TNRC6C

protein-coding

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

Gene summary

Predicted to enable RNA binding activity. Involved in miRNA-mediated post-transcriptional gene silencing; positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; and positive regulation of nuclear-transcribed mRNA poly(A) tail shortening. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001142640.2

Inheritance

—

ClinVar variants

U:285B:10

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr17:77,958,703-78,108,822

External References & Databases

Ensembl (ENSG00000078687)

Transcript & Mutation Effects

hg38 • Region Span ~150.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNRC6C variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 269

not providedTotal: 7

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142640.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	1 clinvar		6
missense			271 clinvar	9 clinvar		280
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	285	10	0	295

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142640.2	RefSeq	NP_001136112.2	22	MANE Select
ENST00000696270.1	Ensembl	ENSP00000512514.1	22	MANE Select
NM_001395508.1	RefSeq	NP_001382437.1	19	Standard
NM_001395509.1	RefSeq	NP_001382438.1	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endoderm Differentiation
Competing endogenous RNAs (ceRNAs) regulate PTEN translation
Signal Transduction
Gene expression (Transcription)
Generic Transcription Pathway

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

Molecular Function

RNA binding
protein binding

Cellular Component

P-body
nucleoplasm
cytosol
micro-ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335749
Coding exons: 19
Length: 104668
Individuals with no LoFs: 124584
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 124648
p: 0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.65	815	959	0.850	0.0000531	11203
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.0029	0.0015	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000093	0.000088	rare
South Asian	0	0.0	absent
Other	0.00067	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.355
RVIS EVS: -1.54
RVIS percentile EVS: 3.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.235

Gene Damage Prediction

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