2P

persistent hyperplastic primary vitreousSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019631

Submitter: Orphanet

Clinical Genomic Database (CGD)

Persistent hyperplastic primary vitreous, autosomal recessiveAR

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 9677055; 21441919; 21474777; 22068589; 22645276Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATOH7 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 118
not specifiedTotal: 46
Persistent hyperplastic primary vitreous, autosomal recessiveTotal: 4
ATOH7-related conditionTotal: 3
Optic nerve hypoplasiaTotal: 2
Foveal hypoplasiaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145178.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
27
clinvar
 30
missense
3
clinvar
1
clinvar
90
clinvar
2
clinvar
1
clinvar
 97
nonsense
3
clinvar
 3
start loss
0
frameshift
4
clinvar
 4
splice donor/acceptor (+/-2bp)
0
Total31100291134
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_145178.4RefSeqNP_660161.11MANE Select
ENST00000373673.5EnsemblENSP00000362777.31MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
atoh7Danio rerio

Structure: retinal bipolar neuron

Quality: increased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • neural retina development
  • regulation of transcription by RNA polymerase II
  • circadian rhythm
  • entrainment of circadian clock
  • optic nerve development

Molecular Function

  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA binding
  • protein dimerization activity

Cellular Component

  • nucleus

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000373673
Coding exons
1
Length
1486
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3055864.90.8930.00000295964
Missense (PolyPhen)2526.2970.95069359
Synonymous-1.213930.51.280.00000138326
Loss of Function0.67723.330.6001.43e-740

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Transcription factor involved in the differentiation of retinal ganglion cells. {ECO:0000250}.;
Disease
DISEASE: Persistent hyperplastic primary vitreous, autosomal recessive (PHPVAR) [MIM:221900]: A developmental eye malformation associated with microphthalmia, cataract, glaucoma, and congenital retinal non-attachment. It is due to failure of the primary vitreous to regress in utero, resulting in the presence of a retrolental fibrovascular membrane with persistence of the posterior portion of the tunica vasculosa lentis and hyaloid artery. Disease manifestations range from a trivial remnant of hyaloid vessels to a dense fibrovascular mass causing lens opacity and retinal detachment. {ECO:0000269|PubMed:21441919, ECO:0000269|PubMed:22068589, ECO:0000269|PubMed:22645276}. Note=The disease is caused by mutations affecting the gene represented in this entry. A 6.5 kb deletion that spans a remote cis regulatory element 20 kb upstream from ATOH7 has been found in PHPVAR patients (PubMed:21441919). {ECO:0000269|PubMed:21441919}.;

Intolerance Scores

LoFtool
0.319
RVIS EVS
0.13
RVIS percentile EVS
62.74

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.801

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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