CCT3

chaperonin containing TCP1 subunit 3, the group of Chaperonins

Basic information

Region (hg38): 1:156308967-156367873

Previous symbols: [ "TRIC5" ]

Links

ENSG00000163468 ∙ NCBI:7203 ∙ OMIM:600114 ∙ HGNC:1616 ∙ Uniprot:P49368 ∙ 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 CCT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT3 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			30			30
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	0	0

Variants in CCT3

This is a list of pathogenic ClinVar variants found in the CCT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156309234-G-A		not specified	Uncertain significance (May 14, 2024)
1-156309284-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-156309285-G-A		See cases	Uncertain significance (Apr 02, 2020)
1-156310679-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-156310969-C-T		not specified	Uncertain significance (Aug 19, 2023)
1-156311005-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-156311089-G-C		not specified	Uncertain significance (Dec 20, 2021)
1-156312087-T-G		not specified	Uncertain significance (May 18, 2023)
1-156312207-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-156317202-C-T		not specified	Uncertain significance (May 11, 2022)
1-156317217-T-C		not specified	Uncertain significance (Dec 15, 2023)
1-156317221-C-T		not specified	Uncertain significance (Dec 20, 2022)
1-156317426-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-156317476-C-G		not specified	Uncertain significance (May 02, 2024)
1-156317508-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-156318932-T-C		not specified	Uncertain significance (May 26, 2023)
1-156318938-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-156318939-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-156318996-C-T		not specified	Uncertain significance (Jun 30, 2022)
1-156320856-A-T		not specified	Uncertain significance (May 26, 2023)
1-156320886-T-C		not specified	Uncertain significance (Jun 07, 2023)
1-156320892-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-156320948-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-156320970-T-C		not specified	Uncertain significance (Jan 18, 2022)
1-156321025-A-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT3	protein_coding	protein_coding	ENST00000295688	14	58906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000187	125587	0	1	125588	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	276	336	0.822	0.0000195	3582
Missense in Polyphen		77	122.77	0.62721		1396
Synonymous	0.461	106	112	0.945	0.00000566	1061
Loss of Function	5.13	0	30.7	0.00	0.00000181	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 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: 0.696

Intolerance Scores

• loftool: 0.0356
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.921
• hipred: Y
• hipred_score: 0.577
• ghis: 0.660

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cct3
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: cct3
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein folding;binding of sperm to zona pellucida;positive regulation of telomere maintenance via telomerase;pore complex assembly;protein stabilization;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
• Cellular component: zona pellucida receptor complex;cytosol;chaperonin-containing T-complex;cytoskeleton;microtubule;plasma membrane;myelin sheath;cell body;extracellular exosome
• Molecular function: RNA binding;protein binding;ATP binding;unfolded protein binding