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

• genetic developmental and epileptic encephalopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GTF3C3 gene.

• not_specified (60 variants)
• NEURODEVELOPMENTAL_DISORDER_WITH_DYSMORPHIC_FACIES,_BRAIN_ANOMALIES,_AND_SEIZURES (9 variants)
• GTF3C3-related_disorder (7 variants)
• Chromosome_2q32-q33_deletion_syndrome (2 variants)
• not_provided (1 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Neurodevelopmental_disorder (1 variants)

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. These statistics are base on transcript: NM_000012086.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense	7		61	2	1	71
nonsense	1		1			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	8	0	62	6	1

Highest pathogenic variant AF is 0.0000397117

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