TRPM3

gene
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Also known as KIAA1616LTRPC3GON-2

Summary

TRPM3 (transient receptor potential cation channel subfamily M member 3, HGNC:17992) is a protein-coding gene on chromosome 9q21.12-q21.13, encoding Transient receptor potential cation channel subfamily M member 3 (Q9HCF6). Constitutively active, non-selective divalent cation-conducting channel that is permeable to Ca(2+), Mn(2+), and Mg(2+), with a high permeability for Ca(2+).

The product of this gene belongs to the family of transient receptor potential (TRP) channels. TRP channels are cation-selective channels important for cellular calcium signaling and homeostasis. The protein encoded by this gene mediates calcium entry, and this entry is potentiated by calcium store depletion. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 80036 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): syndromic complex neurodevelopmental disorder (Definitive, ClinGen) — +6 more curated relationships
  • GWAS associations: 28
  • Clinical variants (ClinVar): 288 total — 4 likely-pathogenic
  • Phenotypes (HPO): 67
  • Druggable target: yes
  • MANE Select transcript: NM_001366145

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17992
Approved symbolTRPM3
Nametransient receptor potential cation channel subfamily M member 3
Location9q21.12-q21.13
Locus typegene with protein product
StatusApproved
AliasesKIAA1616, LTRPC3, GON-2
Ensembl geneENSG00000083067
Ensembl biotypeprotein_coding
OMIM608961
Entrez80036

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 22 protein_coding, 3 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000354500, ENST00000357533, ENST00000358082, ENST00000360823, ENST00000361823, ENST00000377097, ENST00000377101, ENST00000377105, ENST00000377110, ENST00000377111, ENST00000396280, ENST00000396283, ENST00000396285, ENST00000396292, ENST00000408909, ENST00000437699, ENST00000677594, ENST00000677713, ENST00000704565, ENST00000704566, ENST00000704567, ENST00000704568, ENST00000704569, ENST00000704571, ENST00000704573, ENST00000704574, ENST00000704575, ENST00000704576, ENST00000707140, ENST00000715550

RefSeq mRNA: 23 — MANE Select: NM_001366145 NM_001007470, NM_001007471, NM_001366141, NM_001366142, NM_001366143, NM_001366144, NM_001366145, NM_001366146, NM_001366147, NM_001366148, NM_001366149, NM_001366150, NM_001366151, NM_001366152, NM_001366153, NM_001366154, NM_020952, NM_024971, NM_206944, NM_206945, NM_206946, NM_206947, NM_206948

CCDS: CCDS43835, CCDS65064, CCDS6634, CCDS6635, CCDS6636, CCDS6637, CCDS94418, CCDS94419, CCDS94420

Canonical transcript exons

ENST00000677713 — 26 exons

ExonStartEnd
ENSE000014137037062548270625517
ENSE000015770917059103170591205
ENSE000015779427076160170761724
ENSE000015779437078410570784279
ENSE000015782257062007670620365
ENSE000015800117059841970598670
ENSE000015804547063521170635261
ENSE000015808847060334270603470
ENSE000015826957055316070553310
ENSE000015837347061590870616075
ENSE000015839437062519170625331
ENSE000015839727068150670681578
ENSE000015840877054954270549674
ENSE000015850267082784770828018
ENSE000015853347055284470553043
ENSE000015857697063906070639194
ENSE000015876127061060970610749
ENSE000015884217062124470621273
ENSE000016039827064056070640660
ENSE000016104307061886770619095
ENSE000035274957084300370843127
ENSE000035624827086290870863112
ENSE000036417267084637870846591
ENSE000036499587086443270864511
ENSE000039049817112117871121621
ENSE000039069107052906070537405

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 99.00.

FANTOM5 (CAGE): breadth broad, TPM avg 5.7626 / max 764.0838, expressed in 372 samples.

FANTOM5 promoters (19 alternative TSS)

Promoter IDTPM avgSamples expressed
1008831.7925227
1008901.1218196
1008951.0316162
1008910.4969172
1008940.2952107
1008920.2253115
1008820.204755
1009040.188753
1008840.136743
1008930.092555

