GTF3C5

general transcription factor IIIC subunit 5, the group of General transcription factor IIIC complex subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:133030675-133058503

Links

ENSG00000148308 ∙ NCBI:9328 ∙ OMIM:604890 ∙ HGNC:4668 ∙ Uniprot:Q9Y5Q8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GTF3C5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C5 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			50	3		53
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	4	0

Variants in GTF3C5

This is a list of pathogenic ClinVar variants found in the GTF3C5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133031024-G-A		not specified	Uncertain significance (Nov 09, 2024)
9-133031030-G-T		not specified	Uncertain significance (Dec 02, 2022)
9-133031031-A-G		not specified	Uncertain significance (Jan 08, 2024)
9-133031032-T-G		not specified	Uncertain significance (Jan 21, 2025)
9-133031048-G-A		not specified	Uncertain significance (Aug 20, 2024)
9-133031049-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-133031051-G-A		not specified	Likely benign (Jun 06, 2023)
9-133031069-C-T		not specified	Uncertain significance (Apr 22, 2022)
9-133031081-A-G		not specified	Uncertain significance (Feb 13, 2025)
9-133031108-G-A		not specified	Uncertain significance (Feb 11, 2025)
9-133031126-A-G		not specified	Uncertain significance (Jun 16, 2023)
9-133031129-C-G		not specified	Uncertain significance (Jan 16, 2025)
9-133031156-G-A		not specified	Uncertain significance (Aug 23, 2021)
9-133042108-A-G		not specified	Uncertain significance (Jun 05, 2023)
9-133042141-T-C		not specified	Uncertain significance (Feb 25, 2025)
9-133042165-C-T		not specified	Uncertain significance (Mar 22, 2022)
9-133042192-C-T		not specified	Uncertain significance (Jun 11, 2021)
9-133042193-G-T		not specified	Uncertain significance (Jan 27, 2022)
9-133042223-G-T		not specified	Uncertain significance (Apr 12, 2023)
9-133042292-T-A		not specified	Uncertain significance (Jan 26, 2025)
9-133043728-G-C		not specified	Uncertain significance (Dec 17, 2024)
9-133043762-G-A		not specified	Likely benign (Mar 20, 2024)
9-133043772-G-A		not specified	Uncertain significance (Aug 10, 2021)
9-133043812-G-A		not specified	Uncertain significance (Nov 23, 2022)
9-133043817-G-T		Multisystem developmental disorder	Uncertain significance (Feb 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C5	protein_coding	protein_coding	ENST00000372108	12	27815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-8	0.958	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.772	292	332	0.881	0.0000207	3418
Missense in Polyphen		78	108.23	0.7207		1053
Synonymous	-0.999	149	134	1.11	0.00000872	1014
Loss of Function	2.02	17	28.7	0.593	0.00000162	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000698	0.000696
Ashkenazi Jewish	0.000908	0.000893
East Asian	0.000438	0.000435
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000438	0.000435
South Asian	0.0000989	0.0000980
Other	0.000655	0.000652

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: 0.109

Intolerance Scores

• loftool: 0.744
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.83

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.746
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c5
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: transcription by RNA polymerase III;skeletal muscle cell differentiation;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;nucleoplasm
• Molecular function: RNA polymerase III general transcription initiation factor activity;RNA polymerase III type 1 promoter sequence-specific DNA binding;RNA polymerase III type 2 promoter sequence-specific DNA binding;RNA polymerase III transcription regulator recruiting activity;DNA binding;protein binding