OTOP3

otopetrin 3

Basic information

Region (hg38): 17:74935898-74949992

Links

ENSG00000182938 ∙ NCBI:347741 ∙ OMIM:607828 ∙ HGNC:19658 ∙ Uniprot:Q7RTS5 ∙ 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 OTOP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOP3 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				3		3
missense			53	6		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	53	9	0

Variants in OTOP3

This is a list of pathogenic ClinVar variants found in the OTOP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74941450-C-T		not specified	Uncertain significance (May 09, 2023)
17-74941473-G-A		not specified	Likely benign (Aug 12, 2021)
17-74941482-G-A		not specified	Likely benign (Aug 19, 2021)
17-74941498-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-74941552-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-74941555-G-A		not specified	Uncertain significance (May 24, 2024)
17-74941560-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-74941579-G-A		not specified	Uncertain significance (Dec 02, 2021)
17-74941582-A-G		not specified	Uncertain significance (Feb 16, 2023)
17-74941632-T-G		not specified	Uncertain significance (Oct 13, 2023)
17-74941641-A-T		not specified	Uncertain significance (Jul 12, 2022)
17-74941665-G-A		not specified	Likely benign (Jan 05, 2022)
17-74941700-G-A			Likely benign (Jan 01, 2023)
17-74941725-C-T		not specified	Uncertain significance (Mar 11, 2022)
17-74941735-A-G		not specified	Uncertain significance (Aug 17, 2021)
17-74941737-G-A		not specified	Uncertain significance (Dec 16, 2021)
17-74941747-C-G		not specified	Uncertain significance (Oct 26, 2021)
17-74941761-C-G		not specified	Uncertain significance (Feb 12, 2024)
17-74941795-C-G		not specified	Uncertain significance (Jun 05, 2023)
17-74941802-G-C		not specified	Uncertain significance (Sep 28, 2021)
17-74941807-G-A		not specified	Uncertain significance (May 15, 2023)
17-74941924-T-C		not specified	Uncertain significance (Oct 27, 2023)
17-74941949-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-74941976-G-T		not specified	Uncertain significance (Feb 17, 2022)
17-74942013-C-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOP3	protein_coding	protein_coding	ENST00000328801	7	14274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.69e-11	0.311	125452	1	295	125748	0.00118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.20	436	371	1.18	0.0000231	3772
Missense in Polyphen		151	133.81	1.1285		1472
Synonymous	0.527	155	164	0.948	0.0000106	1299
Loss of Function	0.984	19	24.2	0.784	0.00000134	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00265	0.00264
Ashkenazi Jewish	0.00279	0.00278
East Asian	0.000384	0.000381
Finnish	0.000141	0.000139
European (Non-Finnish)	0.00111	0.00111
Middle Eastern	0.000384	0.000381
South Asian	0.00180	0.00180
Other	0.00114	0.000978

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:Q80UF9}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.781
• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.57

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.177

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0680

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otop3
• Phenotype: cellular phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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