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
pigmented layer of retinaUBERON:000178299.00gold quality
dorsal motor nucleus of vagus nerveUBERON:000287093.35gold quality
medial globus pallidusUBERON:000247789.69gold quality
buccal mucosa cellCL:000233689.18gold quality
globus pallidusUBERON:000187588.43gold quality
sural nerveUBERON:001548888.02gold quality
inferior olivary complexUBERON:000212787.39gold quality
lateral globus pallidusUBERON:000247685.24gold quality
cerebellar vermisUBERON:000472084.69gold quality
superior vestibular nucleusUBERON:000722784.61gold quality
substantia nigra pars compactaUBERON:000196584.07gold quality
primary visual cortexUBERON:000243683.87gold quality
medulla oblongataUBERON:000189683.79gold quality
substantia nigra pars reticulataUBERON:000196683.46gold quality
Brodmann (1909) area 23UBERON:001355483.45gold quality
ponsUBERON:000098883.40gold quality
cerebellumUBERON:000203783.17gold quality
choroid plexus epitheliumUBERON:000391183.11gold quality
endothelial cellCL:000011582.20silver quality
cerebellar cortexUBERON:000212982.17gold quality
ventral tegmental areaUBERON:000269182.14gold quality
cerebellar hemisphereUBERON:000224582.02gold quality
right hemisphere of cerebellumUBERON:001489081.46gold quality
postcentral gyrusUBERON:000258181.29gold quality
adult mammalian kidneyUBERON:000008281.06gold quality
occipital lobeUBERON:000202180.71gold quality
cortical plateUBERON:000534380.58gold quality
nephron tubuleUBERON:000123180.28gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.04gold quality
midbrainUBERON:000189179.95gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 9.

ExperimentMarker?Max mean expression
E-HCAD-25yes3568.47
E-GEOD-180759yes3479.28
E-CURD-119yes2359.06
E-GEOD-137537yes1395.93
E-MTAB-9154yes886.93
E-HCAD-35yes86.34
E-MTAB-7316yes22.70
E-GEOD-135922yes18.78
E-GEOD-131882no2498.97
E-MTAB-6108no867.68
E-GEOD-109979no128.63
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EGR1, PAX6

miRNA regulators (miRDB)

84 targeting TRPM3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-MIR-428299.9975.366408
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548AN99.9770.912817
HSA-MIR-50799.9770.111915
HSA-MIR-391099.9571.132227
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-464899.9167.00710
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-449299.8768.253611
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-432099.7565.80793
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-430699.7270.503630
HSA-MIR-10393-3P99.7266.56961
HSA-MIR-6801-5P99.7266.50981

Literature-anchored findings (GeneRIF, showing 40)

