OTOS

otospiralin

Basic information

Region (hg38): 2:240139026-240144562

Links

ENSG00000178602 ∙ NCBI:150677 ∙ OMIM:607877 ∙ HGNC:22644 ∙ Uniprot:Q8NHW6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOS 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in OTOS

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

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

Position	Type	Phenotype	Significance	ClinVar
2-240139190-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-240139199-C-G		not specified	Uncertain significance (Jul 25, 2023)
2-240139204-G-A		not specified	Uncertain significance (Dec 11, 2023)
2-240139207-C-T		not specified	Uncertain significance (Dec 02, 2022)
2-240139346-C-T		not specified	Uncertain significance (Jun 27, 2022)
2-240139353-G-T		not specified	Uncertain significance (Jul 09, 2021)
2-240140077-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-240140086-C-G		not specified	Uncertain significance (Apr 27, 2023)
2-240140280-C-A		not specified	Uncertain significance (May 03, 2023)
2-240140290-G-C		not specified	Uncertain significance (May 02, 2024)
2-240140313-A-T		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOS	protein_coding	protein_coding	ENST00000391989	3	5534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000210	0.164	125723	0	9	125732	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.121	53	50.6	1.05	0.00000274	566
Missense in Polyphen		22	20.276	1.085		214
Synonymous	-0.343	25	22.9	1.09	0.00000150	171
Loss of Function	-0.905	6	4.04	1.49	1.73e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000171	0.000163
South Asian	0.0000986	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be essential for the survival of the neurosensory epithelium of the inner ear. {ECO:0000250}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.746
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.296
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.438

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otos
• Phenotype: skeleton 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)

Gene ontology

• Biological process: sensory perception of sound
• Cellular component: extracellular region