CCT7

chaperonin containing TCP1 subunit 7, the group of Chaperonins

Basic information

Region (hg38): 2:73233419-73253021

Links

ENSG00000135624 ∙ NCBI:10574 ∙ OMIM:605140 ∙ HGNC:1622 ∙ Uniprot:Q99832 ∙ 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 CCT7 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT7 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in CCT7

This is a list of pathogenic ClinVar variants found in the CCT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-73239668-A-T		not specified	Uncertain significance (Jan 16, 2024)
2-73240485-A-G		not specified	Uncertain significance (Jan 18, 2023)
2-73243079-G-C		not specified	Uncertain significance (Nov 17, 2023)
2-73243080-G-T		not specified	Uncertain significance (Jan 09, 2024)
2-73243122-C-T		not specified	Uncertain significance (Sep 07, 2022)
2-73244030-G-A		not specified	Uncertain significance (Sep 13, 2023)
2-73244641-G-A		not specified	Uncertain significance (Aug 22, 2023)
2-73247853-T-C		not specified	Uncertain significance (Oct 12, 2022)
2-73249084-C-G		not specified	Uncertain significance (May 03, 2023)
2-73249103-C-G		not specified	Uncertain significance (Mar 07, 2024)
2-73250331-A-G		not specified	Uncertain significance (Oct 20, 2023)
2-73250420-C-G			Uncertain significance (Nov 01, 2023)
2-73251305-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-73251421-C-G		not specified	Uncertain significance (Feb 08, 2023)
2-73252641-G-C		not specified	Uncertain significance (Dec 17, 2023)
2-73252679-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-73252731-A-T		not specified	Uncertain significance (Jun 21, 2023)
2-73252734-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-73252746-C-T		not specified	Uncertain significance (Dec 16, 2021)
2-73252758-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-73252769-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-73252775-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-73252784-A-G		not specified	Uncertain significance (May 30, 2023)
2-73252803-C-T		Myocardial infarction 1	Pathogenic (Sep 15, 2013)
2-73252817-C-T		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT7	protein_coding	protein_coding	ENST00000258091	12	19602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0164	124795	0	4	124799	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	204	317	0.643	0.0000177	3555
Missense in Polyphen		41	73.83	0.55533		959
Synonymous	-0.326	123	118	1.04	0.00000655	1089
Loss of Function	4.15	3	25.7	0.117	0.00000131	303

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)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {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 (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.447
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.476
• hipred: Y
• hipred_score: 0.831
• ghis: 0.660

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cct7

Zebrafish Information Network

• Gene name: cct7
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: protein folding;binding of sperm to zona pellucida;positive regulation of telomere maintenance via telomerase;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: cytoplasm;cytosol;chaperonin-containing T-complex;microtubule;cell body;extracellular exosome
• Molecular function: protein binding;ATP binding;identical protein binding;unfolded protein binding