  • The hTRPM3 gene is comprised of 24 exons and maps to chromosome 9q-21.12 and is composed of 1555 amino acids with the characteristic six-transmembrane domain of TRPs and is expressed in kidney and, at lesser levels, in brain, testis, and spinal cord (PMID:12672827)
  • TRPM3 is the first ion channel activated by sphingolipids. (PMID:15550678)
  • the divalent cation selectivity of TRPM3 channels is regulated by altenrative splicing (PMID:15824111)
  • we give an overview of the identified TRPM3 variants and compare their functional properties–{REVIEW} (PMID:17217062)
  • TRPM3 may have diverse cellular functions depending on the expression of a particular variant while TRPV4 plays a central role in epithelial homoeostasis by modulating epithelial barrier function [review] (PMID:17233610)
  • TRPM3 did not reveal a otosclerosis-causing mutation (PMID:18224337)
  • data suggest functional relevance of TRPM3 in contractile and proliferating phenotypes of vascular smooth muscle cells (PMID:20360246)
  • Our data establish that TRPM3 channels constitute a regulated entry pathway for zinc ions in pancreatic beta-cells (PMID:20401728)
  • The inhibition of TRPM1 by zinc ions is primarily due to a short stretch of seven amino acids present only in the pore region of TRPM1 but not of TRPM3. (PMID:21278253)
  • Progesterone (0.01-10muM) suppressed TRPM3 activity evoked by pregnenolone sulphate. (PMID:22000496)
  • Calmodulin and S100A1 protein interact with N terminus of TRPM3 channel. (PMID:22451665)
  • TRPM3-ICF deletion mutation variants are regulatory channel subunits fine-tuning TRPM3 channel activity. (PMID:22961981)
  • Data using recombinant proteins expressed in vascular endothelial cells suggest that SigmaR1 (sigma 1-type opioid receptor) is not involved in regulation of calcium signaling via TRPC5/TRPM3 (transient receptor potential cation channels C5/M3). (PMID:23121507)
  • Pregnenolone sulfate is a powerful activator of TRPM3-mediated gene transcription, while transcription is completely inhibited by mefenamic acid in cells expressing activated TRPM3 channels. (PMID:24895737)
  • Missense mutation in the cation channel, TRPM3, underlies inherited cataract and glaucoma. (PMID:25090642)
  • The von Hippel-Lindau tumor suppressor (VHL) represses TRPM3 directly through miR-204 and indirectly through another miR-204 target, Caveolin 1. (PMID:25517751)
  • TRPM3 channel activation changes the gene expression pattern of the cells by activating transcription of c-Jun-, ATF2-, and TCF-controlled genes. (PMID:25576487)
  • The TRPM3 activity is rapidly and reversibly inhibited by activation of phosphatases. (PMID:26123194)
  • TRPM3 is a phosphoinositide-dependent ion channel. (PMID:26123195)
  • Activation of TRPM3 channels increases the transcriptional activation potential of c-Fos in HEK293 cells. (PMID:26493679)
  • Phosphoinositols regulate TRPM3. (PMID:26517445)
  • This is the first study to examine the involvement of TRPM channel gene variations on the risk of SSc incidence. Our results suggest roles of TRPM3 and TRPM5 gene variants in the susceptibility to or clinical expression of Systemic sclerosis (PMID:26546534)
  • rs10780946 TRPM3 polymorphism is associated with asthma-exacerbated respiratory disease susceptibility. (PMID:26891941)
  • this study shows that differential expression of TRPM3 and Ca2+ flux between NK cell subtypes may provide evidence for their role in the pathomechanism involving NK cell cytotoxicity activity in chronic fatigue syndrome/myalgic encephalomyelitis (PMID:27727448)
  • Genetic experiments revealed that the basic region leucine zipper proteins c-Jun and ATF2 and the ternary complex factor Elk-1 are essential to couple TRPM3 channel stimulation with the IL-8 gene. (PMID:28982580)
  • Mutations of lysine residues in calmodulin binding site 2, strongly reduced calmodulin binding and TRPM3 activity indicating the importance of this domain for TRMP3-mediated calcium signaling. (PMID:29880196)
  • In the three-stage genome-wide association study in South Korean population the signal in TRPM3 showed the most robust association with thyroid nodules, and those in MIBP/NKX2-1 also demonstrated a possible association. A rs4745021 variant at TRPM3 reached the genome-wide significance threshold in the meta-analysis. (PMID:30099483)
  • TRPM3 activity is impaired in Chronic Fatigue Syndrome/ Myalgic Encephalomyelitis (CFS/ME) patients suggesting changes in intracellular Ca2+ concentration, which may impact NK cellular functions. This investigation further helps to understand the intracellular-mediated roles in NK cells and confirm the potential role of TRPM3 ion channels in the aetiology and pathomechanism of CFS/ME. (PMID:30134818)
  • The fact that TRPM3 channel stimulation activates Elk-1 connects TRPM3 with the biological functions of Elk-1, including the regulation of proliferation, differentiation, survival, transcription, and cell migration. (PMID:30552902)
  • Study confirmed a significant reduction in amplitude of TRPM3 currents after pregnenolone sulfate stimulation in isolated NK cells from another cohort of CFS/ME patients compared with healthy controls. (PMID:31014226)
  • Our findings suggest that TRPM3 is a locus for ID and epilepsy, and should be included in genetic panels targeting these indications. (PMID:31278393)
  • activation of Gs- and Gq-coupled G-protein-coupled receptors in recombinant cells and sensory neurons inhibits TRPM3 via Gbetagamma liberation (PMID:31451581)
  • Naltrexone Restores Impaired Transient Receptor Potential Melastatin 3 Ion Channel Function in Natural Killer Cells From Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients. (PMID:31736966)
  • Transient receptor potential melastatin 2 channels are overexpressed in myalgic encephalomyelitis/chronic fatigue syndrome patients. (PMID:31796045)
  • Functional expression and pharmacological modulation of TRPM3 in human sensory neurons. (PMID:31985045)
  • Disease-associated mutations in the human TRPM3 render the channel overactive via two distinct mechanisms. (PMID:32343227)
  • Gain of channel function and modified gating properties in TRPM3 mutants causing intellectual disability and epilepsy. (PMID:32427099)
  • Machine-Learned Association of Next-Generation Sequencing-Derived Variants in Thermosensitive Ion Channels Genes with Human Thermal Pain Sensitivity Phenotypes. (PMID:32575443)
  • The structural basis for an on-off switch controlling Gbetagamma-mediated inhibition of TRPM3 channels. (PMID:33122432)
  • TRPM3 channel activation inhibits contraction of the isolated human ureter via CGRP released from sensory nerves. (PMID:33417951)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_reriotrpm3ENSDARG00000039181
mus_musculusTrpm3ENSMUSG00000052387
rattus_norvegicusTrpm3ENSRNOG00000027770
drosophila_melanogasterTrpmFBGN0265194
caenorhabditis_elegansWBGENE00000425
caenorhabditis_elegansgon-2WBGENE00001651
caenorhabditis_elegansWBGENE00004149
caenorhabditis_elegansWBGENE00020972
caenorhabditis_elegansWBGENE00021404
caenorhabditis_elegansWBGENE00021408

