TRPC4AP

transient receptor potential cation channel subfamily C member 4 associated protein, the group of Protein phosphatase 1 regulatory subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 20:35002403-35092807

Previous symbols: [ "C20orf188" ]

Links

ENSG00000100991 ∙ NCBI:26133 ∙ OMIM:608430 ∙ HGNC:16181 ∙ Uniprot:Q8TEL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypothyroidism (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRPC4AP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPC4AP 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				2		2
missense			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in TRPC4AP

This is a list of pathogenic ClinVar variants found in the TRPC4AP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-35003202-C-T		not specified	Uncertain significance (May 26, 2023)
20-35003271-T-G		not specified	Uncertain significance (Aug 14, 2023)
20-35003567-C-T		not specified	Uncertain significance (Apr 26, 2024)
20-35004513-T-C		not specified	Uncertain significance (Apr 12, 2022)
20-35004532-T-C		not specified	Uncertain significance (Jan 04, 2022)
20-35004546-C-T		not specified	Uncertain significance (Feb 16, 2023)
20-35006462-G-C		not specified	Uncertain significance (Feb 15, 2023)
20-35006498-C-T			Likely benign (Mar 01, 2024)
20-35006544-C-G		not specified	Uncertain significance (Aug 30, 2022)
20-35008724-C-G		not specified	Uncertain significance (Mar 11, 2024)
20-35010191-C-T		not specified	Uncertain significance (Sep 22, 2022)
20-35021204-G-A		not specified	Uncertain significance (Nov 21, 2022)
20-35021259-A-C		not specified	Uncertain significance (May 09, 2023)
20-35021260-T-A		not specified	Uncertain significance (Aug 02, 2023)
20-35021272-A-G		not specified	Uncertain significance (Jan 05, 2022)
20-35021273-T-C		not specified	Uncertain significance (May 31, 2022)
20-35021302-G-A		not specified	Uncertain significance (Oct 03, 2022)
20-35021349-A-C		not specified	Uncertain significance (Apr 07, 2022)
20-35035236-G-A		not specified	Uncertain significance (Dec 21, 2022)
20-35044508-G-C		not specified	Uncertain significance (Dec 09, 2023)
20-35044534-A-G		not specified	Uncertain significance (Nov 09, 2021)
20-35044576-G-A		not specified	Uncertain significance (Jun 12, 2023)
20-35044627-A-G		not specified	Uncertain significance (Mar 14, 2023)
20-35044642-G-C		not specified	Uncertain significance (Feb 17, 2022)
20-35049971-C-G		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPC4AP	protein_coding	protein_coding	ENST00000252015	19	90468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.552	0.448	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	368	440	0.836	0.0000244	5226
Missense in Polyphen		91	156.42	0.58176		1941
Synonymous	0.271	170	175	0.974	0.00000937	1557
Loss of Function	4.94	10	46.2	0.216	0.00000274	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000327
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000164	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-specific adapter of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex required for cell cycle control. The DCX(TRUSS) complex specifically mediates the polyubiquitination and subsequent degradation of MYC. Also participates in the activation of NFKB1 in response to ligation of TNFRSF1A, possibly by linking TNFRSF1A to the IKK signalosome. Involved in JNK activation via its interaction with TRAF2. Also involved in elevation of endoplasmic reticulum Ca(2+) storage reduction in response to CHRM1. {ECO:0000269|PubMed:20551172}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0526
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.26

Haploinsufficiency Scores

• pHI: 0.450
• hipred: Y
• hipred_score: 0.775
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.870

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trpc4ap

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;hair follicle maturation;calcium ion transmembrane transport
• Cellular component: plasma membrane;Cul4A-RING E3 ubiquitin ligase complex
• Molecular function: calcium channel activity;protein binding;phosphatase binding