OTOGL

otogelin like

Basic information

Region (hg38): 12:80099536-80380880

Previous symbols: [ "C12orf64" ]

Links

ENSG00000165899 ∙ NCBI:283310 ∙ OMIM:614925 ∙ HGNC:26901 ∙ Uniprot:Q3ZCN5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 84B (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 84B (Definitive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 84B (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 84B (Definitive), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), 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 84B	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	23122586

ClinVar

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

• not provided (657 variants)
• not specified (149 variants)
• Inborn genetic diseases (115 variants)
• Autosomal recessive nonsyndromic hearing loss 84B (44 variants)
• Rare genetic deafness (13 variants)
• Hearing impairment (5 variants)
• OTOGL-related condition (3 variants)
• Nonsyndromic Hearing Loss, Recessive (2 variants)
• - (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOGL 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			7	77	18	102
missense		1	266	17	22	306
nonsense	13	12				25
start loss						0
frameshift	9	11				20
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2	9				11
splice region		1	17	16	8	42
non coding			4	112	124	240
Total	24	33	278	206	164

Highest pathogenic variant AF is 0.0000658

Variants in OTOGL

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

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

Position	Type	Phenotype	Significance	ClinVar
12-80209459-A-G		Autosomal recessive nonsyndromic hearing loss 84B	Pathogenic/Likely pathogenic (Mar 29, 2024)
12-80209465-C-A		not specified • Inborn genetic diseases • Autosomal recessive nonsyndromic hearing loss 84B	Uncertain significance (Aug 01, 2022)
12-80209470-G-A		Rare genetic deafness	Likely pathogenic (Apr 10, 2018)
12-80209486-C-T		Inborn genetic diseases	Uncertain significance (Jan 31, 2022)
12-80209493-TG-T		Autosomal recessive nonsyndromic hearing loss 84B	Pathogenic/Likely pathogenic (Apr 08, 2022)
12-80209509-A-T		Inborn genetic diseases	Uncertain significance (May 03, 2023)
12-80209515-G-A			Uncertain significance (Oct 25, 2019)
12-80209521-A-T			Likely benign (Mar 14, 2023)
12-80209626-A-T			Benign (Nov 12, 2018)
12-80209639-A-G			Benign (Dec 10, 2018)
12-80210549-A-G			Likely benign (Dec 31, 2018)
12-80210860-A-G		not specified	Benign/Likely benign (Jul 03, 2023)
12-80210862-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
12-80210867-A-G			Conflicting classifications of pathogenicity (Dec 22, 2023)
12-80210871-T-C		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
12-80210882-T-C		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
12-80210887-G-A		Rare genetic deafness	Likely pathogenic (Jun 30, 2022)
12-80210892-T-C			Uncertain significance (Aug 10, 2022)
12-80210893-A-G		not specified	Likely benign (Mar 01, 2024)
12-80210987-A-G			Likely benign (Dec 22, 2018)
12-80211020-A-C			Benign (Dec 10, 2018)
12-80211123-T-C			Likely benign (Dec 23, 2018)
12-80211952-C-T		OTOGL-related disorder	Likely benign (Jul 25, 2023)
12-80211953-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 14, 2022)
12-80211955-G-A			Benign (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOGL	protein_coding	protein_coding	ENST00000458043	58	169638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.70e-52	0.00469	124004	2	369	124375	0.00149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.578	1059	1.11e+3	0.951	0.0000543	15358
Missense in Polyphen		422	443.79	0.9509		6119
Synonymous	0.422	373	384	0.973	0.0000198	4033
Loss of Function	2.51	97	128	0.760	0.00000673	1760

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00214
Ashkenazi Jewish	0.00215	0.00209
East Asian	0.00188	0.00180
Finnish	0.000328	0.000324
European (Non-Finnish)	0.00201	0.00187
Middle Eastern	0.00188	0.00180
South Asian	0.00133	0.00121
Other	0.00173	0.00164

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0917

Haploinsufficiency Scores

• pHI: 0.0624
• hipred: N
• hipred_score: 0.491

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otogl

Zebrafish Information Network

• Gene name: otogl
• Affected structure: sagitta
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: sensory perception of sound;L-arabinose metabolic process
• Cellular component: extracellular region
• Molecular function: alpha-L-arabinofuranosidase activity