TAF4
Basic information
Region (hg38): 20:61953468-62065881
Previous symbols: [ "TAF4A", "TAF2C1", "TAF2C" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder, autosomal dominant 73 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 33875846; 35904126 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (55 variants)
- not provided (18 variants)
- not specified (3 variants)
- TAF4-related disorder (1 variants)
- TAF4 related neurodevelopmental disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF4 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 | 5 | |||||
missense | 59 | 64 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 3 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 1 | 66 | 6 | 5 |
Highest pathogenic variant AF is 0.00000695
Variants in TAF4
This is a list of pathogenic ClinVar variants found in the TAF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-61976202-T-C | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
20-61976286-G-A | Inborn genetic diseases | Uncertain significance (Feb 21, 2024) | ||
20-61976291-T-TC | Inborn genetic diseases | Uncertain significance (Jan 18, 2024) | ||
20-61976323-CGG-C | not specified | Uncertain significance (Jan 01, 2020) | ||
20-61976327-G-A | Benign (Jul 20, 2018) | |||
20-61997586-CCT-C | Intellectual developmental disorder, autosomal dominant 73 | Uncertain significance (May 03, 2024) | ||
20-61999102-C-T | Inborn genetic diseases | Uncertain significance (Jun 18, 2021) | ||
20-62000192-G-A | Inborn genetic diseases | Pathogenic (Jan 18, 2024) | ||
20-62000581-G-A | Inborn genetic diseases | Uncertain significance (Dec 20, 2021) | ||
20-62000709-G-GTCA | Uncertain significance (Apr 27, 2023) | |||
20-62003781-C-T | Inborn genetic diseases | Uncertain significance (Dec 14, 2021) | ||
20-62006542-C-T | Inborn genetic diseases | Uncertain significance (Dec 20, 2021) | ||
20-62006572-CA-C | Uncertain significance (Jul 10, 2017) | |||
20-62006590-T-C | Likely benign (Nov 01, 2023) | |||
20-62006614-C-T | Uncertain significance (Oct 26, 2023) | |||
20-62006647-C-T | Inborn genetic diseases | Uncertain significance (Dec 07, 2021) | ||
20-62006648-G-A | Likely benign (May 01, 2022) | |||
20-62006673-G-A | not specified | Uncertain significance (Nov 07, 2023) | ||
20-62006688-G-T | Inborn genetic diseases | Likely benign (Jul 27, 2022) | ||
20-62009062-T-C | Inborn genetic diseases | Uncertain significance (Jan 06, 2023) | ||
20-62009134-G-C | Uncertain significance (Mar 14, 2022) | |||
20-62009161-T-G | Inborn genetic diseases | Uncertain significance (Sep 22, 2022) | ||
20-62010071-G-A | Inborn genetic diseases | Uncertain significance (May 09, 2022) | ||
20-62010092-G-A | Inborn genetic diseases | Uncertain significance (Jan 24, 2023) | ||
20-62010099-C-A | Inborn genetic diseases | Uncertain significance (Nov 10, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TAF4 | protein_coding | protein_coding | ENST00000252996 | 15 | 112342 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.00000195 | 108127 | 0 | 1 | 108128 | 0.00000462 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.68 | 287 | 447 | 0.643 | 0.0000281 | 6715 |
Missense in Polyphen | 95 | 214.62 | 0.44263 | 2374 | ||
Synonymous | -1.82 | 236 | 203 | 1.16 | 0.0000147 | 2473 |
Loss of Function | 5.61 | 0 | 36.7 | 0.00 | 0.00000182 | 436 |
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) | 0.0000100 | 0.0000100 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Part of the TFIID complex, a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Potentiates transcriptional activation by the AF-2S of the retinoic acid, vitamin D3 and thyroid hormone.;
- Pathway
- Huntington,s disease - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);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;Infectious disease;RNA Polymerase II Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53
(Consensus)
Recessive Scores
- pRec
- 0.185
Haploinsufficiency Scores
- pHI
- 0.571
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.690
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.309
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Taf4
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); neoplasm; limbs/digits/tail phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- ovarian follicle development;DNA-templated transcription, initiation;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;viral process;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of signal transduction by p53 class mediator
- Cellular component
- nuclear chromatin;nucleoplasm;transcription factor TFIID complex;cytosol;protein-containing complex;transcription factor TFTC complex;MLL1 complex
- Molecular function
- DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;transcription factor binding;aryl hydrocarbon receptor binding;protein heterodimerization activity