OTOS

protein-coding

otospiralin

Gene summary

Otospiralin is synthesized by nonsensory cells (fibrocytes) of the inner ear, and downregulation of otospiralin in guinea pigs leads to deafness (Lavigne-Rebillard et al., 2003 [PubMed 12687421]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_148961.4

Inheritance

—

ClinVar variants

U:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.49

Max pathogenic AF

—

Genomic locus

chr2:240,139,026-240,144,562

External References & Databases

Ensembl (ENSG00000178602)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OTOS variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_148961.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_148961.4	RefSeq	NP_683764.1	3	MANE Select
ENST00000319460.2	Ensembl	ENSP00000322486.1	3	MANE Select
ENST00000391989.6	Ensembl	ENSP00000375849.2	3	Standard
ENST00000908574.1	Ensembl	ENSP00000578633.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sensory perception of sound

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391989
Coding exons: 3
Length: 5534
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125732
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.121	53	50.6	1.05	0.00000274	566
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.438

Gene Damage Prediction

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