TAF1D
protein-codingTATA-box binding protein associated factor, RNA polymerase I subunit D, the group of Small nucleolar RNA protein coding host genes
Gene summary
TAF1D is a member of the SL1 complex, which includes TBP (MIM 600075) and TAF1A (MIM 604903), TAF1B (MIM 604904), and TAF1C (MIM 604905), and plays a role in RNA polymerase I transcription (Wang et al., 2004 [PubMed 15520167]; Gorski et al., 2007 [PubMed 17318177]).[supplied by OMIM, Jun 2009]
- JOSD3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~54.4 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 TAF1D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024116.4. 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 | 34 | 4 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 36 | 4 | 0 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_077021.1 | 5 | MANE Select | |
| Ensembl | ENSP00000410409.2 | 5 | MANE Select | |
| Ensembl | ENSP00000314971.2 | 5 | Standard | |
| Ensembl | ENSP00000376944.2 | 4 | Standard |
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
- regulation of transcription, DNA-templated
- transcription initiation from RNA polymerase I promoter
- termination of RNA polymerase I transcription
- positive regulation of gene expression, epigenetic
Molecular Function
- DNA binding
- protein binding
Cellular Component
- nucleoplasm
- RNA polymerase transcription factor SL1 complex
- microtubule organizing center
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000448108
- Coding exons
- 5
- Length
- 54444
- Individuals with no LoFs
- 124949
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 124955
- p
- 0.0000240
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.365 | 126 | 138 | 0.913 | 0.00000676 | 1825 |
| Missense (PolyPhen) | 31 | 37.556 | 0.82543 | 589 | ||
| Synonymous | -0.0900 | 47 | 46.2 | 1.02 | 0.00000222 | 488 |
| Loss of Function | 0.719 | 9 | 11.6 | 0.773 | 6.79e-7 | 161 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000062 | 0.000059 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00017 | 0.00016 | 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 (preinitiation 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:17318177}.;
Recessive Scores
- pRec
- 0.0882
Intolerance Scores
- LoFtool
- 0.390
- RVIS EVS
- 0.26
- RVIS percentile EVS
- 70.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |