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): 3:142724033-142807888

Links

ENSG00000144935 ∙ NCBI:7220 ∙ OMIM:602343 ∙ HGNC:12333 ∙ Uniprot:P48995 ∙ 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 TRPC1 gene.

• Inborn genetic diseases (16 variants)

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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	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)
3-142777670-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)
3-142784713-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)
3-142804086-G-A		not specified	Uncertain significance (May 23, 2023)
3-142804108-A-G		not specified	Uncertain significance (Apr 12, 2023)
3-142806178-A-G		not specified	Uncertain significance (Jan 09, 2024)
3-142806198-G-A		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

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: 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. 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