Paralogs (7): TRPM5 (ENSG00000070985), TRPM7 (ENSG00000092439), TRPM6 (ENSG00000119121), TRPM4 (ENSG00000130529), TRPM1 (ENSG00000134160), TRPM2 (ENSG00000142185), TRPM8 (ENSG00000144481)

Protein

Protein identifiers

Transient receptor potential cation channel subfamily M member 3Q9HCF6 (reviewed: Q9HCF6)

Alternative names: Long transient receptor potential channel 3, Melastatin-2

All UniProt accessions (21): Q9HCF6, A0A7I2V4C9, A0A7I2V4E8, A0A994J4I2, A0A994J4R7, A0A994J557, A0A994J563, A0A994J743, A0A994J747, A0A994J7I1, A0AA34QVQ9, A0AAQ5BIH5, A2A3F3, A2A3F4, A2A3F7, E9PBI7, G5E9G1, H0Y3D4, H7BYP1, Q4VXD4, Q504Y1

UniProt curated annotations — full annotation on UniProt →

Function. Constitutively active, non-selective divalent cation-conducting channel that is permeable to Ca(2+), Mn(2+), and Mg(2+), with a high permeability for Ca(2+). However, can be enhanced by increasing temperature and by ligands, including the endogenous neurosteroid pregnenolone sulfate and sphingosine-1 and suppressed by intracellular Mg(2+). Implicated in a variety of cellular processes, including insulin/peptide secretion, vascular constriction and dilation, noxious heat sensing, inflammatory and spontaneous pain sensitivity. In neurons of the dorsal root ganglia, functions as thermosensitive channel for the detection of noxious heat and spontaneous pain. Suggested to function as an ionotropic steroid receptor in beta-cell, indeed pregnenolone sulfate leads to Ca(2+) influx and enhanced insulin secretion. Mediates Zn(2+) uptake into the lumen of pancreatic beta cell secretory granules, thereby regulating insulin secretion. Forms heteromultimeric ion channels with TRPM1 which are permeable for Ca(2+) and Zn(2+) ions. Exists as multiple splice variants which differ significantly in their biophysical properties.

Subunit / interactions. Homotetramer. Interacts with TRPM1; the interaction results in the formation of a heteromultimeric cation channel complex that are functionally different from the homomeric channels.

Subcellular location. Cell membrane.

Tissue specificity. Expressed primarily in the kidney and, at lower levels, in brain, testis, ovary, pancreas and spinal cord. Expression in the brain and kidney was determined at protein level. In the kidney, expressed predominantly in the collecting tubular epithelium in the medulla, medullary rays, and periglomerular regions; in the brain, highest levels are found in the cerebellum, choroid plexus, the locus coeruleus, the posterior thalamus and the substantia nigra. Down-regulated in renal tumors compared to normal kidney. Expressed in the lens.

Disease relevance. Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (NEDFSS) [MIM:620224] An autosomal dominant disorder characterized by global developmental delay, moderate to severely impaired intellectual development, poor or absent speech, congenital hypotonia, dysmorphic facial features, exotropia, and musculoskeletal issues such as hip dysplasia, hip dislocation and scoliosis. About half of patients develop various types of seizures. The disease is caused by variants affecting the gene represented in this entry. Cataract 50 with or without glaucoma (CTRCT50) [MIM:620253] A form of cataract, an opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. CTRCT50 is an autosomal dominant form characterized by early onset. Affected individuals may also exhibit high-tension glaucoma and variable anterior segment defects. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Activated by the neurosteroid pregnelonone sulfate (PregS); PregS activates the channel by shifting its current-voltage activation curve toward more negative membrane potentials and also potentiates temperature-induced activation. Activated by sphingosine. Activated by heat. Intracellular Ca(2+) inhibits TRPM3 probably via interaction with Ca(2+)/calmodulin. Intracellular Mg(2+) inhibits TRPM3 activity. Both intracellular and extracellular protons block TRPM3 through probable binding sites in the pore region. Positively regulated by phosphoinositide phosphoinositol 4,5-biphosphate (PI(4,5)P2). Strongly inhibited by activation of G(i)-coupled receptors via direct binding with G-betagamma-subunits of heterotrimeric G-proteins.

