OTOP1

otopetrin 1

Basic information

Region (hg38): 4:4188726-4226929

Links

ENSG00000163982

∙ NCBI:133060 ∙ OMIM:607806 ∙ HGNC:19656 ∙ Uniprot:Q7RTM1 ∙ 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 OTOP1 gene.

not_specified (105 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTOP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000177998.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			100 clinvar	5 clinvar		105
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	100	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTOP1	protein_coding	protein_coding	ENST00000296358	6	38087

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.84e-24	0.0000125	125515	0	233	125748	0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.664	356	322	1.10	0.0000179	3874
Missense in Polyphen		117	106.19	1.1018		1369
Synonymous	-0.312	141	136	1.03	0.00000804	1267
Loss of Function	-1.95	30	20.5	1.47	0.00000103	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.000554	0.000554
European (Non-Finnish)	0.00130	0.00129
Middle Eastern	0.000436	0.000435
South Asian	0.000915	0.000915
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Proton-selective channel that specifically transports protons into cells (PubMed:29371428). Proton channel activity is only weakly-sensitive to voltage (By similarity). 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 (PubMed:29371428). In the vestibular system of the inner ear, required for the formation and function of otoconia, which are calcium carbonate crystals that sense gravity and acceleration (By similarity). Probably acts by maintaining the pH appropriate for formation of otoconia (By similarity). Regulates purinergic control of intracellular calcium in vestibular supporting cells (By similarity). May be involved in sour taste perception in sour taste cells by mediating entry of protons within the cytosol (By similarity). Also involved in energy metabolism, by reducing adipose tissue inflammation and protecting from obesity-induced metabolic dysfunction (By similarity). {ECO:0000250|UniProtKB:Q80VM9, ECO:0000269|PubMed:29371428}.;

Intolerance Scores

loftool: 0.927
rvis_EVS: 0.42
rvis_percentile_EVS: 77.26

Haploinsufficiency Scores

pHI: 0.0944
hipred: N
hipred_score: 0.264
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Otop1
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype;

Zebrafish Information Network

Gene name: otop1
Affected structure: otolith
Phenotype tag: abnormal
Phenotype quality: quality

Gene ontology

Biological process: detection of gravity;biomineral tissue development;cellular response to insulin stimulus;inner ear morphogenesis;negative regulation of interferon-gamma-mediated signaling pathway;proton transmembrane transport
Cellular component: integral component of plasma membrane
Molecular function: proton channel activity