GTF3C4

general transcription factor IIIC subunit 4, the group of Lysine acetyltransferases|General transcription factor IIIC complex subunits

Basic information

Region (hg38): 9:132670035-132694953

Links

ENSG00000125484 ∙ NCBI:9329 ∙ OMIM:604892 ∙ HGNC:4667 ∙ Uniprot:Q9UKN8 ∙ 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 GTF3C4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C4 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				1		1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in GTF3C4

This is a list of pathogenic ClinVar variants found in the GTF3C4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132670058-G-T		not specified	Uncertain significance (Jan 31, 2024)
9-132670065-G-A		not specified	Uncertain significance (May 30, 2024)
9-132670071-G-T		not specified	Uncertain significance (Jul 25, 2023)
9-132670095-G-C		not specified	Uncertain significance (May 30, 2024)
9-132670111-G-A		not specified	Uncertain significance (Apr 06, 2024)
9-132670173-G-T		not specified	Uncertain significance (Dec 21, 2022)
9-132670191-C-G		not specified	Uncertain significance (Nov 19, 2024)
9-132670604-C-A		not specified	Uncertain significance (Oct 12, 2021)
9-132670606-C-T		not specified	Uncertain significance (Apr 18, 2023)
9-132670630-C-T		not specified	Uncertain significance (Nov 26, 2024)
9-132670638-G-A		not specified	Uncertain significance (May 10, 2022)
9-132670645-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-132670741-G-A		not specified	Uncertain significance (Mar 14, 2023)
9-132670753-C-G		not specified	Uncertain significance (May 16, 2023)
9-132670755-C-T		not specified	Uncertain significance (May 24, 2024)
9-132670780-A-G		not specified	Uncertain significance (Mar 11, 2024)
9-132670794-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-132670868-G-A			Likely benign (Jan 01, 2023)
9-132670917-A-T		not specified	Uncertain significance (Aug 26, 2024)
9-132670926-C-T		not specified	Uncertain significance (Oct 14, 2021)
9-132670938-A-G		not specified	Uncertain significance (Feb 15, 2024)
9-132678076-C-T		not specified	Uncertain significance (Apr 25, 2023)
9-132678100-A-G		not specified	Uncertain significance (Jul 02, 2024)
9-132678218-T-C		not specified	Uncertain significance (Apr 23, 2024)
9-132678478-G-A		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C4	protein_coding	protein_coding	ENST00000372146	5	24921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.259	0.741	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	302	445	0.678	0.0000232	5384
Missense in Polyphen		98	177.65	0.55166		2186
Synonymous	0.148	173	175	0.986	0.00000985	1602
Loss of Function	3.85	7	29.6	0.236	0.00000142	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000938	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for RNA polymerase III to make a number of small nuclear and cytoplasmic RNAs, including 5S RNA, tRNA, and adenovirus-associated (VA) RNA of both cellular and viral origin. Has histone acetyltransferase activity (HAT) with unique specificity for free and nucleosomal H3. May cooperate with GTF3C5 in facilitating the recruitment of TFIIIB and RNA polymerase through direct interactions with BRF1, POLR3C and POLR3F. May be localized close to the A box.
• 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: 0.245

Intolerance Scores

• loftool: 0.494
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.756
• ghis: 0.558

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c4

Gene ontology

• Biological process: transcription by RNA polymerase III;transcription initiation from RNA polymerase III promoter;histone acetylation;5S class rRNA transcription by RNA polymerase III;tRNA transcription by RNA polymerase III;positive regulation of catalytic activity
• Cellular component: transcription factor TFIIIC complex;nucleus;nucleoplasm;mitochondrion
• Molecular function: DNA binding;histone acetyltransferase activity;protein binding;enzyme activator activity