CCT6A

chaperonin containing TCP1 subunit 6A, the group of Chaperonins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 7:56051685-56063989

Previous symbols: [ "CCT6" ]

Links

ENSG00000146731 ∙ NCBI:908 ∙ OMIM:104613 ∙ HGNC:1620 ∙ Uniprot:P40227 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCT6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT6A 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	1
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	1

Variants in CCT6A

This is a list of pathogenic ClinVar variants found in the CCT6A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-56051889-C-T		not specified	Uncertain significance (Jul 11, 2023)
7-56054411-A-G		not specified	Uncertain significance (Mar 28, 2022)
7-56054415-C-T		not specified	Uncertain significance (Oct 25, 2023)
7-56054424-A-C		not specified	Uncertain significance (Sep 08, 2024)
7-56054499-C-T		not specified	Uncertain significance (Sep 27, 2021)
7-56055693-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-56055733-T-A		not specified	Uncertain significance (Dec 15, 2022)
7-56055751-C-G		not specified	Uncertain significance (May 02, 2023)
7-56055768-C-G		not specified	Uncertain significance (Dec 28, 2022)
7-56056323-T-G		not specified	Uncertain significance (Mar 06, 2025)
7-56056345-A-G		not specified	Uncertain significance (Dec 12, 2023)
7-56057996-A-C		not specified	Uncertain significance (Dec 29, 2024)
7-56058028-G-A		not specified	Uncertain significance (Sep 28, 2021)
7-56058051-G-T		not specified	Uncertain significance (Jun 25, 2024)
7-56058063-T-C		not specified	Uncertain significance (Mar 06, 2023)
7-56058073-C-G		not specified	Uncertain significance (Jun 26, 2024)
7-56058376-G-C		not specified	Uncertain significance (Dec 17, 2024)
7-56058394-C-T		not specified	Uncertain significance (Nov 13, 2024)
7-56058447-G-T		not specified	Uncertain significance (Oct 02, 2023)
7-56058455-A-C		not specified	Uncertain significance (Jul 19, 2023)
7-56058456-A-G		not specified	Uncertain significance (Sep 27, 2022)
7-56059583-T-G		not specified	Likely benign (Feb 01, 2025)
7-56059631-G-C		not specified	Uncertain significance (Jul 20, 2021)
7-56059633-A-G		not specified	Uncertain significance (Jul 05, 2024)
7-56060353-C-G		not specified	Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT6A	protein_coding	protein_coding	ENST00000275603	14	12360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00468	125735	0	3	125738	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	222	282	0.788	0.0000138	3472
Missense in Polyphen		20	55.37	0.36121		806
Synonymous	-0.457	106	100	1.06	0.00000517	1030
Loss of Function	4.23	2	24.7	0.0810	0.00000114	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
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). 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: 0.438

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.771
• ghis: 0.651

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cct6a

Gene ontology

• Biological process: protein folding;positive regulation of telomere maintenance via telomerase;protein stabilization;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;extracellular exosome
• Molecular function: RNA binding;protein binding;ATP binding;unfolded protein binding;WD40-repeat domain binding