TAF12
TATA-box binding protein associated factor 12, the group of General transcription factor IID complex subunits |SAGA complex
Basic information
Region (hg38): 1:28587828-28648291
Previous symbols: [ "TAF2J" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF12 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 11 | 11 | ||||
| Total | 0 | 0 | 19 | 0 | 0 |
Variants in TAF12
This is a list of pathogenic ClinVar variants found in the TAF12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-28592578-A-C | not specified | Uncertain significance (Jun 18, 2021) | ||
| 1-28592614-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 1-28592637-G-C | not specified | Uncertain significance (Jan 22, 2024) | ||
| 1-28592692-G-A | not specified | Uncertain significance (Jun 13, 2022) | ||
| 1-28593717-G-A | not specified | Uncertain significance (Jun 28, 2023) | ||
| 1-28593781-A-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 1-28593906-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 1-28593929-G-C | not specified | Uncertain significance (Aug 16, 2022) | ||
| 1-28594032-G-T | not specified | Uncertain significance (Nov 28, 2023) | ||
| 1-28594053-T-C | not specified | Uncertain significance (Aug 04, 2023) | ||
| 1-28594075-G-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-28594077-C-A | not specified | Uncertain significance (May 31, 2022) | ||
| 1-28603558-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 1-28605389-T-C | not specified | Uncertain significance (Jan 10, 2022) | ||
| 1-28605412-C-T | not specified | Uncertain significance (Nov 02, 2023) | ||
| 1-28605416-T-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| 1-28605424-G-C | not specified | Uncertain significance (May 07, 2024) | ||
| 1-28621936-C-T | not specified | Uncertain significance (Apr 07, 2022) | ||
| 1-28621963-A-G | not specified | Uncertain significance (Dec 15, 2023) | ||
| 1-28621969-A-G | not specified | Uncertain significance (Aug 17, 2021) | ||
| 1-28621981-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 1-28622014-G-C | not specified | Uncertain significance (Jan 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TAF12 | protein_coding | protein_coding | ENST00000263974 | 5 | 53763 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.950 | 0.0498 | 125640 | 0 | 4 | 125644 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.29 | 55 | 89.4 | 0.615 | 0.00000476 | 1050 |
| Missense in Polyphen | 2 | 11.849 | 0.16879 | 158 | ||
| Synonymous | -0.0763 | 33 | 32.4 | 1.02 | 0.00000163 | 311 |
| Loss of Function | 2.85 | 0 | 9.44 | 0.00 | 4.85e-7 | 105 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TAFs components-TIIFD are essential for mediating regulation of RNA polymerase transcription.;
- Pathway
- Basal transcription factors - Homo sapiens (human);Eukaryotic Transcription Initiation;Disease;Gene expression (Transcription);Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;HIV Transcription Initiation;RNA Polymerase II Transcription;Chromatin modifying enzymes;Infectious disease;RNA Polymerase II Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;HATs acetylate histones;Regulation of TP53 Activity through Phosphorylation;Chromatin organization;C-MYC pathway;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.121
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.33
Haploinsufficiency Scores
- pHI
- 0.473
- hipred
- Y
- hipred_score
- 0.824
- ghis
- 0.509
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Taf12
- Phenotype
Gene ontology
- Biological process
- DNA-templated transcription, initiation;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;histone H3 acetylation;positive regulation of DNA-binding transcription factor activity;RNA polymerase II preinitiation complex assembly;regulation of signal transduction by p53 class mediator;positive regulation of nucleic acid-templated transcription
- Cellular component
- SAGA complex;nucleus;nucleoplasm;transcription factor TFIID complex;STAGA complex;transcription factor TFTC complex;SLIK (SAGA-like) complex
- Molecular function
- RNA polymerase II activating transcription factor binding;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;histone acetyltransferase activity;protein binding;transcription factor binding;TBP-class protein binding;protein heterodimerization activity