CCT4

chaperonin containing TCP1 subunit 4, the group of Chaperonins

Basic information

Region (hg38): 2:61868085-61888671

Links

ENSG00000115484 ∙ NCBI:10575 ∙ OMIM:605142 ∙ HGNC:1617 ∙ Uniprot:P50991 ∙ 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 CCT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT4 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	27	0	1

Variants in CCT4

This is a list of pathogenic ClinVar variants found in the CCT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-61869493-C-A		not specified	Uncertain significance (Feb 16, 2023)
2-61869514-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-61872086-C-T		not specified	Uncertain significance (Jun 17, 2022)
2-61872125-C-T		CCT4-related disorder • not specified	Uncertain significance (Sep 17, 2021)
2-61872201-T-C		not specified	Uncertain significance (Oct 20, 2021)
2-61872260-T-C		not specified	Uncertain significance (Jun 02, 2023)
2-61873035-C-G		not specified	Uncertain significance (Apr 17, 2024)
2-61873102-G-T		not specified	Uncertain significance (May 30, 2024)
2-61873107-A-C		not specified	Uncertain significance (Jun 04, 2024)
2-61873242-C-T		not specified	Uncertain significance (Dec 08, 2023)
2-61876109-C-A		not specified	Uncertain significance (Apr 13, 2022)
2-61876120-G-A		CCT4-related disorder	Uncertain significance (Jul 30, 2024)
2-61876168-A-C		not specified	Uncertain significance (Dec 12, 2023)
2-61876191-C-T		not specified	Uncertain significance (Nov 13, 2023)
2-61876200-T-C		not specified	Uncertain significance (Jul 12, 2023)
2-61876944-A-C		not specified	Uncertain significance (Jun 17, 2024)
2-61877027-C-T		not specified	Uncertain significance (Dec 13, 2021)
2-61877432-C-T		not specified	Uncertain significance (Dec 05, 2022)
2-61877447-G-T		not specified	Uncertain significance (Oct 05, 2023)
2-61877481-T-C		not specified	Uncertain significance (Mar 15, 2024)
2-61878877-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-61878906-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-61878931-G-A		not specified	Uncertain significance (Oct 05, 2021)
2-61878947-C-A		not specified	Uncertain significance (Aug 04, 2023)
2-61878958-T-C		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT4	protein_coding	protein_coding	ENST00000394440	14	20716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000969	125712	0	2	125714	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	240	288	0.833	0.0000141	3474
Missense in Polyphen		68	116.09	0.58576		1488
Synonymous	-1.45	117	98.6	1.19	0.00000449	1103
Loss of Function	4.64	2	28.9	0.0692	0.00000183	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
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;b cell survival pathway;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: 0.513

Intolerance Scores

• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.726
• hipred: Y
• hipred_score: 0.825
• ghis: 0.709

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cct4

Zebrafish Information Network

• Gene name: cct4
• 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;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
• Cellular component: zona pellucida receptor complex;nucleoplasm;centrosome;cytosol;chaperonin-containing T-complex;microtubule;melanosome;cell projection;cell body;extracellular exosome
• Molecular function: RNA binding;protein binding;ATP binding;unfolded protein binding