GTF3C6

general transcription factor IIIC subunit 6, the group of General transcription factor IIIC complex subunits

Basic information

Region (hg38): 6:110958706-110967890

Previous symbols: [ "C6orf51" ]

Links

ENSG00000155115 ∙ NCBI:112495 ∙ OMIM:611784 ∙ HGNC:20872 ∙ Uniprot:Q969F1 ∙ 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 GTF3C6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C6 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in GTF3C6

This is a list of pathogenic ClinVar variants found in the GTF3C6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-110958792-G-C		not specified	Likely benign (Nov 03, 2023)
6-110958806-G-A		not specified	Uncertain significance (Mar 03, 2025)
6-110959200-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-110959230-G-A		not specified	Uncertain significance (Sep 19, 2023)
6-110960430-G-C		not specified	Uncertain significance (May 20, 2024)
6-110960432-C-T		not specified	Uncertain significance (Jan 09, 2025)
6-110962442-A-G		not specified	Uncertain significance (Feb 13, 2025)
6-110962445-A-C		not specified	Uncertain significance (Oct 26, 2024)
6-110967513-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-110967547-C-G		not specified	Uncertain significance (Dec 28, 2022)
6-110967630-T-C		not specified	Uncertain significance (Jan 26, 2023)
6-110967657-T-C		not specified	Uncertain significance (Sep 10, 2024)
6-110967662-G-A		not specified	Uncertain significance (Feb 05, 2025)
6-110967725-C-T		not specified	Uncertain significance (Oct 30, 2024)
6-110967726-C-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C6	protein_coding	protein_coding	ENST00000329970	6	9331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000283	0.805	125728	0	16	125744	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	98	111	0.886	0.00000491	1422
Missense in Polyphen		20	27.405	0.72978		377
Synonymous	-1.19	47	37.7	1.25	0.00000186	362
Loss of Function	1.15	7	11.1	0.628	5.34e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in RNA polymerase III-mediated transcription. Integral, tightly associated component of the DNA-binding TFIIIC2 subcomplex that directly binds tRNA and virus-associated RNA promoters. {ECO:0000269|PubMed:17409385}.
• Pathway: Gene expression (Transcription);RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 1 Promoter;RNA Polymerase III Transcription Initiation From Type 2 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.351
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0830
• hipred: N
• hipred_score: 0.189
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c6

Gene ontology

• Biological process: transcription by RNA polymerase III;5S class rRNA transcription by RNA polymerase III;tRNA transcription by RNA polymerase III
• Cellular component: transcription factor TFIIIC complex;nucleoplasm;nuclear body
• Molecular function: DNA binding;protein binding