CCT6B

chaperonin containing TCP1 subunit 6B, the group of Chaperonins

Basic information

Region (hg38): 17:34927858-34981078

Links

ENSG00000132141 ∙ NCBI:10693 ∙ OMIM:610730 ∙ HGNC:1621 ∙ Uniprot:Q92526 ∙ 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 CCT6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT6B 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	29	1	1

Variants in CCT6B

This is a list of pathogenic ClinVar variants found in the CCT6B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-34928067-C-G		not specified	Uncertain significance (May 11, 2022)
17-34928088-A-G		not specified	Uncertain significance (Sep 01, 2021)
17-34928098-T-C		not specified	Uncertain significance (Dec 15, 2022)
17-34928112-A-G		not specified	Uncertain significance (Oct 12, 2022)
17-34929013-T-C		not specified	Uncertain significance (May 24, 2024)
17-34931051-C-A		not specified	Uncertain significance (Aug 02, 2023)
17-34932371-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-34932381-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-34932416-G-T		not specified	Uncertain significance (Jul 19, 2022)
17-34932437-T-C		not specified	Uncertain significance (Aug 28, 2023)
17-34932494-A-G		not specified	Uncertain significance (Jun 11, 2021)
17-34939204-T-C		not specified	Likely benign (Aug 04, 2023)
17-34939627-T-G		not specified	Uncertain significance (Oct 05, 2023)
17-34939654-C-A		not specified	Uncertain significance (Aug 22, 2023)
17-34939667-G-T		not specified	Uncertain significance (Feb 14, 2023)
17-34939685-C-T		not specified	Uncertain significance (Apr 18, 2023)
17-34940552-T-C		not specified	Uncertain significance (Jun 27, 2023)
17-34942494-A-G		not specified	Uncertain significance (Aug 28, 2023)
17-34942585-C-G		not specified	Uncertain significance (Nov 15, 2021)
17-34942883-T-C		not specified	Uncertain significance (Aug 23, 2021)
17-34942885-C-T			Likely benign (Jun 01, 2024)
17-34942908-T-C			Benign (Dec 31, 2019)
17-34952044-C-T		not specified	Uncertain significance (Jan 31, 2024)
17-34954439-T-A		not specified	Uncertain significance (Apr 09, 2024)
17-34954593-G-A		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT6B	protein_coding	protein_coding	ENST00000314144	14	53220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.67e-11	0.382	125529	3	214	125746	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0435	275	273	1.01	0.0000130	3436
Missense in Polyphen		67	58.298	1.1493		824
Synonymous	-0.331	98	93.9	1.04	0.00000455	1038
Loss of Function	1.08	19	24.8	0.766	0.00000114	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00156	0.00155
Ashkenazi Jewish	0.000215	0.000198
East Asian	0.000230	0.000217
Finnish	0.0000961	0.0000924
European (Non-Finnish)	0.000431	0.000422
Middle Eastern	0.000230	0.000217
South Asian	0.00424	0.00412
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. {ECO:0000305|PubMed:8812458}.
• 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: 0.119

Intolerance Scores

• loftool: 0.980
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.649
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.710

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Cct6b

Gene ontology

• Biological process: protein folding;spermatogenesis;protein transport;chaperone-mediated protein complex assembly;toxin transport
• Cellular component: cytosol;chaperonin-containing T-complex
• Molecular function: ATP binding;protein transporter activity;unfolded protein binding