CCT2

chaperonin containing TCP1 subunit 2, the group of Chaperonins

Basic information

Region (hg38): 12:69585425-69601570

Links

ENSG00000166226 ∙ NCBI:10576 ∙ OMIM:605139 ∙ HGNC:1615 ∙ Uniprot:P78371 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leber congenital amaurosis (Limited), mode of inheritance: AR
• Leber congenital amaurosis 9 (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCT2 gene.

• not provided (291 variants)
• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT2 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			1	62	2	65
missense			156	1		157
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			7	14	1	22
non coding			2	45	6	53
Total	0	0	161	108	8

Variants in CCT2

This is a list of pathogenic ClinVar variants found in the CCT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-69585530-C-G			Uncertain significance (Feb 04, 2021)
12-69585531-C-T			Likely benign (Dec 15, 2021)
12-69585533-G-A			Likely benign (Dec 28, 2019)
12-69585537-C-A			Likely benign (Aug 31, 2022)
12-69585540-C-T			Likely benign (Jul 19, 2023)
12-69585541-T-G			Likely benign (Aug 01, 2022)
12-69585544-C-T			Likely benign (Mar 14, 2022)
12-69586252-C-T			Likely benign (Jul 07, 2023)
12-69586262-C-T			Likely benign (May 15, 2023)
12-69586276-C-T			Uncertain significance (Sep 12, 2022)
12-69586280-C-G			Uncertain significance (Jan 15, 2024)
12-69586289-C-A			Uncertain significance (Nov 06, 2020)
12-69586289-C-T			Uncertain significance (Feb 01, 2022)
12-69586290-T-G			Likely benign (Nov 04, 2023)
12-69586295-A-C		not specified	Uncertain significance (Nov 18, 2022)
12-69586299-C-T			Likely benign (Dec 11, 2023)
12-69586302-T-C			Benign (Jan 13, 2024)
12-69586334-C-G			Uncertain significance (Jun 05, 2021)
12-69586340-G-A			Uncertain significance (May 10, 2022)
12-69586340-G-C			Uncertain significance (Feb 08, 2022)
12-69586353-T-C			Likely benign (Oct 13, 2022)
12-69586354-G-C			Likely benign (Nov 16, 2021)
12-69586357-C-T			Likely benign (Dec 11, 2023)
12-69586361-G-C			Benign (Jan 31, 2024)
12-69586736-C-T			Likely benign (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT2	protein_coding	protein_coding	ENST00000299300	16	16237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00147	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	226	298	0.759	0.0000151	3503
Missense in Polyphen		36	95.194	0.37818		1218
Synonymous	0.0724	97	97.9	0.991	0.00000500	1054
Loss of Function	4.54	2	27.8	0.0719	0.00000146	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000533	0.0000527
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: Neutrophil degranulation;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;Innate Immune System;Immune System;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: 0.506

Intolerance Scores

• loftool: 0.361
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.783
• ghis: 0.721

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cct2

Zebrafish Information Network

• Gene name: cct2
• 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;neutrophil degranulation;protein stabilization;chaperone mediated protein folding independent of cofactor;chaperone-mediated protein complex assembly;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;extracellular region;cytosol;chaperonin-containing T-complex;microtubule;azurophil granule lumen;myelin sheath;cell body;extracellular exosome
• Molecular function: protein binding;ATP binding;ubiquitin protein ligase binding;protein folding chaperone;unfolded protein binding