ATOH1
atonal bHLH transcription factor 1, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 4:93828753-93830964
Links
Phenotypes
GenCC
Source:
- hearing loss, autosomal dominant 89 (Limited), mode of inheritance: AD
- hearing loss, autosomal dominant 89 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Deafness, autosomal dominant 89 | AD | Audiologic/Otolaryngologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development | Audiologic/Otolaryngologic | 33111345 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (54 variants)
- ATOH1-related_disorder (12 variants)
- not_provided (5 variants)
- Hearing_loss,_autosomal_dominant_89 (2 variants)
- Dominant_progressive_sensorineural_hearing_loss (1 variants)
- Pontoneocerebellar_hypoplasia (1 variants)
- Hearing_loss (1 variants)
- Global_developmental_delay (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATOH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005172.2. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 58 | 62 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 1 | 59 | 3 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATOH1 | protein_coding | protein_coding | ENST00000306011 | 1 | 1180 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0178 | 0.902 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.134 | 215 | 210 | 1.03 | 0.00000942 | 2273 |
| Missense in Polyphen | 66 | 82.323 | 0.80172 | 933 | ||
| Synonymous | -1.46 | 113 | 94.9 | 1.19 | 0.00000446 | 768 |
| Loss of Function | 1.48 | 4 | 8.70 | 0.460 | 3.70e-7 | 99 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator. Activates E box-dependent transcription in collaboration with TCF3/E47, but the activity is completely antagonized by the negative regulator of neurogenesis HES1. Plays a role in the differentiation of subsets of neural cells by activating E box-dependent transcription (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.283
Intolerance Scores
- loftool
- rvis_EVS
- -0.11
- rvis_percentile_EVS
- 45.26
Haploinsufficiency Scores
- pHI
- 0.768
- hipred
- Y
- hipred_score
- 0.694
- ghis
- 0.403
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.577
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atoh1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- atoh1a
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- neuron migration;transcription by RNA polymerase II;Notch signaling pathway;axon guidance;central nervous system development;cerebral cortex development;inner ear morphogenesis;auditory receptor cell fate specification;auditory receptor cell fate determination;negative regulation of apoptotic process;positive regulation of inner ear auditory receptor cell differentiation;positive regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;chromatin DNA binding;protein dimerization activity