GTF3C3

general transcription factor IIIC subunit 3, the group of General transcription factor IIIC complex subunits|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:196763035-196799725

Links

ENSG00000119041 ∙ NCBI:9330 ∙ OMIM:604888 ∙ HGNC:4666 ∙ Uniprot:Q9Y5Q9 ∙ 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 GTF3C3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C3 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			31			31
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1				1
non coding						0
Total	0	0	32	0	0

Variants in GTF3C3

This is a list of pathogenic ClinVar variants found in the GTF3C3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-196764580-T-C		not specified	Uncertain significance (Jul 13, 2021)
2-196764591-G-A		not specified	Uncertain significance (Sep 01, 2024)
2-196764594-T-A		not specified	Uncertain significance (Jun 23, 2023)
2-196764594-T-G		not specified	Uncertain significance (Feb 08, 2025)
2-196764642-T-C		not specified	Uncertain significance (Dec 11, 2024)
2-196766579-G-C		GTF3C3-related disorder	Likely benign (Feb 21, 2022)
2-196766608-T-C		not specified	Uncertain significance (Feb 05, 2025)
2-196766634-C-G		Chromosome 2q32-q33 deletion syndrome	Uncertain significance (Oct 13, 2024)
2-196766683-C-T		NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES, BRAIN ANOMALIES, AND SEIZURES	Pathogenic (May 15, 2025)
2-196766684-G-A		NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES, BRAIN ANOMALIES, AND SEIZURES	Pathogenic (May 15, 2025)
2-196769985-C-G		not specified	Uncertain significance (Dec 24, 2024)
2-196770026-T-G		not specified	Uncertain significance (Apr 19, 2024)
2-196771753-G-C		not specified	Uncertain significance (Apr 28, 2023)
2-196771828-A-G		not specified	Uncertain significance (Apr 10, 2023)
2-196771859-G-A		NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES, BRAIN ANOMALIES, AND SEIZURES	Pathogenic (May 15, 2025)
2-196771859-G-C		not specified	Uncertain significance (Dec 24, 2024)
2-196771910-G-A		not specified	Uncertain significance (Feb 12, 2024)
2-196771915-T-C		not specified	Uncertain significance (May 03, 2023)
2-196771932-C-T		not specified	Uncertain significance (Nov 08, 2024)
2-196772906-G-A		GTF3C3-related disorder	Likely benign (May 21, 2019)
2-196773022-A-G		not specified	Uncertain significance (Jan 17, 2024)
2-196773065-G-C		GTF3C3-related disorder	Likely benign (Dec 02, 2019)
2-196773130-C-T		not specified	Uncertain significance (Nov 13, 2023)
2-196773131-G-A		GTF3C3-related disorder	Likely benign (May 24, 2019)
2-196773142-C-T		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C3	protein_coding	protein_coding	ENST00000263956	18	36694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.97e-7	1.00	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	321	480	0.669	0.0000249	5826
Missense in Polyphen		72	132.23	0.5445		1520
Synonymous	1.89	136	167	0.814	0.00000822	1647
Loss of Function	3.82	19	47.4	0.401	0.00000266	593

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000695
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000219	0.000217
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.000171	0.000163
Other	0.000326	0.000326

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.
• Pathway: Gene expression (Transcription);rna polymerase iii 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: 0.246

Intolerance Scores

• loftool: 0.819
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.343
• hipred: Y
• hipred_score: 0.648
• ghis: 0.669

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c3

Gene ontology

• Biological process: transcription by RNA polymerase III;5S class rRNA transcription by RNA polymerase III;tRNA transcription by RNA polymerase III;RNA polymerase III preinitiation complex assembly
• Cellular component: transcription factor TFIIIC complex;nucleus;nucleoplasm;nucleolus;nuclear membrane
• Molecular function: RNA polymerase III general transcription initiation factor activity;RNA polymerase III transcription regulator recruiting activity;DNA binding;protein binding