Similarity. Belongs to the transient receptor (TC 1.A.4) family. LTrpC subfamily. TRPM3 sub-subfamily.

Isoforms (11)

UniProt IDNamesCanonical?
Q9HCF6-11, TRPM3fyes
Q9HCF6-22, TRPM3a
Q9HCF6-33, TRPM3b
Q9HCF6-44, TRPM3d
Q9HCF6-55, TRPM3e
Q9HCF6-66, TRPM3c
Q9HCF6-77
Q9HCF6-88
Q9HCF6-1010
Q9HCF6-1111
Q9HCF6-1212

RefSeq proteins (23): NP_001007471, NP_001007472, NP_001353070, NP_001353071, NP_001353072, NP_001353073, NP_001353074, NP_001353075, NP_001353076, NP_001353077, NP_001353078, NP_001353079, NP_001353080, NP_001353081, NP_001353082, NP_001353083, NP_066003, NP_079247, NP_996827, NP_996828, NP_996829, NP_996830, NP_996831 (=MANE)

Domains & families (InterPro)

IDNameType
IPR005821Ion_trans_domDomain
IPR032415TRPM_tetraDomain
IPR037162TRPM_tetra_sfHomologous_superfamily
IPR041491TRPM_SLOGDomain
IPR050927TRPMFamily
IPR057366TRPM-likeDomain

Pfam: PF00520, PF16519, PF18139, PF25508

Catalyzed reactions (Rhea), 4 shown:

  • Mn(2+)(in) = Mn(2+)(out) (RHEA:28699)
  • Zn(2+)(in) = Zn(2+)(out) (RHEA:29351)
  • Ca(2+)(in) = Ca(2+)(out) (RHEA:29671)
  • Mg(2+)(in) = Mg(2+)(out) (RHEA:29827)

UniProt features (54 total): splice variant 10, sequence variant 8, topological domain 7, region of interest 7, transmembrane region 6, compositionally biased region 4, sequence conflict 4, binding site 3, mutagenesis site 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9J84ELECTRON MICROSCOPY4.21

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HCF6-F164.700.15

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 796; 1017; 1018

Mutagenesis-validated functional residues (3):

PositionPhenotype
1084enhances ph sensitivity.
1087enhances ph sensitivity.
1098less sensitivity toward protons.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-3295583TRP channels

MSigDB gene sets: 311 (showing top): GOBP_PROTEIN_HOMOTETRAMERIZATION, GOBP_TRANSITION_METAL_ION_TRANSPORT, FOXO4_01, GOBP_MONOATOMIC_CATION_TRANSPORT, IRF7_01, GATA3_01, PU1_Q6, AACTTT_UNKNOWN, GOBP_PROTEIN_HOMOOLIGOMERIZATION, ZHANG_BREAST_CANCER_PROGENITORS_UP, IK3_01, GOBP_CALCIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_PROTEIN_TETRAMERIZATION, GOBP_TRANSMEMBRANE_TRANSPORT, TGGAAA_NFAT_Q4_01

GO Biological Process (10): monoatomic cation transport (GO:0006812), calcium ion transport (GO:0006816), protein homotetramerization (GO:0051289), calcium ion transmembrane transport (GO:0070588), zinc ion transmembrane transport (GO:0071577), monoatomic cation transmembrane transport (GO:0098655), monoatomic ion transport (GO:0006811), monoatomic ion transmembrane transport (GO:0034220), protein tetramerization (GO:0051262), transmembrane transport (GO:0055085)

GO Molecular Function (7): monoatomic cation channel activity (GO:0005261), calcium channel activity (GO:0005262), calmodulin binding (GO:0005516), phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), G-protein beta/gamma-subunit complex binding (GO:0031683), monoatomic ion channel activity (GO:0005216), metal ion transmembrane transporter activity (GO:0046873)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Stimuli-sensing channels1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
monoatomic ion transport2
metal ion transport2
monoatomic cation transmembrane transport2
transport2
monoatomic cation transmembrane transporter activity2
protein homooligomerization1
protein tetramerization1
calcium ion transport1
zinc ion transport1
monoatomic cation transport1
monoatomic ion transmembrane transport1
transmembrane transport1
protein complex oligomerization1
cellular process1
monoatomic ion channel activity1
monoatomic cation channel activity1
calcium ion transmembrane transporter activity1
protein binding1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
protein-containing complex binding1
monoatomic ion transmembrane transporter activity1
channel activity1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

1132 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRPM3TRPV2Q9Y5S1822
TRPM3TRPA1O75762813
TRPM3TRPV1Q8NER1792
TRPM3TRPV3Q8NET8784
TRPM3TRPV4Q9HBA0784
TRPM3PKD2Q13563750
TRPM3TRPC1P48995716
TRPM3TJP2Q9UDY2684
TRPM3KLF9Q13886667
TRPM3MCOLN1Q9GZU1622
TRPM3TRPC6Q9Y210599
TRPM3CALM1P02593568
TRPM3PKD2L1Q9P0L9564
TRPM3ANK1P16157563
TRPM3S100A1P23297534

IntAct

22 interactions, top by confidence:

ABTypeScore
PHC1CBX4psi-mi:“MI:0914”(association)0.790
OSMIL6STpsi-mi:“MI:0914”(association)0.760
CHCHD10CLPXpsi-mi:“MI:0914”(association)0.640
NHLH2AP3B1psi-mi:“MI:0914”(association)0.530
PRR20ESIAH2psi-mi:“MI:0914”(association)0.530
H1-7psi-mi:“MI:0914”(association)0.350
LRP3TMEM131Lpsi-mi:“MI:0914”(association)0.350
SENP3POTEFpsi-mi:“MI:0914”(association)0.350
TFPTKRBA1psi-mi:“MI:0914”(association)0.350
CXCL14DCTN6psi-mi:“MI:0914”(association)0.350
ZRSR2U2SURPpsi-mi:“MI:0914”(association)0.350
DDX54SYNCRIPpsi-mi:“MI:0914”(association)0.350
AKAP17ANOS1APpsi-mi:“MI:0914”(association)0.350
GNLYPRKCIpsi-mi:“MI:0914”(association)0.350
DDX54MYO1Fpsi-mi:“MI:0914”(association)0.350
BHLHA15RNASEH1psi-mi:“MI:0914”(association)0.350
CLEC3AMACROH2A1psi-mi:“MI:0914”(association)0.350
TNFRSF13BCYBApsi-mi:“MI:0914”(association)0.350
DDX54CLPXpsi-mi:“MI:0914”(association)0.350
ESRRGTTRpsi-mi:“MI:0914”(association)0.350

BioGRID (30): TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS), TRPM3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IMY7, A0JPA0, A2AP18, A8DYE2, J9SQF3, O00329, O35904, O75038, P0C1Q3, P0C588, P19687, P33402, P48736, P97557, Q02108, Q09M05, Q148L1, Q1LWG4, Q2TV84, Q2WEA5, Q3USB7, Q4ZHS0, Q502J0, Q5EBA1, Q60565, Q62688, Q69ZF7, Q6P4Q7, Q6PA06, Q7L5N7, Q7TN37, Q7Z2W7, Q7Z4N2, Q80YD1, Q8BTI9, Q8BYI6, Q8BZN2, Q8CIR4, Q8NHH9, Q8R455

Diamond homologs: A0A0R4IMY7, A7T1N0, A8DYE2, E9PTA2, J9SQF3, O94759, Q2TV84, Q2WEA5, Q5XIG0, Q7TN37, Q7Z2W7, Q7Z4N2, Q8BVU5, Q8R455, Q8R4D5, Q8TD43, Q91YD4, Q9BW91, Q9ESQ5, Q9HCF6, Q9JJH7, Q9NZQ8, S5UH55, Q09297, Q8CIR4, Q923J1, Q925B3, Q96QT4, Q9BX84, Q93971, O00418, O01991, P42527, P90648, Q54SF9, Q6B9X6, Q8MY12, Q54DK4, Q86TB3, Q91ZB0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

288 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic4
Uncertain significance221
Likely benign24
Benign16

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1516729NM_001366145.2(TRPM3):c.3428G>A (p.Arg1143Lys)Likely pathogenic
2412979NM_001366145.2(TRPM3):c.3431A>G (p.Tyr1144Cys)Likely pathogenic
2580894NM_001366145.2(TRPM3):c.3397T>C (p.Ser1133Pro)Likely pathogenic
4077407NM_001366145.2(TRPM3):c.1840-25_1852delLikely pathogenic

SpliceAI

6379 predictions. Top by Δscore:

VariantEffectΔscore
9:70537401:CCACC:Cacceptor_gain1.0000
9:70537402:CACC:Cacceptor_gain1.0000
9:70537402:CACCC:Cacceptor_gain1.0000
9:70537404:CC:Cacceptor_gain1.0000
9:70537404:CCCT:Cacceptor_loss1.0000
9:70537405:CC:Cacceptor_gain1.0000
9:70537405:CCTG:Cacceptor_loss1.0000
9:70537406:C:CCacceptor_gain1.0000
9:70537406:C:CGacceptor_loss1.0000
9:70537407:T:Cacceptor_loss1.0000
9:70549537:CACA:Cdonor_loss1.0000
9:70549538:ACACC:Adonor_loss1.0000
9:70549539:CACCT:Cdonor_loss1.0000
9:70549540:ACCT:Adonor_loss1.0000
9:70549541:CCTTT:Cdonor_gain1.0000
9:70549551:G:Cdonor_gain1.0000
9:70549560:AT:Adonor_gain1.0000
9:70549670:GAGTT:Gacceptor_gain1.0000
9:70549671:AGTT:Aacceptor_gain1.0000
9:70549672:GTT:Gacceptor_gain1.0000
9:70549673:TT:Tacceptor_gain1.0000
9:70549673:TTC:Tacceptor_loss1.0000
9:70549674:TCTG:Tacceptor_loss1.0000
9:70549675:C:CCacceptor_gain1.0000
9:70549675:C:CGacceptor_loss1.0000
9:70549677:G:Cacceptor_gain1.0000
9:70552305:T:TAdonor_gain1.0000
9:70552842:A:ACdonor_gain1.0000
9:70552843:C:CCdonor_gain1.0000
9:70552843:CT:Cdonor_gain1.0000

AlphaMissense

11420 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000003962 (9:70933707 T>G), RS1000007117 (9:71110524 T>C), RS1000015646 (9:70697684 T>C), RS1000020072 (9:71380843 A>G), RS1000020852 (9:70565022 C>A,T), RS1000021828 (9:71283096 C>T), RS1000022517 (9:70651845 A>C), RS1000022830 (9:70872503 G>T), RS1000029266 (9:71396737 C>A), RS1000033783 (9:70670828 C>T), RS1000035167 (9:70702121 G>A,T), RS1000036384 (9:70933462 A>T), RS1000041967 (9:70785347 T>G), RS1000046705 (9:71165102 C>A,G,T), RS1000050630 (9:70924028 C>T)

Disease associations

OMIM: gene MIM:608961 | disease phenotypes: MIM:620224, MIM:620253, MIM:253250, MIM:612292

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizuresDefinitiveAutosomal dominant
cataract 50 with or without glaucomaStrongAutosomal dominant
autosomal dominant non-syndromic intellectual disabilitySupportiveAutosomal dominant
intellectual disabilityLimitedAutosomal dominant
schizophreniaLimitedAutosomal dominant
cataract-glaucoma syndromeLimitedAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
syndromic complex neurodevelopmental disorderDefinitiveAD
cataract 50 with or without glaucomaModerateAD

Mondo (10): neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (MONDO:0859365), prostate cancer (MONDO:0008315), intellectual disability (MONDO:0001071), neurodevelopmental disorder (MONDO:0700092), cataract 50 with or without glaucoma (MONDO:0859382), mulibrey nanism (MONDO:0009664), Birk-Barel syndrome (MONDO:0012856), autosomal dominant non-syndromic intellectual disability (MONDO:0015802), schizophrenia (MONDO:0005090), cataract-glaucoma syndrome (MONDO:0015567)

Orphanet (5): Familial prostate cancer (Orphanet:1331), Birk-Barel syndrome (Orphanet:166108), Autosomal dominant non-syndromic intellectual disability (Orphanet:178469), Mulibrey nanism (Orphanet:2576), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

67 total (30 of 67 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000054Micropenis
HP:0000154Wide mouth
HP:0000218High palate
HP:0000262Turricephaly
HP:0000294Low anterior hairline
HP:0000322Short philtrum
HP:0000324Facial asymmetry
HP:0000337Broad forehead
HP:0000347Micrognathia
HP:0000414Bulbous nose
HP:0000463Anteverted nares
HP:0000470Short neck
HP:0000473Torticollis
HP:0000486Strabismus
HP:0000490Deeply set eye
HP:0000501Glaucoma
HP:0000506Telecanthus
HP:0000508Ptosis
HP:0000518Cataract
HP:0000541Retinal detachment
HP:0000577Exotropia
HP:0000582Upslanted palpebral fissure
HP:0000729Autistic behavior
HP:0000750Delayed speech and language development
HP:0000767Pectus excavatum
HP:0000996Facial capillary hemangioma
HP:0001182Tapered finger
HP:0001249Intellectual disability

