TRPC5

transient receptor potential cation channel subfamily C member 5, the group of Transient receptor potential cation channels|Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing

Basic information

Region (hg38): X:111768011-112082776

Links

ENSG00000072315 ∙ NCBI:7224 ∙ OMIM:300334 ∙ HGNC:12337 ∙ Uniprot:Q9UL62 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRPC5 gene.

• TRPC5-related_disorder (113 variants)
• not_specified (44 variants)
• not_provided (12 variants)
• Intellectual_disability (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPC5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012471.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	52	5	58
missense			75	5		80
nonsense						0
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	57	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPC5	protein_coding	protein_coding	ENST00000262839	10	308462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000270	125411	1	2	125414	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.27	197	375	0.525	0.0000288	6435
Missense in Polyphen		65	175.8	0.36975		2948
Synonymous	-0.413	146	140	1.04	0.0000104	1869
Loss of Function	4.72	1	27.9	0.0358	0.00000213	484

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000761	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000132	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.0000549	0.0000327
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. Has also been shown to be calcium-selective (By similarity). May also be activated by intracellular calcium store depletion. {ECO:0000250, ECO:0000269|PubMed:16284075}.
• Pathway: Axon guidance - Homo sapiens (human);ion channels and their functional role in vascular endothelium;Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.0223
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.792
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0289

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Trpc5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: calcium ion transport;manganese ion transport;positive regulation of cytosolic calcium ion concentration;nervous system development;positive regulation of cell population proliferation;positive regulation of peptidyl-threonine phosphorylation;neuron differentiation;positive regulation of axon extension;negative regulation of dendrite morphogenesis;regulation of cytosolic calcium ion concentration;calcium ion transmembrane transport;regulation of membrane hyperpolarization
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;dendrite;growth cone;cation channel complex;calcium channel complex;neuronal cell body;membrane raft
• Molecular function: actin binding;calcium channel activity;protein binding;store-operated calcium channel activity;clathrin binding;actinin binding;ATPase binding;inositol 1,4,5 trisphosphate binding