TNRC6C

trinucleotide repeat containing adaptor 6C, the group of TNRC6 adaptor family

Basic information

Region (hg38): 17:77958702-78108822

Links

ENSG00000078687 ∙ NCBI:57690 ∙ OMIM:610741 ∙ HGNC:29318 ∙ Uniprot:Q9HCJ0 ∙ 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 TNRC6C gene.

• Inborn genetic diseases (79 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNRC6C 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			79	2		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	80	2	0

Variants in TNRC6C

This is a list of pathogenic ClinVar variants found in the TNRC6C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-78049087-A-G		not specified	Uncertain significance (Jun 24, 2022)
17-78049133-A-G		not specified	Uncertain significance (Feb 05, 2024)
17-78049144-G-A		not specified	Uncertain significance (Mar 04, 2024)
17-78049207-G-T		not specified	Uncertain significance (Dec 21, 2023)
17-78049255-T-C		not specified	Uncertain significance (Mar 12, 2024)
17-78049273-G-A		not specified	Uncertain significance (Mar 16, 2022)
17-78049283-T-C		not specified	Uncertain significance (Jan 11, 2023)
17-78049297-G-A		not specified	Uncertain significance (Jul 09, 2021)
17-78049307-G-A			Uncertain significance (Sep 01, 2022)
17-78049408-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-78049414-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-78049445-G-T		not specified	Uncertain significance (Feb 10, 2022)
17-78049450-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-78049475-G-A		not specified	Uncertain significance (Nov 05, 2021)
17-78049486-G-A		not specified	Uncertain significance (Jan 20, 2023)
17-78049487-G-T		not specified	Uncertain significance (Feb 27, 2024)
17-78049495-A-T		not specified	Uncertain significance (Apr 19, 2023)
17-78049582-G-A		not specified	Uncertain significance (Nov 13, 2023)
17-78049607-A-G		not specified	Uncertain significance (Jan 03, 2024)
17-78049630-A-G		not specified	Uncertain significance (Dec 15, 2022)
17-78049646-A-G		not specified	Uncertain significance (Jan 31, 2023)
17-78049799-A-G			Uncertain significance (Jan 01, 2024)
17-78049805-T-C		not specified	Uncertain significance (Dec 13, 2022)
17-78049877-C-T		not specified	Uncertain significance (Sep 01, 2021)
17-78049969-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNRC6C	protein_coding	protein_coding	ENST00000335749	19	104668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.67e-9	124584	0	64	124648	0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	815	959	0.850	0.0000531	11203
Missense in Polyphen		275	377.27	0.72891		4402
Synonymous	1.10	364	392	0.929	0.0000250	3504
Loss of Function	7.42	4	72.0	0.0556	0.00000341	761

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00286	0.00286
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000931	0.0000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000665	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in RNA-mediated gene silencing by micro- RNAs (miRNAs). Required for miRNA-dependent translational repression of complementary mRNAs by argonaute family proteins. As scaffoldng protein associates with argonaute proteins bound to partially complementary mRNAs and simultaneously can recruit CCR4- NOT and PAN deadenylase complexes. {ECO:0000269|PubMed:19304925, ECO:0000269|PubMed:21981923, ECO:0000269|PubMed:21984184, ECO:0000269|PubMed:21984185}.
• Pathway: Endoderm Differentiation;Competing endogenous RNAs (ceRNAs) regulate PTEN translation;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;RNA Polymerase II Transcription;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Regulation of PTEN mRNA translation;PTEN Regulation;PIP3 activates AKT signaling;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;Regulation of RUNX1 Expression and Activity;Estrogen-dependent gene expression;ESR-mediated signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1;Post-transcriptional silencing by small RNAs;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.355
• rvis_EVS: -1.54
• rvis_percentile_EVS: 3.34

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.776
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnrc6c
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: Wnt signaling pathway, calcium modulating pathway;positive regulation of gene expression;negative regulation of gene expression;posttranscriptional gene silencing by RNA;gene silencing by miRNA;miRNA mediated inhibition of translation;regulation of megakaryocyte differentiation;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
• Cellular component: P-body;nucleoplasm;cytosol;micro-ribonucleoprotein complex
• Molecular function: RNA binding;protein binding