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GeneE
9 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
GTF3C3
general transcription factor IIIC subunit 3
Chromosome 2 Β· 2q33.1
NCBI Gene: 9330Ensembl: ENSG00000119041.12HGNC: HGNC:4666UniProt: Q9Y5Q9
138PubMed Papers
21Diseases
0Drugs
11Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleusnuclear membranetranscription factor TFIIIC complexnucleoplasmneurodegenerative diseasechromosome 2q32-q33 deletion syndromeIntellectual disabilityGlobal developmental delay
✦AI Summary

GTF3C3 encodes a key DNA-binding component of transcription factor IIIC (TFIIIC), which is essential for RNA polymerase III-mediated transcription of non-coding RNAs including tRNAs and 5S rRNA 1. As an integral subunit of the TFIIIC2 complex, GTF3C3 directly binds tRNA and virus-associated RNA promoters to facilitate transcription initiation 2. Biallelic GTF3C3 variants cause autosomal recessive neurodevelopmental disorder characterized by intellectual disability, microcephaly, distinctive dysmorphic facies, seizures, and cerebellar/frontal lobe anomalies 13. Pathogenic missense variants disrupt intra- and intermolecular protein interactions, resulting in loss-of-function effects confirmed by RNA polymerase III reporter assays 3. Some variants introduce cryptic splice sites causing mRNA missplicing 3. Animal models demonstrate that GTF3C3 loss recapitulates human clinical features including seizure susceptibility and motor impairments, with reduced RNA polymerase III target gene expression 13. The discovery of GTF3C3 as a disease gene expands understanding of TFIIIC-linked neurodevelopmental pathologies and highlights the critical role of RNA polymerase III transcription in normal brain development.

Sources cited
1
GTF3C3 is a key TFIIIC component; biallelic variants cause microcephaly, developmental delay, intellectual disability, dysmorphic facies, brain atrophy with cerebellar involvement, and seizures; zebrafish knockout shows reduced Pol III target gene expression
PMID: 40040844
2
GTF3C3 missense variants disrupt protein interactions and cause loss-of-function in Pol III reporter assays; one variant introduces cryptic splice site; neuronal Gtf3c3 loss in Drosophila causes seizure-like behavior, motor impairment, and learning deficits
PMID: 39636576
3
TFIIIC complex (including GTF3C3) regulates RNA polymerase III transcription of tRNA, 5S rRNA and 7SL RNA genes
PMID: 26038315
4
GTF3C3 is confirmed as an intellectual disability-associated gene following previous single-family reports
PMID: 28940097
5
GTF3C3 supports candidacy as a neurodevelopmental disorder gene with recessive inheritance pattern
PMID: 30552426
Disease Associationsβ“˜21
neurodegenerative diseaseOpen Targets
0.45Moderate
chromosome 2q32-q33 deletion syndromeOpen Targets
0.30Weak
Intellectual disabilityOpen Targets
0.25Weak
Global developmental delayOpen Targets
0.25Weak
SeizureOpen Targets
0.25Weak
complex neurodevelopmental disorderOpen Targets
0.18Weak
Neurodevelopmental disorderOpen Targets
0.12Weak
spinal cord injuryOpen Targets
0.09Suggestive
adrenal gland hyperfunctionOpen Targets
0.04Suggestive
hyperaldosteronismOpen Targets
0.04Suggestive
generalized dystoniaOpen Targets
0.02Suggestive
depressive disorderOpen Targets
0.02Suggestive
anxiety disorderOpen Targets
0.02Suggestive
neoplasmOpen Targets
0.02Suggestive
breast cancerOpen Targets
0.01Suggestive
nasopharyngeal carcinomaOpen Targets
0.01Suggestive
microcephalyOpen Targets
0.01Suggestive
obesityOpen Targets
0.00Suggestive
Brain atrophyOpen Targets
0.00Suggestive
epilepsyOpen Targets
0.00Suggestive
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizuresUniProt
Pathogenic Variants11
NM_012086.5(GTF3C3):c.1708C>T (p.Arg570Ter)Likely pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜…β˜†β˜†β˜†2026β†’ Residue 570
NM_012086.5(GTF3C3):c.538C>T (p.Pro180Ser)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 180
NM_012086.5(GTF3C3):c.1390+3A>GLikely pathogenic
Chromosome 2q32-q33 deletion syndrome|Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜…β˜†β˜†β˜†2024
NM_012086.5(GTF3C3):c.503C>T (p.Ala168Val)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 168
NM_012086.5(GTF3C3):c.2420G>A (p.Arg807His)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 807
NM_012086.5(GTF3C3):c.1279G>T (p.Val427Phe)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 427
NM_012086.5(GTF3C3):c.514T>G (p.Cys172Gly)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 172
NM_012086.5(GTF3C3):c.2149C>T (p.Arg717Ter)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 717
NM_012086.5(GTF3C3):c.1525G>A (p.Ala509Thr)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 509
NM_012086.5(GTF3C3):c.1436A>G (p.Tyr479Cys)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 479
NM_012086.5(GTF3C3):c.2419C>T (p.Arg807Cys)Pathogenic
Neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
β˜†β˜†β˜†β˜†2025β†’ Residue 807
View on ClinVar β†—
Related Genes
TBPProtein interaction100%BDP1Protein interaction100%CPSF2Protein interaction100%CPSF1Protein interaction100%GTF3C2Protein interaction98%GTF3C5Protein interaction98%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
90%
Brain
71%
Ovary
68%
Lung
62%
Liver
60%
Gene Interaction Network
Click a node to explore
GTF3C3TBPBDP1CPSF2CPSF1GTF3C2GTF3C5
PROTEIN STRUCTURE
Preparing viewer…
PDB8CLK Β· 3.50 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.98LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.72 [0.54–0.98]
RankingsWhere GTF3C3 stands among ~20K protein-coding genes
  • #3,337of 20,598
    Most Researched138 Β· top quartile
  • #2,744of 5,498
    Most Pathogenic Variants11
  • #9,383of 17,882
    Most Constrained (LOEUF)0.98
Genes detectedGTF3C3
Sources retrieved9 papers
Response timeβ€”
πŸ“„ Sources
9β–Ό
1
Expanding the genetic heterogeneity of intellectual disability.
PMID: 28940097
Hum Genet Β· 2017
1.00
2
Biallelic variants in
PMID: 40040844
Brain Commun Β· 2025
0.89
3
Biallelic variants in GTF3C3 result in an autosomal recessive disorder with intellectual disability.
PMID: 39636576
Genet Med Β· 2025
0.78
4
Landscape of protein-protein interactions during hepatitis C virus assembly and release.
PMID: 38230952
Microbiol Spectr Β· 2024
0.67
5
Ectodermal dysplasia-like syndrome with mental retardation due to contiguous gene deletion: further clinical and molecular delineation of del(2q32) syndrome.
PMID: 20034071
Am J Med Genet A Β· 2010
0.56