GTF3C2

general transcription factor IIIC subunit 2, the group of General transcription factor IIIC complex subunits|WD repeat domain containing

Basic information

Region (hg38): 2:27325848-27356999

Links

ENSG00000115207 ∙ NCBI:2976 ∙ OMIM:604883 ∙ HGNC:4665 ∙ Uniprot:Q8WUA4 ∙ 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 GTF3C2 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF3C2 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in GTF3C2

This is a list of pathogenic ClinVar variants found in the GTF3C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27326698-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-27326733-G-A		not specified	Uncertain significance (May 27, 2022)
2-27326775-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-27326854-C-A		not specified	Uncertain significance (Mar 20, 2023)
2-27327240-C-T		not specified	Uncertain significance (Aug 09, 2021)
2-27328071-T-C		not specified	Uncertain significance (Jan 22, 2024)
2-27328119-G-A		not specified	Uncertain significance (Jun 13, 2022)
2-27328125-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-27329227-G-A		not specified	Uncertain significance (May 24, 2023)
2-27329278-A-T		not specified	Uncertain significance (Aug 17, 2021)
2-27329455-A-C		not specified	Uncertain significance (Oct 29, 2021)
2-27329478-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-27335613-C-T		not specified	Uncertain significance (Dec 08, 2023)
2-27335927-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-27336224-G-T			Likely benign (Jun 01, 2022)
2-27337275-G-A		not specified	Uncertain significance (Feb 27, 2024)
2-27337932-T-C		not specified	Uncertain significance (Jul 14, 2023)
2-27337945-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-27337963-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-27341958-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-27342033-A-C		not specified	Likely benign (Jan 10, 2022)
2-27342175-C-A		not specified	Uncertain significance (Sep 20, 2023)
2-27342911-G-C		not specified	Uncertain significance (Jun 18, 2021)
2-27342976-G-C		not specified	Uncertain significance (Sep 29, 2023)
2-27343072-C-T		not specified	Uncertain significance (Aug 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF3C2	protein_coding	protein_coding	ENST00000359541	18	31153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00560	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	377	524	0.719	0.0000295	5827
Missense in Polyphen		71	153.65	0.4621		1631
Synonymous	-0.812	211	197	1.07	0.0000105	1916
Loss of Function	5.95	10	59.5	0.168	0.00000405	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

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. May play a direct role in stabilizing interactions of TFIIIC2 with TFIIIC1.
• Pathway: Gene expression (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: 0.235

Intolerance Scores

• loftool: 0.482
• rvis_EVS: -1.4
• rvis_percentile_EVS: 4.22

Haploinsufficiency Scores

• pHI: 0.559
• hipred: Y
• hipred_score: 0.736
• ghis: 0.680

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf3c2

Gene ontology

• Biological process: transcription by RNA polymerase III;5S class rRNA transcription by RNA polymerase III;tRNA transcription by RNA polymerase III
• Cellular component: transcription factor TFIIIC complex;nucleoplasm
• Molecular function: RNA polymerase III general transcription initiation factor activity;DNA binding;protein binding