OTOL1

otolin 1, the group of C1q and TNF related

Basic information

Region (hg38): 3:161496807-161503942

Links

ENSG00000182447 ∙ NCBI:131149 ∙ ∙ HGNC:34071 ∙ Uniprot:A6NHN0 ∙ 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 OTOL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOL1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in OTOL1

This is a list of pathogenic ClinVar variants found in the OTOL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-161496908-A-G		not specified	Uncertain significance (Jan 10, 2022)
3-161497097-T-G		not specified	Uncertain significance (Aug 21, 2023)
3-161497130-T-C		not specified	Uncertain significance (Nov 21, 2023)
3-161499178-A-C		not specified	Uncertain significance (Oct 25, 2022)
3-161499242-G-T		not specified	Uncertain significance (Aug 16, 2022)
3-161499249-A-G		not specified	Uncertain significance (Jul 14, 2023)
3-161502327-G-C		not specified	Uncertain significance (Jan 29, 2024)
3-161502363-G-T		not specified	Uncertain significance (Jan 17, 2024)
3-161503089-G-C		not specified	Uncertain significance (Jan 04, 2022)
3-161503098-G-C		not specified	Uncertain significance (May 23, 2023)
3-161503102-C-G		not specified	Uncertain significance (Aug 23, 2021)
3-161503151-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-161503196-G-A		not specified	Uncertain significance (Jun 02, 2024)
3-161503229-A-G		not specified	Uncertain significance (Sep 30, 2021)
3-161503247-T-A		not specified	Uncertain significance (Jun 09, 2022)
3-161503262-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-161503344-G-A		not specified	Likely benign (Apr 26, 2023)
3-161503403-G-A		not specified	Uncertain significance (Jul 20, 2021)
3-161503472-A-G		not specified	Uncertain significance (May 08, 2023)
3-161503536-C-T		not specified	Uncertain significance (May 30, 2024)
3-161503546-C-A		not specified	Uncertain significance (Oct 05, 2023)
3-161503590-A-G		not specified	Uncertain significance (Jan 31, 2023)
3-161503640-G-A		not specified	Uncertain significance (Jun 06, 2023)
3-161503640-G-C		not specified	Uncertain significance (Feb 23, 2023)
3-161503679-T-C		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOL1	protein_coding	protein_coding	ENST00000327928	4	7135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-15	0.00180	124536	0	92	124628	0.000369

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.967	270	229	1.18	0.0000114	3042
Missense in Polyphen		77	69.35	1.1103		847
Synonymous	-0.0368	85	84.6	1.01	0.00000441	970
Loss of Function	-1.09	20	15.4	1.30	8.81e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000343	0.000342
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00168	0.00167
Finnish	0.000511	0.000511
European (Non-Finnish)	0.000313	0.000301
Middle Eastern	0.00168	0.00167
South Asian	0.000230	0.000229
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Collagen-like protein specifically expressed in the inner ear, which provides an organic scaffold for otoconia, a calcium carbonate structure in the saccule and utricle of the ear. Acts as a scaffold for biomineralization: sequesters calcium and forms interconnecting fibrils between otoconia that are incorporated into the calcium crystal structure. Together with OC90, modulates calcite crystal morphology and growth kinetics. {ECO:0000250|UniProtKB:Q4ZJM7}.

Intolerance Scores

• loftool: 0.456
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Otol1

Gene ontology

• Biological process: extracellular matrix organization;otolith mineralization;protein homooligomerization
• Cellular component: extracellular region;collagen trimer;extracellular space;extracellular matrix
• Molecular function: extracellular matrix structural constituent;calcium ion binding