GTF3C2

protein-coding

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

Gene summary

Enables RNA polymerase III general transcription initiation factor activity. Contributes to DNA binding activity. Involved in transcription initiation at RNA polymerase III promoter. Located in nucleoplasm. Part of transcription factor TFIIIC complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001035521.3

Inheritance

—

ClinVar variants

U:102B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr2:27,325,849-27,356,999

External References & Databases

Ensembl (ENSG00000115207)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GTF3C2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001035521.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			97 clinvar	4 clinvar		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	102	5	0	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001035521.3	RefSeq	NP_001030598.1	18	MANE Select
ENST00000264720.8	Ensembl	ENSP00000264720.3	18	MANE Select
NM_001318909.4	RefSeq	NP_001305838.2	18	Standard
NM_001388380.3	RefSeq	NP_001375309.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

transcription by RNA polymerase III
5S class rRNA transcription by RNA polymerase III
tRNA transcription by RNA polymerase III

Molecular Function

RNA polymerase III general transcription initiation factor activity
DNA binding
protein binding

Cellular Component

transcription factor TFIIIC complex
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359541
Coding exons: 18
Length: 31153
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.29	377	524	0.719	0.0000295	5827
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.235

Intolerance Scores

LoFtool: 0.482
RVIS EVS: -1.4
RVIS percentile EVS: 4.22

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Indispensability pred.: E
Indispensability score: 0.974

Gene Damage Prediction

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