CCT8L2

chaperonin containing TCP1 subunit 8 like 2

Basic information

Region (hg38): 22:16590750-16592810

Links

ENSG00000198445 ∙ NCBI:150160 ∙ ∙ HGNC:15553 ∙ Uniprot:Q96SF2 ∙ 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 CCT8L2 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCT8L2 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			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	1

Variants in CCT8L2

This is a list of pathogenic ClinVar variants found in the CCT8L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-16590942-A-G		not specified	Likely benign (Dec 12, 2023)
22-16590974-C-A		not specified	Uncertain significance (Feb 06, 2024)
22-16590990-C-T		not specified	Uncertain significance (Jul 27, 2022)
22-16591125-G-A		not specified	Likely benign (Feb 05, 2024)
22-16591126-G-T		not specified	Uncertain significance (Nov 12, 2021)
22-16591133-C-G		not specified	Likely benign (Aug 28, 2023)
22-16591151-A-G		not specified	Uncertain significance (Jan 02, 2024)
22-16591362-C-T		not specified	Uncertain significance (Feb 22, 2023)
22-16591368-C-A		not specified	Uncertain significance (May 16, 2022)
22-16591370-T-C		not specified	Uncertain significance (Jan 03, 2024)
22-16591395-G-A		not specified	Uncertain significance (Feb 22, 2023)
22-16591415-C-T		not specified	Uncertain significance (Oct 17, 2023)
22-16591419-T-A		not specified	Uncertain significance (Jun 22, 2023)
22-16591521-G-T			Benign (Nov 08, 2017)
22-16591560-C-G		not specified	Uncertain significance (Jun 24, 2022)
22-16591567-C-A		not specified	Uncertain significance (Oct 02, 2023)
22-16591611-C-T		not specified	Uncertain significance (Sep 23, 2023)
22-16591614-C-T		not specified	Likely benign (Jan 30, 2024)
22-16591617-T-C		not specified	Uncertain significance (Mar 01, 2024)
22-16591638-T-C		not specified	Uncertain significance (Nov 08, 2022)
22-16591729-G-A			Likely benign (Nov 01, 2022)
22-16591773-G-A		not specified	Uncertain significance (Oct 12, 2021)
22-16591776-C-A		not specified	Uncertain significance (Mar 01, 2023)
22-16591789-A-C		not specified	Uncertain significance (Mar 23, 2022)
22-16591824-G-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCT8L2	protein_coding	protein_coding	ENST00000359963	1	2034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000159	0.246	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0418	311	313	0.993	0.0000178	3564
Missense in Polyphen		99	96.442	1.0265		1134
Synonymous	-0.770	146	135	1.08	0.00000820	1249
Loss of Function	0.0874	9	9.29	0.969	4.02e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible molecular chaperone; assists the folding of proteins upon ATP hydrolysis. {ECO:0000250|UniProtKB:P40227}.

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.75

Haploinsufficiency Scores

• pHI: 0.449
• hipred: N
• hipred_score: 0.317
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: inorganic anion transport;potassium ion transmembrane transport
• Cellular component: chaperonin-containing T-complex
• Molecular function: anion channel activity;ATP binding;calcium-activated potassium channel activity