OTOR

otoraplin, the group of MIA family

Basic information

Region (hg38): 20:16748357-16770062

Links

ENSG00000125879 ∙ NCBI:56914 ∙ OMIM:606067 ∙ HGNC:8517 ∙ Uniprot:Q9NRC9 ∙ 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 OTOR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOR 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				1		1
missense			6	1	1	8
nonsense						0
start loss					1	1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	2

Variants in OTOR

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

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

Position	Type	Phenotype	Significance	ClinVar
20-16748403-T-C		not specified	Benign (Mar 29, 2016)
20-16748433-G-T		not specified	Uncertain significance (Dec 03, 2021)
20-16748471-G-T		not specified	Uncertain significance (Dec 13, 2023)
20-16748493-T-C		OTOR-related disorder	Benign (Oct 17, 2019)
20-16748891-A-G		not specified	Uncertain significance (Apr 30, 2024)
20-16748894-A-G		not specified	Uncertain significance (Jul 12, 2023)
20-16748904-T-C		OTOR-related disorder	Likely benign (Jul 15, 2019)
20-16748926-A-G		not specified	Uncertain significance (Dec 04, 2023)
20-16749943-A-T		not specified	Uncertain significance (Oct 27, 2021)
20-16749973-G-A		not specified	Likely benign (Jan 31, 2024)
20-16751108-T-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOR	protein_coding	protein_coding	ENST00000246081	4	21705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00488	0.708	125717	0	19	125736	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.458	82	71.1	1.15	0.00000385	829
Missense in Polyphen		26	23.387	1.1117		287
Synonymous	-0.207	27	25.7	1.05	0.00000157	230
Loss of Function	0.718	4	5.88	0.680	2.45e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000370	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000527
Middle Eastern	0.000370	0.000326
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.486
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.325

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otor

Gene ontology

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