GeneBe

GTF2B

protein-coding

general transcription factor IIB, the group of General transcription factors

Gene summary

This gene encodes the general transcription factor IIB, one of the ubiquitous factors required for transcription initiation by RNA polymerase II. The protein localizes to the nucleus where it forms a complex (the DAB complex) with transcription factors IID and IIA. Transcription factor IIB serves as a bridge between IID, the factor which initially recognizes the promoter sequence, and RNA polymerase II. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001514.6

Inheritance

—

ClinVar variants

U:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr1:88,852,633-88,891,944

External References & Databases

Ensembl (ENSG00000137947)NCBI Gene (2959)OMIM (189963)HGNC:4648GenCCUniProt (Q00403)AlphaFoldClinVar (GTF2B)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~39.3 kb
Loading mutation effect viewer...

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 GTF2B variants in ClinVar

1 Conditions Cataloged
not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001514.6. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
15
clinvar
 15
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00180018
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001514.6RefSeqNP_001505.17MANE Select
ENST00000370500.10EnsemblENSP00000359531.57MANE Select
ENST00000418217.1EnsemblENSP00000402345.16Standard
ENST00000448623.5EnsemblENSP00000415741.17Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Basal transcription factors - Homo sapiens (human)
  • Viral carcinogenesis - Homo sapiens (human)
  • Epstein-Barr virus infection - Homo sapiens (human)
  • Eukaryotic Transcription Initiation
  • Disease

Biological Process

  • transcriptional start site selection at RNA polymerase II promoter
  • DNA-templated transcription, initiation
  • transcription by RNA polymerase II
  • transcription initiation from RNA polymerase II promoter
  • protein acetylation

Molecular Function

  • RNA polymerase II core promoter sequence-specific DNA binding
  • RNA polymerase II complex binding
  • core promoter binding
  • RNA polymerase II complex recruiting activity
  • histone acetyltransferase activity

Cellular Component

  • nucleus
  • nucleoplasm
  • transcription factor TFIID complex
  • chromosome
  • nuclear body

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000370500
Coding exons
7
Length
39013
Individuals with no LoFs
125730
Homozygous LoFs
0
Heterozygous LoFs
17
Defined
125747
p
0.0000676
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.53841790.4680.000009292068
Missense (PolyPhen)1963.8950.29736721
Synonymous0.09405959.90.9850.00000300625
Loss of Function1.82917.10.5260.00000117171

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.000100.000099rare
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000880.000088rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: General transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). Involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA (PubMed:1876184, PubMed:1946368, PubMed:1517211, PubMed:3818643, PubMed:3029109, PubMed:8413225, PubMed:8515820, PubMed:8516311, PubMed:8516312, PubMed:7601352, PubMed:9420329, PubMed:12931194, PubMed:27193682). Together with the TATA box-bound TBP forms the core initiation complex and provides a bridge between TBP and the Pol II-TFIIF complex (PubMed:8504927, PubMed:8413225, PubMed:8515820, PubMed:8516311, PubMed:8516312). Released from the PIC early following the onset of transcription during the initiation and elongation transition and reassociates with TBP during the next transcription cycle (PubMed:7601352). Associates with chromatin to core promoter- specific regions (PubMed:12931194, PubMed:24441171). Binds to two distinct DNA core promoter consensus sequence elements in a TBP- independent manner; these IIB-recognition elements (BREs) are localized immediately upstream (BREu), 5'-[GC][GC][GA]CGCC-3', and downstream (BREd), 5'-[GA]T[TGA][TG][GT][TG][TG]-3', of the TATA box element (PubMed:9420329, PubMed:16230532, PubMed:7675079, PubMed:10619841). Modulates transcription start site selection (PubMed:10318856). Exhibits also autoacetyltransferase activity that contributes to the activated transcription (PubMed:12931194). {ECO:0000269|PubMed:10318856, ECO:0000269|PubMed:10619841, ECO:0000269|PubMed:12931194, ECO:0000269|PubMed:1517211, ECO:0000269|PubMed:16230532, ECO:0000269|PubMed:1876184, ECO:0000269|PubMed:1946368, ECO:0000269|PubMed:24441171, ECO:0000269|PubMed:27193682, ECO:0000269|PubMed:3029109, ECO:0000269|PubMed:3818643, ECO:0000269|PubMed:7601352, ECO:0000269|PubMed:7675079, ECO:0000269|PubMed:8413225, ECO:0000269|PubMed:8504927, ECO:0000269|PubMed:8515820, ECO:0000269|PubMed:8516311, ECO:0000269|PubMed:8516312, ECO:0000269|PubMed:9420329}.;

Recessive Scores

pRec
0.350

Intolerance Scores

RVIS EVS
0.1
RVIS percentile EVS
61.28

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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