TRPV1

transient receptor potential cation channel subfamily V member 1, the group of Transient receptor potential cation channels|Ankyrin repeat domain containing

Basic information

Region (hg38): 17:3565443-3609411

Previous symbols: [ "VR1" ]

Links

ENSG00000196689 ∙ NCBI:7442 ∙ OMIM:602076 ∙ HGNC:12716 ∙ Uniprot:Q8NER1 ∙ 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 TRPV1 gene.

• Inborn genetic diseases (43 variants)
• not provided (18 variants)
• Malignant hyperthermia of anesthesia (1 variants)
• Nephropathic cystinosis (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 TRPV1 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				5	3	8
missense		1	41	6	2	50
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	1	42	11	7

Variants in TRPV1

This is a list of pathogenic ClinVar variants found in the TRPV1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3566826-C-T		not specified	Uncertain significance (Feb 01, 2023)
17-3566832-C-T		not specified	Uncertain significance (Aug 26, 2022)
17-3566858-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-3566978-C-T		not specified	Uncertain significance (Jan 10, 2023)
17-3571516-C-T			Likely benign (Jun 13, 2018)
17-3571589-T-G		not specified	Uncertain significance (Apr 17, 2023)
17-3572182-C-T		not specified	Uncertain significance (Jan 08, 2024)
17-3572188-C-T		Malignant hyperthermia of anesthesia	Uncertain significance (Feb 26, 2021)
17-3572231-C-A		not specified	Uncertain significance (Dec 12, 2023)
17-3573719-T-G		not specified	Uncertain significance (Jun 30, 2022)
17-3573863-C-T			Likely benign (Jun 05, 2018)
17-3573871-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-3573879-A-C			Benign (Apr 16, 2018)
17-3573890-A-G		not specified	Uncertain significance (May 11, 2022)
17-3573898-G-A		not specified	Uncertain significance (Dec 28, 2023)
17-3573900-C-T			Benign (Jun 10, 2018)
17-3573901-G-A			Likely benign (Jul 06, 2018)
17-3577139-G-C			Likely benign (Jul 19, 2018)
17-3577170-C-T		not specified	Uncertain significance (Mar 07, 2024)
17-3577612-C-T		not specified	Uncertain significance (Oct 20, 2023)
17-3577644-G-T		not specified	Uncertain significance (Feb 13, 2024)
17-3577668-C-T		not specified	Uncertain significance (Sep 07, 2022)
17-3580491-T-C			Benign (Jul 19, 2018)
17-3583394-G-T			Likely benign (Aug 15, 2018)
17-3583414-T-G		not specified	Uncertain significance (Feb 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPV1	protein_coding	protein_coding	ENST00000571088	15	31655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-16	0.127	124996	0	166	125162	0.000663

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.466	475	504	0.942	0.0000311	5421
Missense in Polyphen		167	176.58	0.94577		1848
Synonymous	-1.43	258	230	1.12	0.0000168	1626
Loss of Function	1.15	29	36.5	0.795	0.00000186	417

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00207	0.00202
Ashkenazi Jewish	0.000310	0.000298
East Asian	0.000640	0.000608
Finnish	0.00164	0.00162
European (Non-Finnish)	0.000555	0.000538
Middle Eastern	0.000640	0.000608
South Asian	0.000366	0.000359
Other	0.000331	0.000328

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand-activated non-selective calcium permeant cation channel involved in detection of noxious chemical and thermal stimuli. Seems to mediate proton influx and may be involved in intracellular acidosis in nociceptive neurons. Involved in mediation of inflammatory pain and hyperalgesia. Sensitized by a phosphatidylinositol second messenger system activated by receptor tyrosine kinases, which involves PKC isozymes and PCL. Activation by vanilloids, like capsaicin, and temperatures higher than 42 degrees Celsius, exhibits a time- and Ca(2+)-dependent outward rectification, followed by a long-lasting refractory state. Mild extracellular acidic pH (6.5) potentiates channel activation by noxious heat and vanilloids, whereas acidic conditions (pH <6) directly activate the channel. Can be activated by endogenous compounds, including 12-hydroperoxytetraenoic acid and bradykinin. Acts as ionotropic endocannabinoid receptor with central neuromodulatory effects. Triggers a form of long-term depression (TRPV1-LTD) mediated by the endocannabinoid anandamine in the hippocampus and nucleus accumbens by affecting AMPA receptors endocytosis. {ECO:0000250|UniProtKB:O35433, ECO:0000269|PubMed:11050376, ECO:0000269|PubMed:11226139, ECO:0000269|PubMed:11243859, ECO:0000269|PubMed:12077606}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Serotonin and anxiety;Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels;Trk receptor signaling mediated by PI3K and PLC-gamma;Trk receptor signaling mediated by the MAPK pathway (Consensus)

Recessive Scores

• pRec: 0.258

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.16

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Trpv1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;fever generation;microglial cell activation;diet induced thermogenesis;peptide secretion;negative regulation of systemic arterial blood pressure;lipid metabolic process;cell surface receptor signaling pathway;chemosensory behavior;negative regulation of heart rate;negative regulation of mitochondrial membrane potential;glutamate secretion;cellular response to heat;positive regulation of apoptotic process;response to peptide hormone;positive regulation of nitric oxide biosynthetic process;behavioral response to pain;sensory perception of mechanical stimulus;thermoception;detection of temperature stimulus involved in thermoception;detection of temperature stimulus involved in sensory perception of pain;detection of chemical stimulus involved in sensory perception of pain;release of sequestered calcium ion into cytosol;protein homotetramerization;excitatory postsynaptic potential;smooth muscle contraction involved in micturition;positive regulation of gastric acid secretion;calcium ion transmembrane transport;cellular response to alkaloid;cellular response to ATP;cellular response to tumor necrosis factor;cellular response to acidic pH;cellular response to temperature stimulus;negative regulation of establishment of blood-brain barrier;calcium ion import across plasma membrane;response to capsazepine;cellular response to nerve growth factor stimulus
• Cellular component: mitochondrion;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;integral component of membrane;cell junction;intrinsic component of plasma membrane;dendritic spine membrane;neuronal cell body;postsynaptic membrane
• Molecular function: transmembrane signaling receptor activity;ion channel activity;extracellular ligand-gated ion channel activity;excitatory extracellular ligand-gated ion channel activity;calcium channel activity;protein binding;calmodulin binding;ATP binding;calcium-release channel activity;chloride channel regulator activity;phosphatidylinositol binding;identical protein binding;metal ion binding;phosphoprotein binding;temperature-gated ion channel activity