GTF3C1

general transcription factor IIIC subunit 1, the group of General transcription factor IIIC complex subunits

Basic information

Region (hg38): 16:27459555-27549913

Links

ENSG00000077235 ∙ NCBI:2975 ∙ OMIM:603246 ∙ HGNC:4664 ∙ Uniprot:Q12789 ∙ 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 GTF3C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C1 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			2		6	8
missense		1	127	11	2	141
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	1	129	11	8

Variants in GTF3C1

This is a list of pathogenic ClinVar variants found in the GTF3C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-27461397-G-A		not specified	Uncertain significance (Sep 26, 2024)
16-27461406-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-27461489-G-A		not specified	Uncertain significance (Oct 21, 2024)
16-27461493-T-C		not specified	Uncertain significance (Jun 25, 2024)
16-27461497-G-C		not specified	Uncertain significance (Apr 04, 2024)
16-27461516-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-27461531-C-T		not specified	Uncertain significance (Apr 11, 2023)
16-27461532-G-A		not specified	Uncertain significance (May 04, 2023)
16-27461541-T-C		not specified	Uncertain significance (Feb 08, 2025)
16-27462344-G-A		not specified	Uncertain significance (Jan 03, 2024)
16-27462348-C-T			Benign (Jan 12, 2018)
16-27462371-G-T		Esophageal atresia/tracheoesophageal fistula	Likely pathogenic (Jul 01, 2019)
16-27462373-C-T		not specified	Likely benign (May 11, 2022)
16-27462458-G-A		not specified	Uncertain significance (Jun 01, 2023)
16-27463548-G-A		not specified	Likely benign (Mar 13, 2023)
16-27463575-C-T		not specified	Uncertain significance (Apr 22, 2024)
16-27464359-C-T		not specified	Uncertain significance (Feb 01, 2025)
16-27464430-G-A		not specified	Uncertain significance (Jul 19, 2023)
16-27464454-G-A		not specified	Uncertain significance (Nov 13, 2024)
16-27464484-T-A		not specified	Uncertain significance (Apr 20, 2024)
16-27464502-A-T		not specified	Uncertain significance (Apr 01, 2024)
16-27464527-G-C			Benign (Dec 31, 2019)
16-27464530-G-A		not specified	Uncertain significance (May 17, 2023)
16-27464532-G-A		not specified	Likely benign (Feb 28, 2024)
16-27464536-G-A		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C1	protein_coding	protein_coding	ENST00000356183	37	90359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.99e-10	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.26	950	1.28e+3	0.743	0.0000816	13820
Missense in Polyphen		252	458.97	0.54905		4694
Synonymous	-0.786	543	520	1.04	0.0000344	4153
Loss of Function	8.52	11	105	0.104	0.00000582	1157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.000194	0.000185
European (Non-Finnish)	0.0000721	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for RNA polymerase III-mediated transcription. Component of TFIIIC that initiates transcription complex assembly on tRNA and is required for transcription of 5S rRNA and other stable nuclear and cytoplasmic RNAs. Binds to the box B promoter element.
• 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: 0.286

Intolerance Scores

• loftool: 0.282
• rvis_EVS: -1.71
• rvis_percentile_EVS: 2.51

Haploinsufficiency Scores

• pHI: 0.489
• hipred: Y
• hipred_score: 0.694
• ghis: 0.543

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c1
• 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;transcription initiation from RNA polymerase III promoter;rRNA transcription;tRNA transcription;5S class rRNA transcription by RNA polymerase III;tRNA transcription by RNA polymerase III
• Cellular component: transcription factor TFIIIC complex;nucleus;nucleoplasm;nucleolus;membrane;ribonucleoprotein complex
• 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;DNA binding;protein binding