OTOA

otoancorin

Basic information

Region (hg38): 16:21663967-21761935

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
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 22 (Definitive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), 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 (300 variants)
• not specified (59 variants)
• Autosomal recessive nonsyndromic hearing loss 22 (40 variants)
• Inborn genetic diseases (33 variants)
• Rare genetic deafness (7 variants)
• OTOA-related condition (4 variants)
• Hearing impairment (2 variants)
• Usher syndrome (1 variants)
• Hearing loss, autosomal recessive (1 variants)
• Autosomal recessive nonsyndromic hearing loss 7 (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.

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	48	5	55
missense		2	110	6	2	120
nonsense	4	3				7
start loss						0
frameshift	13	7				20
inframe indel						0
splice donor/acceptor (+/-2bp)	5	6				11
splice region		1	3	17	1	22
non coding			1	70	46	117
Total	22	18	113	124	53

Highest pathogenic variant AF is 0.0000263

Variants in OTOA

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

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

Position	Type	Phenotype	Significance	ClinVar
16-21678250-A-T			Likely benign (Jul 10, 2018)
16-21678407-CAT-C			Likely benign (Oct 04, 2019)
16-21678407-C-CAT			Benign (Oct 07, 2019)
16-21678452-G-GTA			Benign (Aug 21, 2019)
16-21678454-G-A			Benign (Aug 15, 2019)
16-21678470-T-A			Benign (Jun 24, 2018)
16-21678526-A-G			Likely benign (Aug 14, 2023)
16-21678532-G-A			Likely benign (Jan 07, 2024)
16-21678534-CAT-C			Pathogenic (Aug 05, 2023)
16-21678538-C-T			Likely benign (Nov 17, 2023)
16-21678542-C-T			Uncertain significance (Sep 21, 2022)
16-21678558-T-A		not specified	Benign (Feb 01, 2024)
16-21678571-A-C			Likely benign (Sep 20, 2023)
16-21678571-A-T			Conflicting classifications of pathogenicity (Aug 18, 2023)
16-21678577-G-A			Likely benign (Jan 07, 2024)
16-21678583-TAC-T			Pathogenic (Jul 14, 2023)
16-21678586-A-G			Likely benign (Jan 24, 2024)
16-21678592-A-G			Likely benign (Mar 22, 2023)
16-21678600-G-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
16-21678606-G-A			Likely pathogenic (Sep 01, 2023)
16-21678606-G-T			Pathogenic (Dec 22, 2023)
16-21678614-T-C			Likely benign (Jul 19, 2023)
16-21678895-A-G			Likely benign (Sep 05, 2023)
16-21678898-C-A			Likely benign (Dec 29, 2022)
16-21678898-C-G			Likely benign (Nov 08, 2023)

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