TRPC1
transient receptor potential cation channel subfamily C member 1, the group of Transient receptor potential cation channels|Ankyrin repeat domain containing
Basic information
Region (hg38): 3:142724034-142807888
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPC1 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 | 0 | |||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 25 | 0 | 0 |
Variants in TRPC1
This is a list of pathogenic ClinVar variants found in the TRPC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-142724579-C-G | not specified | Uncertain significance (Feb 23, 2023) | ||
| 3-142724609-C-T | not specified | Uncertain significance (Feb 12, 2024) | ||
| 3-142724623-T-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 3-142724646-C-A | not specified | Uncertain significance (Jul 11, 2023) | ||
| 3-142724665-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 3-142724678-T-G | not specified | Uncertain significance (Dec 22, 2023) | ||
| 3-142736460-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 3-142736462-A-C | not specified | Uncertain significance (Sep 20, 2023) | ||
| 3-142748322-T-C | not specified | Uncertain significance (Aug 12, 2022) | ||
| 3-142748333-C-T | not specified | Uncertain significance (Oct 06, 2022) | ||
| 3-142748457-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 3-142777645-A-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 3-142777670-C-T | not specified | Uncertain significance (Jan 10, 2022) | ||
| 3-142777742-G-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 3-142780938-C-G | not specified | Uncertain significance (May 11, 2022) | ||
| 3-142780946-G-A | not specified | Uncertain significance (May 14, 2024) | ||
| 3-142781010-T-G | not specified | Uncertain significance (May 08, 2024) | ||
| 3-142784713-C-T | Malignant tumor of prostate | Uncertain significance (-) | ||
| 3-142784893-T-C | not specified | Uncertain significance (Mar 29, 2022) | ||
| 3-142785011-T-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 3-142785019-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 3-142791084-C-T | not specified | Uncertain significance (Aug 03, 2022) | ||
| 3-142792828-A-G | not specified | Uncertain significance (Jan 26, 2022) | ||
| 3-142792921-G-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 3-142803982-T-C | not specified | Uncertain significance (Aug 21, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRPC1 | protein_coding | protein_coding | ENST00000476941 | 13 | 83815 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0129 | 0.987 | 125718 | 0 | 26 | 125744 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.05 | 242 | 417 | 0.580 | 0.0000218 | 5218 |
| Missense in Polyphen | 98 | 190.07 | 0.51559 | 2376 | ||
| Synonymous | 0.901 | 132 | 146 | 0.905 | 0.00000710 | 1487 |
| Loss of Function | 4.10 | 11 | 38.5 | 0.286 | 0.00000222 | 470 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000422 | 0.000422 |
| Ashkenazi Jewish | 0.000213 | 0.000198 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.000324 | 0.000185 |
| European (Non-Finnish) | 0.000106 | 0.0000703 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. Seems to be also activated by intracellular calcium store depletion. {ECO:0000269|PubMed:15016832}.;
- Pathway
- Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Axon guidance - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Cell-type Dependent Selectivity of CCK2R Signaling;VEGFA-VEGFR2 Signaling Pathway;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Stimuli-sensing channels;Ion channel transport;Signaling by the B Cell Receptor (BCR);Immune System;Adaptive Immune System;Ion homeostasis;eumelanin biosynthesis;Transport of small molecules;Cardiac conduction;Muscle contraction;TRP channels
(Consensus)
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- loftool
- 0.316
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.548
- hipred
- Y
- hipred_score
- 0.725
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.580
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trpc1
- 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); digestive/alimentary phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- trpc1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- increased curvature
Gene ontology
- Biological process
- calcium ion transport;manganese ion transport;melanin biosynthetic process;positive regulation of release of sequestered calcium ion into cytosol;regulation of cytosolic calcium ion concentration;response to calcium ion;calcium ion transmembrane transport;regulation of cardiac conduction
- Cellular component
- plasma membrane;integral component of plasma membrane;cation channel complex;receptor complex
- Molecular function
- cation channel activity;calcium channel activity;protein binding;store-operated calcium channel activity;inositol 1,4,5 trisphosphate binding