CNOT10

CCR4-NOT transcription complex subunit 10, the group of Tetratricopeptide repeat domain containing|CCR4-NOT transcription complex

Basic information

Region (hg38): 3:32685145-32773875

Links

ENSG00000182973 ∙ NCBI:25904 ∙ ∙ HGNC:23817 ∙ Uniprot:Q9H9A5 ∙ 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 CNOT10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT10 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			45			45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	1	0

Variants in CNOT10

This is a list of pathogenic ClinVar variants found in the CNOT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-32685464-G-A		not specified	Uncertain significance (Aug 12, 2024)
3-32703874-G-A		not specified	Uncertain significance (Dec 09, 2023)
3-32703877-C-G		not specified	Uncertain significance (Jan 16, 2025)
3-32703886-A-G		not specified	Uncertain significance (Dec 30, 2024)
3-32703916-C-G		not specified	Uncertain significance (Nov 07, 2024)
3-32708690-A-C		not specified	Uncertain significance (Oct 06, 2022)
3-32708719-G-A		not specified	Uncertain significance (Oct 25, 2024)
3-32708721-A-T		not specified	Uncertain significance (Nov 13, 2024)
3-32708742-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-32708760-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-32708761-G-A		not specified	Uncertain significance (Jan 10, 2022)
3-32713247-G-A		not specified	Uncertain significance (May 23, 2023)
3-32713274-A-G		not specified	Uncertain significance (Dec 28, 2024)
3-32713345-C-T		not specified	Likely benign (Oct 21, 2024)
3-32713347-A-G		not specified	Uncertain significance (Nov 28, 2023)
3-32716238-A-G		not specified	Uncertain significance (Jun 06, 2022)
3-32716258-C-T		not specified	Uncertain significance (Oct 06, 2022)
3-32716300-A-C		not specified	Uncertain significance (Nov 13, 2023)
3-32716303-A-C		not specified	Uncertain significance (Jan 17, 2023)
3-32717167-C-T		not specified	Uncertain significance (Feb 10, 2022)
3-32717196-T-C		not specified	Uncertain significance (Aug 10, 2021)
3-32717222-G-A		not specified	Uncertain significance (May 10, 2024)
3-32720118-C-T		not specified	Uncertain significance (Aug 10, 2021)
3-32720121-C-T		not specified	Uncertain significance (May 05, 2023)
3-32720177-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNOT10	protein_coding	protein_coding	ENST00000454516	19	88731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0181	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	316	419	0.755	0.0000207	5281
Missense in Polyphen		80	136.52	0.58601		1770
Synonymous	1.57	125	149	0.837	0.00000768	1475
Loss of Function	5.10	7	43.1	0.162	0.00000207	560

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000439
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 CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4- NOT complex. {ECO:0000269|PubMed:23221646}.
• Pathway: RNA degradation - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Metabolism of RNA;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Deadenylation of mRNA;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.65

Haploinsufficiency Scores

• pHI: 0.208
• hipred: Y
• hipred_score: 0.629
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnot10

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;mRNA catabolic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;negative regulation of translation;gene silencing by RNA
• Cellular component: nucleus;cytosol;membrane;CCR4-NOT complex
• Molecular function: protein binding