OTOP2

otopetrin 2

Basic information

Region (hg38): 17:74922950-74933912

Links

ENSG00000183034 ∙ NCBI:92736 ∙ OMIM:607827 ∙ HGNC:19657 ∙ Uniprot:Q7RTS6 ∙ 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 OTOP2 gene.

• not provided (3 variants)
• Usher syndrome type 1G (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOP2 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			33	2	2	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	4		24	5		33
Total	4	0	57	7	2

Highest pathogenic variant AF is 0.00000657

Variants in OTOP2

This is a list of pathogenic ClinVar variants found in the OTOP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74922954-G-A			Uncertain significance (Feb 19, 2022)
17-74922961-C-T		Usher syndrome type 1G	Pathogenic (Feb 20, 2021)
17-74922961-CAG-C			Pathogenic (Dec 01, 2023)
17-74922973-G-T			Uncertain significance (Feb 02, 2022)
17-74922974-T-A		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
17-74922978-G-A			Likely benign (Oct 01, 2022)
17-74922980-C-T		Inborn genetic diseases	Uncertain significance (Apr 20, 2024)
17-74922984-C-T			Likely benign (Oct 18, 2021)
17-74922986-C-T		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
17-74922988-T-TC		Usher syndrome type 1G	Pathogenic (Feb 28, 2023)
17-74922989-C-CG			Pathogenic (Jan 15, 2024)
17-74922990-G-A		not specified	Likely benign (Sep 03, 2010)
17-74922991-G-A		not specified • Usher syndrome type 1G	Conflicting classifications of pathogenicity (Oct 17, 2022)
17-74922998-T-G		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
17-74923004-C-T		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
17-74923009-C-T			Uncertain significance (Aug 16, 2022)
17-74923028-G-C		Usher syndrome type 1	Uncertain significance (Mar 23, 2022)
17-74923029-C-T			Likely benign (Oct 13, 2022)
17-74923031-C-G		not specified • USH1G-related disorder	Uncertain significance (Sep 19, 2019)
17-74923044-C-G			Likely benign (Mar 11, 2022)
17-74923045-C-T			Uncertain significance (Jul 25, 2022)
17-74923046-G-A			Uncertain significance (Sep 27, 2022)
17-74923048-G-A			Uncertain significance (Jul 07, 2023)
17-74923052-C-G		Usher syndrome type 1G	Uncertain significance (May 22, 2022)
17-74923052-C-T			Uncertain significance (Jun 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOP2	protein_coding	protein_coding	ENST00000331427	6	9638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.59e-14	0.0223	125654	0	94	125748	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.306	334	350	0.954	0.0000204	3634
Missense in Polyphen		102	112.36	0.90781		1221
Synonymous	0.662	145	156	0.932	0.00000999	1190
Loss of Function	0.108	21	21.5	0.975	0.00000119	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000897	0.000887
Ashkenazi Jewish	0.000597	0.000595
East Asian	0.000437	0.000435
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000456	0.000448
Middle Eastern	0.000437	0.000435
South Asian	0.000230	0.000229
Other	0.000819	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-selective channel that specifically transports protons into cells. Proton-selective channel activity is probably required in cell types that use changes in intracellular pH for cell signaling or to regulate biochemical or developmental processes. {ECO:0000250|UniProtKB:Q80SX5}.

Intolerance Scores

• loftool: 0.823
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.88

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.275
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otop2

Gene ontology

• Biological process: proton transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: proton channel activity