TAF1B
protein-codingTATA-box binding protein associated factor, RNA polymerase I subunit B
Gene summary
Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes one of the SL1-specific TAFs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~91.0 kbGenCC 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 TAF1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005680.3. 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 | 1 | 1 | ||||
| missense | 73 | 3 | 76 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 80 | 3 | 0 | 83 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005671.3 | 15 | MANE Select | |
| Ensembl | ENSP00000263663.4 | 15 | MANE Select | |
| RefSeq | NP_001305905.1 | 8 | Standard | |
| RefSeq | NP_001305906.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| taf1b | Danio rerio | Structure: head Quality: pointed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- B-WICH complex positively regulates rRNA expression
- Positive epigenetic regulation of rRNA expression
- SIRT1 negatively regulates rRNA expression
- NoRC negatively regulates rRNA expression
- Negative epigenetic regulation of rRNA expression
Biological Process
- RNA polymerase I preinitiation complex assembly
- transcription, DNA-templated
- transcription initiation from RNA polymerase I promoter
- termination of RNA polymerase I transcription
- nucleolar large rRNA transcription by RNA polymerase I
Molecular Function
- RNA polymerase I CORE element sequence-specific DNA binding
- protein binding
- TBP-class protein binding
- metal ion binding
Cellular Component
- nucleus
- nucleoplasm
- RNA polymerase transcription factor SL1 complex
- RNA polymerase I core factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263663
- Coding exons
- 15
- Length
- 91063
- Individuals with no LoFs
- 125612
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 135
- Defined
- 125748
- p
- 0.000541
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.775 | 257 | 294 | 0.873 | 0.0000144 | 3868 |
| Missense (PolyPhen) | 61 | 88.515 | 0.68915 | 1189 | ||
| Synonymous | -0.265 | 105 | 102 | 1.03 | 0.00000516 | 1012 |
| Loss of Function | 1.44 | 27 | 36.3 | 0.743 | 0.00000171 | 462 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.00052 | 0.00046 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00060 | 0.00049 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00079 | 0.00071 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of RNA polymerase I core factor complex that acts as a GTF2B/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment as a component of the SL1/TIF-IB complex and, possibly, directly through its interaction with RRN3. {ECO:0000269|PubMed:15970593, ECO:0000269|PubMed:21921198, ECO:0000269|PubMed:21921199, ECO:0000269|PubMed:7491500, ECO:0000269|PubMed:7801123, ECO:0000269|PubMed:7801130}.;
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- LoFtool
- 0.941
- RVIS EVS
- 0.76
- RVIS percentile EVS
- 86.8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.713
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |