TAF6L
protein-codingTATA-box binding protein associated factor 6 like, the group of SAGA complex
Gene summary
Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a protein that is a component of the PCAF histone acetylase complex and structurally similar to one of the histone-like TAFs, TAF6. The PCAF histone acetylase complex, which is composed of more than 20 polypeptides some of which are TAFs, is required for myogenic transcription and differentiation. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.0 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 TAF6L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006473.4. 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 | 2 | 2 | ||||
| missense | 86 | 4 | 90 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 92 | 4 | 0 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006464.1 | 10 | MANE Select | |
| Ensembl | ENSP00000294168.3 | 10 | MANE Select | |
| Ensembl | ENSP00000435443.1 | 2 | Standard | |
| Ensembl | ENSP00000435116.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Basal transcription factors - Homo sapiens (human)
- Herpes simplex infection - Homo sapiens (human)
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
Biological Process
- chromatin organization
- chromatin remodeling
- regulation of transcription by RNA polymerase II
- transcription by RNA polymerase II
- transcription initiation from RNA polymerase II promoter
Molecular Function
- RNA polymerase II activating transcription factor binding
- DNA binding
- DNA-binding transcription factor activity
- transcription coactivator activity
- histone acetyltransferase activity
Cellular Component
- histone deacetylase complex
- SAGA complex
- nucleus
- nucleoplasm
- transcription factor TFIID complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000294168
- Coding exons
- 10
- Length
- 16040
- Individuals with no LoFs
- 125727
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125748
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.846 | 308 | 353 | 0.873 | 0.0000195 | 3903 |
| Missense (PolyPhen) | 60 | 77.558 | 0.77361 | 793 | ||
| Synonymous | -0.968 | 171 | 156 | 1.10 | 0.00000849 | 1379 |
| Loss of Function | 3.40 | 7 | 25.5 | 0.274 | 0.00000133 | 275 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000064 | 0.000062 | rare |
| South Asian | 0.00011 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a component of the PCAF complex. The PCAF complex is capable of efficiently acetylating histones in a nucleosomal context. The PCAF complex could be considered as the human version of the yeast SAGA complex.;
Recessive Scores
- pRec
- 0.0909
Intolerance Scores
- LoFtool
- 0.333
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 29.31
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.832
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |