TRPM2

protein-coding

transient receptor potential cation channel subfamily M member 2, the group of Transient receptor potential cation channels|Nudix hydrolase family

Gene summary

The protein encoded by this gene forms a tetrameric cation channel that is permeable to calcium, sodium, and potassium and is regulated by free intracellular ADP-ribose. The encoded protein is activated by oxidative stress and confers susceptibility to cell death. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. Additional transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2016]

Previous symbols:
  • TRPC7

MANE transcript

NM_003307.4

Inheritance

—

ClinVar variants

U:292B:64

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr21:44,350,163-44,443,081

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~92.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRPM2 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 292
not providedTotal: 59

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003307.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
12
clinvar
9
clinvar
23
missense
284
clinvar
29
clinvar
12
clinvar
325
nonsense
1
clinvar
1
clinvar
1
clinvar
3
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total002924222356
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003307.4RefSeqNP_003298.232MANE Select
ENST00000397928.6EnsemblENSP00000381023.132MANE Select
NM_001320350.2RefSeqNP_001307279.233Standard
NM_001320351.2RefSeqNP_001307280.231Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Oxytocin signaling pathway - Homo sapiens (human)
  • NOD-like receptor signaling pathway - Homo sapiens (human)
  • Ectoderm Differentiation
  • Neutrophil degranulation
  • Stimuli-sensing channels

Biological Process

  • temperature homeostasis
  • dendritic cell chemotaxis
  • calcium ion transport
  • response to purine-containing compound
  • calcium-mediated signaling using intracellular calcium source

Molecular Function

  • cation channel activity
  • calcium channel activity
  • sodium channel activity
  • calcium ion binding
  • calcium-release channel activity

Cellular Component

  • lysosome
  • lysosomal membrane
  • plasma membrane
  • integral component of plasma membrane
  • cytoplasmic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000397928
Coding exons
32
Length
92919
Individuals with no LoFs
124953
Homozygous LoFs
3
Heterozygous LoFs
792
Defined
125748
p
0.00317
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.3359889591.030.00006469817
Missense (PolyPhen)310299.151.03633043
Synonymous-3.295164291.200.00003262943
Loss of Function0.7207076.80.9110.00000370827

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00190.0018notable
Latino/Admixed American0.00420.0042notable
Ashkenazi Jewish0.0110.011notable
East Asian0.00150.0014notable
Finnish0.000560.00055rare
European (Non-Finnish)0.00290.0029notable
South Asian0.00400.0039notable
Other0.00430.0042notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Isoform 1: Nonselective, voltage-independent cation channel that mediates Na(+) and Ca(2+) influx, leading to increased cytoplasmic Ca(2+) levels (PubMed:11960981, PubMed:12594222, PubMed:11385575, PubMed:11509734, PubMed:11804595, PubMed:15561722, PubMed:16601673, PubMed:19171771, PubMed:20660597, PubMed:27383051, PubMed:27068538). Extracellular calcium passes through the channel and increases channel activity by binding to the cytoplasmic domain and stabilizing the channel in an open conformation (PubMed:19171771). Also contributes to Ca(2+) release from intracellular stores in response to ADP-ribose (PubMed:19454650). Plays a role in numerous processes that involve signaling via intracellular Ca(2+) levels (Probable). Besides, mediates the release of lysosomal Zn(2+) stores in response to reactive oxygen species, leading to increased cytosolic Zn(2+) levels (PubMed:25562606, PubMed:27068538). Activated by moderate heat (35 to 40 degrees Celsius) (PubMed:16601673). Activated by intracellular ADP-ribose, beta-NAD (NAD(+)) and similar compounds, and by oxidative stress caused by reactive oxygen or nitrogen species (PubMed:11960981, PubMed:11385575, PubMed:11509734, PubMed:11804595, PubMed:15561722, PubMed:16601673, PubMed:19171771, PubMed:27383051, PubMed:27068538). The precise physiological activators are under debate; the true, physiological activators may be ADP-ribose and ADP-ribose-2'-phosphate (PubMed:20650899, PubMed:25918360). Activation by ADP-ribose and beta-NAD is strongly increased by moderate heat (35 to 40 degrees Celsius) (PubMed:16601673). Likewise, reactive oxygen species lower the threshold for activation by moderate heat (37 degrees Celsius) (PubMed:22493272). Plays a role in mediating behavorial and physiological responses to moderate heat and thereby contributes to body temperature homeostasis. Plays a role in insulin secretion, a process that requires increased cytoplasmic Ca(2+) levels (By similarity). Required for normal IFNG and cytokine secretion and normal innate immune immunity in response to bacterial infection. Required for normal phagocytosis and cytokine release by macrophages exposed to zymosan (in vitro). Plays a role in dendritic cell differentiation and maturation, and in dendritic cell chemotaxis via its role in regulating cytoplasmic Ca(2+) levels (By similarity). Plays a role in the regulation of the reorganization of the actin cytoskeleton and filopodia formation in response to reactive oxygen species via its role in increasing cytoplasmic Ca(2+) and Zn(2+) levels (PubMed:27068538). Confers susceptibility to cell death following oxidative stress (PubMed:12594222, PubMed:25562606). {ECO:0000250|UniProtKB:Q91YD4, ECO:0000269|PubMed:11385575, ECO:0000269|PubMed:11509734, ECO:0000269|PubMed:11804595, ECO:0000269|PubMed:11960981, ECO:0000269|PubMed:12594222, ECO:0000269|PubMed:15561722, ECO:0000269|PubMed:16601673, ECO:0000269|PubMed:19171771, ECO:0000269|PubMed:19454650, ECO:0000269|PubMed:20650899, ECO:0000269|PubMed:20660597, ECO:0000269|PubMed:22493272, ECO:0000269|PubMed:25562606, ECO:0000269|PubMed:25918360, ECO:0000269|PubMed:27068538, ECO:0000269|PubMed:27383051, ECO:0000305}.; FUNCTION: Isoform 3: Lacks cation channel activity and negatively regulates the channel activity of isoform 1. Negatively regulates susceptibility to cell death in reposponse to oxidative stress. {ECO:0000269|PubMed:12594222}.;

Recessive Scores

pRec
0.0973

Intolerance Scores

LoFtool
0.797
RVIS EVS
1
RVIS percentile EVS
90.56

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.606

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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