TCP1

t-complex 1, the group of Chaperonins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 6:159778498-159789703

Links

ENSG00000120438 ∙ NCBI:6950 ∙ OMIM:186980 ∙ HGNC:11655 ∙ Uniprot:P17987 ∙ 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 TCP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	3		6
Total	0	0	25	3	0

Variants in TCP1

This is a list of pathogenic ClinVar variants found in the TCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-159778654-G-A			Likely benign (Apr 11, 2018)
6-159778677-G-T		not specified	Uncertain significance (Nov 08, 2022)
6-159778705-C-G		not specified	Uncertain significance (Mar 29, 2022)
6-159778740-A-G		not specified	Likely benign (Mar 01, 2023)
6-159778753-T-C		not specified	Likely benign (Dec 28, 2022)
6-159778761-A-G		not specified	Uncertain significance (Apr 13, 2023)
6-159779075-A-T		not specified	Uncertain significance (Apr 18, 2023)
6-159779077-C-T		not specified	Uncertain significance (Mar 20, 2024)
6-159779254-G-A		not specified	Uncertain significance (Jun 03, 2022)
6-159779631-T-G		not specified	Uncertain significance (Jan 06, 2023)
6-159779645-T-C		not specified	Uncertain significance (Mar 23, 2023)
6-159779910-G-C		not specified	Uncertain significance (Apr 27, 2022)
6-159780073-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-159780076-C-G		not specified	Uncertain significance (Jun 02, 2023)
6-159780444-T-G		not specified	Uncertain significance (Nov 10, 2022)
6-159780465-C-G		not specified	Uncertain significance (Nov 28, 2023)
6-159780491-T-A		not specified	Uncertain significance (Jul 19, 2023)
6-159780956-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-159780990-C-T		not specified	Uncertain significance (May 03, 2023)
6-159781082-G-C		not specified	Uncertain significance (Apr 15, 2024)
6-159781099-A-G		not specified	Uncertain significance (May 26, 2024)
6-159783969-G-A		not specified	Uncertain significance (Apr 08, 2024)
6-159784007-G-T		not specified	Uncertain significance (Aug 25, 2021)
6-159784050-C-T		not specified	Uncertain significance (Jul 31, 2023)
6-159784825-T-C		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCP1	protein_coding	protein_coding	ENST00000321394	12	11252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00473	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	228	307	0.742	0.0000152	3649
Missense in Polyphen		32	91.91	0.34817		1180
Synonymous	-0.935	117	105	1.12	0.00000506	1110
Loss of Function	4.23	2	24.7	0.0811	0.00000123	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000554	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000554	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.
• Pathway: Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Metabolism of proteins;Chaperonin-mediated protein folding;Formation of tubulin folding intermediates by CCT/TriC;Association of TriC/CCT with target proteins during biosynthesis;Protein folding;Prefoldin mediated transfer of substrate to CCT/TriC;Folding of actin by CCT/TriC;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;BBSome-mediated cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.656

Intolerance Scores

• loftool: 0.301
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.359
• hipred: Y
• hipred_score: 0.831
• ghis: 0.611

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcp1

Zebrafish Information Network

• Gene name: tcp1
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein folding;tubulin complex assembly;binding of sperm to zona pellucida;positive regulation of telomere maintenance via telomerase;interleukin-12-mediated signaling pathway;translocation of peptides or proteins into host cell cytoplasm;protein stabilization;positive regulation of telomerase activity;scaRNA localization to Cajal body;toxin transport;positive regulation of establishment of protein localization to telomere;positive regulation of protein localization to Cajal body;positive regulation of telomerase RNA localization to Cajal body;regulation of macrophage apoptotic process
• Cellular component: pericentriolar material;acrosomal vesicle;zona pellucida receptor complex;nuclear heterochromatin;Golgi apparatus;centrosome;cytosol;chaperonin-containing T-complex;microtubule;myelin sheath;cell body;extracellular exosome
• Molecular function: RNA binding;protein binding;ATP binding;ubiquitin protein ligase binding;unfolded protein binding