OTOA

otoancorin

Basic information

Region (hg38): 16:21663968-21761935

Previous symbols: [ "DFNB22" ]

Links

ENSG00000155719

∙ NCBI:146183 ∙ OMIM:607038 ∙ HGNC:16378 ∙ Uniprot:Q7RTW8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

autosomal recessive nonsyndromic hearing loss 22 (Strong), mode of inheritance: AR
autosomal recessive nonsyndromic hearing loss 22 (Strong), mode of inheritance: AR
autosomal recessive nonsyndromic hearing loss 22 (Definitive), mode of inheritance: AR
hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
autosomal recessive nonsyndromic hearing loss 22 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 22	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	11972037; 19888295

ClinVar

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

not_provided (568 variants)
Inborn_genetic_diseases (101 variants)
not_specified (61 variants)
Autosomal_recessive_nonsyndromic_hearing_loss_22 (51 variants)
OTOA-related_disorder (23 variants)
Rare_genetic_deafness (9 variants)
Hearing_impairment (4 variants)
Hearing_loss,_autosomal_recessive (3 variants)
Autosomal_recessive_nonsyndromic_hearing_loss_7 (2 variants)
Nonsyndromic_genetic_hearing_loss (1 variants)
nonsyndromic_sensorineural_hearing_loss (1 variants)
Schizophrenia (1 variants)
Usher_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144672.4. 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			3 clinvar	168 clinvar	3 clinvar	174
missense	1 clinvar	14 clinvar	192 clinvar	16 clinvar		223
nonsense	11 clinvar	6 clinvar				17
start loss						0
frameshift	27 clinvar	10 clinvar				37
splice donor/acceptor (+/-2bp)	5 clinvar	15 clinvar				20
Total	44	45	195	184	3

Highest pathogenic variant AF is 0.0035015864

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOA	protein_coding	protein_coding	ENST00000388958	28	82216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-10	1.00	125622	1	125	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.281	463	480	0.964	0.0000263	7383
Missense in Polyphen		121	139.03	0.87034		2507
Synonymous	0.507	191	200	0.954	0.0000117	2262
Loss of Function	3.29	24	48.8	0.492	0.00000240	700

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000535	0.000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000679	0.000668
Middle Eastern	0.000653	0.000653
South Asian	0.000558	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: May act as an adhesion molecule.;
Disease: DISEASE: Deafness, autosomal recessive, 22 (DFNB22) [MIM:607039]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:11972037}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

pRec: 0.0953

Intolerance Scores

loftool: 0.616
rvis_EVS: -0.82
rvis_percentile_EVS: 11.98

Haploinsufficiency Scores

pHI: 0.290
hipred: N
hipred_score: 0.448
ghis: 0.414

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.350

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Otoa
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); hearing/vestibular/ear phenotype;

Gene ontology

Biological process: cell-matrix adhesion;sensory perception of sound;transmission of nerve impulse
Cellular component: extracellular region;plasma membrane;cell surface;apical plasma membrane;anchored component of membrane
Molecular function