TNRC6A

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

Basic information

Region (hg38): 16:24610208-24827632

Previous symbols: [ "TNRC6" ]

Links

ENSG00000090905 ∙ NCBI:27327 ∙ OMIM:610739 ∙ HGNC:11969 ∙ Uniprot:Q8NDV7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy, familial adult myoclonic, 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, familial adult myoclonic, 6	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29507423

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNRC6A gene.

• Inborn genetic diseases (68 variants)
• not provided (15 variants)
• Epilepsy, familial adult myoclonic, 6 (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNRC6A 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				2	4	6
missense			66	5	5	76
nonsense						0
start loss						0
frameshift						0
inframe indel			1	1	1	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	2	4
Total	0	0	68	9	12

Variants in TNRC6A

This is a list of pathogenic ClinVar variants found in the TNRC6A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-24750807-AAAG-A		Epilepsy, familial adult myoclonic, 6	Uncertain significance (Oct 08, 2021)
16-24758355-T-C		not specified	Uncertain significance (Aug 08, 2023)
16-24776944-A-T		not specified	Uncertain significance (May 11, 2022)
16-24776954-G-C		not specified	Uncertain significance (Dec 02, 2022)
16-24776988-C-G		not specified	Uncertain significance (Jan 31, 2024)
16-24777054-A-G			Likely benign (May 01, 2022)
16-24777089-A-C		not specified	Uncertain significance (Feb 28, 2023)
16-24777101-AGCAGCCACAGCC-A		Epilepsy, familial adult myoclonic, 6	Benign (Sep 10, 2021)
16-24777160-C-T		not specified	Uncertain significance (Jan 18, 2022)
16-24777175-G-A		not specified	Uncertain significance (Dec 14, 2022)
16-24777228-G-A			Benign (Dec 31, 2019)
16-24777324-T-A		Epilepsy, familial adult myoclonic, 6	Benign (Sep 10, 2021)
16-24777344-G-A		not specified	Uncertain significance (Jan 30, 2024)
16-24789277-G-A		not specified	Uncertain significance (Apr 22, 2022)
16-24789303-T-A		not specified	Uncertain significance (Jun 23, 2023)
16-24789312-A-G		not specified	Uncertain significance (Oct 06, 2022)
16-24789349-A-G		not specified	Uncertain significance (Oct 20, 2023)
16-24789367-C-T		not specified	Likely benign (Aug 15, 2023)
16-24789465-A-G		not specified	Uncertain significance (Jan 03, 2024)
16-24789550-A-C		not specified	Uncertain significance (May 18, 2023)
16-24789598-C-A		not specified	Uncertain significance (Apr 13, 2022)
16-24789652-G-A		not specified	Uncertain significance (Jan 18, 2023)
16-24789742-A-G		not specified	Uncertain significance (Jan 22, 2024)
16-24789757-T-C		not specified	Uncertain significance (Aug 08, 2023)
16-24789806-T-G		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNRC6A	protein_coding	protein_coding	ENST00000395799	25	97938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.34e-10	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	951	1.05e+3	0.902	0.0000558	12885
Missense in Polyphen		249	333.56	0.74649		3869
Synonymous	-0.711	398	380	1.05	0.0000212	3786
Loss of Function	8.38	9	98.9	0.0910	0.00000502	1050

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.0000798	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in RNA-mediated gene silencing by both micro-RNAs (miRNAs) and short interfering RNAs (siRNAs). Required for miRNA-dependent repression of translation and for siRNA- dependent endonucleolytic cleavage of complementary mRNAs by argonaute family proteins. As a scaffolding protein, associates with argonaute proteins bound to partially complementary mRNAs, and can simultaneously recruit CCR4-NOT and PAN deadenylase complexes. {ECO:0000269|PubMed:16284622, ECO:0000269|PubMed:16284623, ECO:0000269|PubMed:17596515, ECO:0000269|PubMed:17671087, ECO:0000269|PubMed:19056672, ECO:0000269|PubMed:19304925}.
• Pathway: 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;Transcriptional regulation by small RNAs;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: 0.114

Intolerance Scores

• loftool: 0.231
• rvis_EVS: -1.02
• rvis_percentile_EVS: 7.88

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.762
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnrc6a
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; hematopoietic 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)

Gene ontology

• Biological process: Wnt signaling pathway, calcium modulating pathway;cellular response to starvation;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;regulation of gene silencing by miRNA
• Cellular component: P-body;nucleoplasm;Golgi apparatus;cytosol;micro-ribonucleoprotein complex;intracellular membrane-bounded organelle
• Molecular function: RNA binding;protein binding