ATOH7

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

Basic information

Region (hg38): 10:68230595-68232113

Links

ENSG00000179774 ∙ NCBI:220202 ∙ OMIM:609875 ∙ HGNC:13907 ∙ Uniprot:Q8N100 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• persistent hyperplastic primary vitreous, autosomal recessive (Limited), mode of inheritance: AR
• persistent hyperplastic primary vitreous (Supportive), mode of inheritance: AD
• anterior segment dysgenesis 7 (Supportive), mode of inheritance: AR
• persistent hyperplastic primary vitreous, autosomal recessive (Strong), mode of inheritance: AR
• persistent hyperplastic primary vitreous, autosomal recessive (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Persistent hyperplastic primary vitreous, autosomal recessive	AR	General	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	Ophthalmologic	9677055; 21441919; 21474777; 22068589; 22645276

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATOH7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATOH7 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	23	2	27
missense		1	81		1	83
nonsense			3			3
start loss						0
frameshift			4			4
inframe indel			5			5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	1	95	23	7

Variants in ATOH7

This is a list of pathogenic ClinVar variants found in the ATOH7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-68231223-G-A		not specified	Uncertain significance (May 20, 2024)
10-68231225-G-A			Likely benign (Oct 23, 2023)
10-68231229-A-G			Uncertain significance (Aug 07, 2022)
10-68231232-T-C			Uncertain significance (Apr 11, 2021)
10-68231242-C-T			Uncertain significance (Oct 15, 2021)
10-68231243-G-A			Likely benign (Mar 15, 2022)
10-68231243-G-C			Likely benign (Mar 09, 2022)
10-68231245-G-C		not specified	Uncertain significance (Jan 19, 2024)
10-68231252-G-A			Likely benign (Nov 25, 2022)
10-68231268-C-T			Uncertain significance (Sep 24, 2021)
10-68231270-G-A			Likely benign (Aug 16, 2022)
10-68231274-A-G			Uncertain significance (Jul 19, 2022)
10-68231276-C-A		not specified	Uncertain significance (Jan 24, 2024)
10-68231282-C-T			Likely benign (Jun 23, 2023)
10-68231289-G-T		not specified	Uncertain significance (May 20, 2024)
10-68231295-T-G			Uncertain significance (Jun 01, 2022)
10-68231302-C-G			Uncertain significance (Jul 25, 2022)
10-68231303-C-G			Likely benign (Aug 29, 2023)
10-68231313-A-C		not specified	Uncertain significance (Jan 17, 2024)
10-68231315-GT-G			Uncertain significance (Mar 15, 2022)
10-68231318-G-A			Likely benign (Apr 24, 2023)
10-68231322-T-C		not specified	Uncertain significance (Sep 06, 2022)
10-68231323-C-T			Uncertain significance (Aug 09, 2019)
10-68231330-G-C			Uncertain significance (Oct 24, 2022)
10-68231331-A-C			Uncertain significance (Jan 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATOH7	protein_coding	protein_coding	ENST00000373673	1	1486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0509	0.707	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.305	58	64.9	0.893	0.00000295	964
Missense in Polyphen		25	26.297	0.95069		359
Synonymous	-1.21	39	30.5	1.28	0.00000138	326
Loss of Function	0.677	2	3.33	0.600	1.43e-7	40

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: 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

Haploinsufficiency Scores

• pHI: 0.713
• hipred: N
• hipred_score: 0.490
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Atoh7
• Phenotype: vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype

Zebrafish Information Network

• Gene name: atoh7
• Affected structure: retinal bipolar neuron
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: neural retina development;regulation of transcription by RNA polymerase II;circadian rhythm;entrainment of circadian clock;optic nerve development;cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein dimerization activity