TAF1A
protein-codingTATA-box binding protein associated factor, RNA polymerase I subunit A
Gene summary
This gene encodes a subunit of the RNA polymerase I complex, Selectivity Factor I (SLI). The encoded protein is a TATA box-binding protein-associated factor that plays a role in the assembly of the RNA polymerase I preinitiation complex. Alternate splicing results in multiple transcript variants encoding multiple isoforms.[provided by RefSeq, Jan 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~32.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015470
Submitter: Orphanet
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TAF1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005681.4. 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 | 0 | |||||
| missense | 47 | 4 | 1 | 52 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 4 | 1 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005672.1 | 10 | MANE Select | |
| Ensembl | ENSP00000327072.6 | 10 | MANE Select | |
| RefSeq | NP_001188465.1 | 10 | Standard | |
| RefSeq | NP_647603.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| taf1a | Danio rerio | Structure: whole organism Quality: decreased life span 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
- transcription by RNA polymerase I
- transcription initiation from RNA polymerase I promoter
- termination of RNA polymerase I transcription
- transcription by RNA polymerase II
- positive regulation of gene expression, epigenetic
Molecular Function
- DNA binding
- protein binding
Cellular Component
- RNA polymerase I transcription factor complex
- nucleoplasm
- microtubule cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000350027
- Coding exons
- 10
- Length
- 32032
- Individuals with no LoFs
- 125673
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 70
- Defined
- 125743
- p
- 0.000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 186 | 229 | 0.814 | 0.0000110 | 2980 |
| Missense (PolyPhen) | 52 | 68.838 | 0.7554 | 945 | ||
| Synonymous | 0.127 | 80 | 81.5 | 0.982 | 0.00000396 | 758 |
| Loss of Function | 1.56 | 18 | 26.7 | 0.674 | 0.00000119 | 349 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00070 | 0.00058 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00034 | 0.00033 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (pre- initiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation probably is primarily dependent on the rate of association of SL1/TIF-IB with the rDNA promoter. SL1/TIF-IB is involved in stabilization of nucleolar transcription factor 1/UBTF on rDNA. Formation of SL1/TIF-IB excludes the association of TBP with TFIID subunits. {ECO:0000269|PubMed:15970593, ECO:0000269|PubMed:7801123}.;
Recessive Scores
- pRec
- 0.0680
Intolerance Scores
- LoFtool
- 0.626
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.888
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |