GeneBe

TRPC3

transient receptor potential cation channel subfamily C member 3, the group of Transient receptor potential cation channels|Ankyrin repeat domain containing

Basic information

Region (hg38): 4:121874481-121952060

Links

ENSG00000138741 ∙ NCBI:7222 ∙ OMIM:602345 ∙ HGNC:12335 ∙ Uniprot:Q13507 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • spinocerebellar ataxia type 41 (Supportive), mode of inheritance: AD
  • spinocerebellar ataxia type 41 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spinocerebellar ataxia 41ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic25477146

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRPC3 gene.

  • not_provided (138 variants)
  • not_specified (48 variants)
  • TRPC3-related_disorder (11 variants)
  • Spinocerebellar_ataxia_type_41 (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001130698.2. 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.

EffectPLPVUSLBBSum
synonymous
42
clinvar
5
clinvar
 47
missense
108
clinvar
1
clinvar
2
clinvar
 111
nonsense
3
clinvar
 3
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 1 0 111 43 7
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRPC3protein_codingprotein_codingENST00000379645 1272728
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.08e-70.9991256910571257480.000227
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.842675120.5220.00003036053
Missense in Polyphen69188.070.366892048
Synonymous1.371802050.8780.00001381758
Loss of Function3.011838.00.4730.00000196470

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004860.000483
Ashkenazi Jewish0.0001020.0000992
East Asian0.001260.00125
Finnish0.00009250.0000924
European (Non-Finnish)0.0001500.000149
Middle Eastern0.001260.00125
South Asian0.00009810.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Thought to form a receptor-activated non-selective calcium permeant cation channel. Probably is operated by a phosphatidylinositol second messenger system activated by receptor tyrosine kinases or G-protein coupled receptors. Activated by diacylglycerol (DAG) in a membrane-delimited fashion, independently of protein kinase C, and by inositol 1,4,5- triphosphate receptors (ITPR) with bound IP3. May also be activated by internal calcium store depletion. {ECO:0000269|PubMed:20095964, ECO:0000269|PubMed:8646775, ECO:0000269|PubMed:9417057, ECO:0000269|PubMed:9930701}.;
Pathway
Axon guidance - Homo sapiens (human);BDNF-TrkB Signaling;Signaling by GPCR;Signal Transduction;ion channels and their functional role in vascular endothelium;Stimuli-sensing channels;Ion channel transport;Transport of small molecules;Effects of PIP2 hydrolysis;Platelet activation, signaling and aggregation;Hemostasis;TRP channels;Elevation of cytosolic Ca2+ levels;Platelet calcium homeostasis;Platelet homeostasis;G alpha (q) signalling events;GPCR downstream signalling;Trk receptor signaling mediated by PI3K and PLC-gamma (Consensus)

Recessive Scores

pRec
0.246

Intolerance Scores

loftool
0.195
rvis_EVS
-1.24
rvis_percentile_EVS
5.41

Haploinsufficiency Scores

pHI
0.349
hipred
Y
hipred_score
0.737
ghis
0.589

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.762

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trpc3
Phenotype
growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system 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);

Gene ontology

Biological process
calcium ion transport;manganese ion transport;single fertilization;phototransduction;positive regulation of calcium ion transport into cytosol;platelet activation;response to ATP;regulation of cytosolic calcium ion concentration;response to calcium ion;calcium ion transmembrane transport;positive regulation of cardiac muscle hypertrophy in response to stress
Cellular component
plasma membrane;integral component of plasma membrane;cation channel complex
Molecular function
calcium channel activity;protein binding;store-operated calcium channel activity;inositol 1,4,5 trisphosphate binding