GWAS associations

28 associations (top):

StudyTraitp-value
GCST000785_8Longevity1.000000e-06
GCST001875_3Pubertal anthropometrics8.000000e-07
GCST002868_17Response to serotonin reuptake inhibitors in major depressive disorder4.000000e-06
GCST003219_27Advanced age-related macular degeneration3.000000e-08
GCST003262_570Post bronchodilator FEV13.000000e-06
GCST004068_44Venous thromboembolism adjusted for sickle cell variant rs77121243-T3.000000e-07
GCST006069_67Time-dependent creatinine clearance change response to tenofovir treatment in HIV infection (time and treatment arm interaction)9.000000e-06
GCST006387_1Thyroid nodules2.000000e-08
GCST007576_147Chronotype1.000000e-08
GCST008161_82Waist circumference adjusted for body mass index2.000000e-06
GCST009391_637Metabolite levels1.000000e-07
GCST010002_320Refractive error3.000000e-39
GCST010320_1PR interval5.000000e-11
GCST010321_15PR interval2.000000e-12
GCST010577_7Crohn’s disease5.000000e-06
GCST010796_3480Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-09
GCST010796_3481Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-08
GCST010796_3482Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08
GCST010796_3483Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08
GCST010796_3484Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-08
GCST010796_3485Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_3486Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_3487Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-08
GCST010796_3488Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-08
GCST010796_3489Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-08
GCST010988_397Adult body size1.000000e-11
GCST011494_46Daytime nap3.000000e-10
GCST012299_13Schizophrenia, bipolar disorder or major depressive disorder x sex interaction (3df)9.000000e-06

EFO canonical traits (12, from GWAS)

EFO IDTrait name
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:1001492atrophic macular degeneration
EFO:0004314forced expiratory volume
EFO:0007934creatinine clearance measurement
EFO:1001436thyroid nodule
EFO:0008328chronotype measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0010504inositol measurement
EFO:0004462PR interval
EFO:0004327electrocardiography
EFO:0007828daytime rest measurement
EFO:0008343sex interaction measurement

MeSH disease descriptors (5)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D050336Mulibrey NanismC05.116.099.343.796; C16.320.240.875
D065886Neurodevelopmental DisordersF03.625
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
C567357Birk-Barel Mental Retardation Dysmorphism Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3559708 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2043144TRPM30.000

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: vgic — Transient Receptor Potential channels (TRP)

Most potent curated ligand interactions (17 total), top 17:

LigandActionAffinityParameter
isosakuranetinChannel blocker7.3pIC50
primidoneChannel blocker6.2pIC50
CIM0216Activation6.1pEC50
maprotilineChannel blocker5.8pIC50
clotrimazoleAgonist5.52pEC50
naringeninChannel blocker5.2pIC50
diclofenacChannel blocker5.2pIC50
(S)-liquiritigeninChannel blocker5.2pIC50
sphingosineAgonist4.9pEC50
pregnenolone sulphateActivator4.9pEC50
dihydrosphingosineAgonist4.7pEC50
Gd3+Antagonist4.0pIC50
2-APBAntagonist4.0pIC50
La3+Antagonist4.0pIC50
chloroformAntagonist3.78pIC50
halothaneAntagonist3.28pIC50
Mg2+Antagonist2.0pIC50

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, increases expression5
methylmercuric chloridedecreases expression, increases expression3
entinostatdecreases expression, affects cotreatment2
Vorinostataffects cotreatment, increases expression2
Aflatoxin B1increases methylation, decreases methylation2
propionaldehydedecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
2,5,2’,5’-tetrachlorobiphenylincreases expression1
trichostatin Adecreases expression, increases expression1
sodium arseniteaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
Resveratrolaffects cotreatment, decreases expression1
Arsenic Trioxideincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Amphotericin Bdecreases expression1
Benzo(a)pyreneaffects methylation1
Carbamazepineaffects expression1
Copperaffects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Endosulfandecreases expression1
Methamphetamineaffects response to substance1
Sarinincreases expression1
Smokeincreases expression1
Thimerosalincreases expression1
Tretinoindecreases expression1
Zincincreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4411010BindingInhibition of TRPM3 channel (unknown origin)Discovery of a Potent and Selective TRPC5 Inhibitor, Efficacious in a Focal Segmental Glomerulosclerosis Model. — ACS Med Chem Lett

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D9V0Ubigene HEK293 TRPM3 KOTransformed cell lineFemale

Clinical trials (associated diseases)

600 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia