TAF1

TATA-box binding protein associated factor 1, the group of Bromodomain containing|General transcription factor IID complex subunits |Lysine acetyltransferases

Basic information

Region (hg38): X:71366221-71532374

Previous symbols: [ "TAF2A", "BA2R", "CCG1", "CCGS", "DYT3" ]

Links

ENSG00000147133 ∙ NCBI:6872 ∙ OMIM:313650 ∙ HGNC:11535 ∙ Uniprot:P21675 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked dystonia-parkinsonism (Moderate), mode of inheritance: XL
• X-linked dystonia-parkinsonism (Supportive), mode of inheritance: XL
• X-linked intellectual disability-global development delay-facial dysmorphism-sacral caudal remnant syndrome (Supportive), mode of inheritance: XL
• intellectual disability, X-linked, syndromic 33 (Definitive), mode of inheritance: XL
• intellectual disability, X-linked, syndromic 33 (Strong), mode of inheritance: XL
• X-linked dystonia-parkinsonism (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dystonia 3, torsion, X-linked; Mental retardation, X-linked, syndromic 33	XL	Neurologic	Dystonia 3, torsion, X-linked may be responsive to levodopa	Craniofacial; Musculoskeletal; Neurologic	15596620; 17273961; 26637982

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF1 gene.

• not provided (337 variants)
• Intellectual disability, X-linked, syndromic 33 (51 variants)
• Inborn genetic diseases (35 variants)
• not specified (9 variants)
• Heart, malformation of (8 variants)
• TAF1-related condition (7 variants)
• X-linked dystonia-parkinsonism;Intellectual disability, X-linked, syndromic 33 (6 variants)
• X-linked dystonia-parkinsonism (4 variants)
• Intellectual disability (3 variants)
• TAF1-related syndromic intellectual disability (2 variants)
• See cases (2 variants)
• Autism spectrum disorder (1 variants)
• Marfanoid habitus and intellectual disability (1 variants)
• TAF1-related X-linked syndromic intellectual disability (1 variants)
• Intellectual disability, X-linked, syndromic 33;X-linked dystonia-parkinsonism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1 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			4	49	24	77
missense	5	19	171	19	9	223
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel			7	1		8
splice donor/acceptor (+/-2bp)	1	1	1			3
splice region			7	17	3	27
non coding			9	27	25	61
Total	6	21	193	96	58

Variants in TAF1

This is a list of pathogenic ClinVar variants found in the TAF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-71366318-G-A			Uncertain significance (Nov 27, 2023)
X-71366321-C-G			Uncertain significance (Aug 12, 2022)
X-71366329-C-A			Uncertain significance (Jul 21, 2022)
X-71366336-C-T			Likely benign (Mar 01, 2022)
X-71366335-G-GCTGCTGCGGACAGCAGCTACCATCA			Benign (Mar 17, 2023)
X-71366339-C-T			Benign (Jan 07, 2024)
X-71366341-G-A			Likely benign (Jan 03, 2022)
X-71366341-G-C			Benign (Dec 27, 2023)
X-71366342-C-T			Uncertain significance (Oct 05, 2023)
X-71366346-C-T		not specified • TAF1-related disorder	Benign (Jan 18, 2024)
X-71366350-A-T			Likely benign (Aug 14, 2018)
X-71366350-AG-TT			Uncertain significance (Sep 13, 2022)
X-71366351-G-T			Likely benign (Feb 11, 2023)
X-71366352-C-G			Uncertain significance (Apr 08, 2022)
X-71366357-A-G			Benign (Oct 03, 2023)
X-71366367-C-T			Uncertain significance (Sep 19, 2019)
X-71366368-C-T			Likely benign (Sep 01, 2018)
X-71366373-T-C			Uncertain significance (Aug 10, 2023)
X-71366375-A-T		Intellectual disability, X-linked, syndromic 33 • Heart, malformation of	Likely pathogenic; association (Jun 13, 2020)
X-71366402-T-G			Uncertain significance (May 01, 2023)
X-71366418-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 18, 2023)
X-71366421-TTTC-T			Uncertain significance (Jan 12, 2023)
X-71366428-A-T			Uncertain significance (Aug 30, 2019)
X-71366438-C-T			Uncertain significance (Dec 11, 2023)
X-71366461-C-G		TAF1-related disorder	Benign (Jan 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1	protein_coding	protein_coding	ENST00000276072	38	166111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.15e-11	125612	3	14	125629	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.49	326	748	0.436	0.0000596	12563
Missense in Polyphen		82	312.02	0.2628		5365
Synonymous	-1.07	272	250	1.09	0.0000182	3522
Loss of Function	7.69	0	68.9	0.00	0.00000538	1203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000535	0.000397
East Asian	0.000794	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.000794	0.000598
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Largest component and core scaffold of the TFIID basal transcription factor complex (PubMed:25412659, PubMed:27007846). Contains novel N- and C-terminal Ser/Thr kinase domains which can autophosphorylate or transphosphorylate other transcription factors. Phosphorylates TP53 on 'Thr-55' which leads to MDM2- mediated degradation of TP53. Phosphorylates GTF2A1 and GTF2F1 on Ser residues. Possesses DNA-binding activity (PubMed:25412659). Essential for progression of the G1 phase of the cell cycle (PubMed:11278496, PubMed:15053879, PubMed:2038334, PubMed:8450888, PubMed:8625415, PubMed:9660973, PubMed:9858607). Exhibits histone acetyltransferase activity towards histones H3 and H4 (PubMed:15870300). {ECO:0000269|PubMed:11278496, ECO:0000269|PubMed:15053879, ECO:0000269|PubMed:15870300, ECO:0000269|PubMed:2038334, ECO:0000269|PubMed:25412659, ECO:0000269|PubMed:27007846, ECO:0000269|PubMed:8450888, ECO:0000269|PubMed:8625415, ECO:0000269|PubMed:9660973, ECO:0000269|PubMed:9858607}.
• Disease: DISEASE: Dystonia 3, torsion, X-linked (DYT3) [MIM:314250]: A X- linked dystonia-parkinsonism disorder. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. DYT3 is characterized by severe progressive torsion dystonia followed by parkinsonism. It has a well-defined pathology of extensive neuronal loss and mosaic gliosis in the striatum (caudate nucleus and putamen) which appears to resemble that in Huntington disease. {ECO:0000269|PubMed:12928496, ECO:0000269|PubMed:17273961}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, X-linked, syndromic, 33 (MRXS33) [MIM:300966]: A mental retardation syndrome characterized by intellectual deficit, delayed psychomotor development, delayed speech and language, and characteristic facial features. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:26637982}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Basal transcription factors - Homo sapiens (human);MECP2 and Associated Rett Syndrome;Disease;Gene expression (Transcription);hypoxia and p53 in the cardiovascular system;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;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.152
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.73

Haploinsufficiency Scores

• pHI: 0.651
• hipred: Y
• hipred_score: 0.746
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Taf1

Zebrafish Information Network

• Gene name: taf1
• Affected structure: optic tectum
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: protein polyubiquitination;DNA-templated transcription, initiation;regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein phosphorylation;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;cell cycle;negative regulation of gene expression;negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage;viral process;histone acetylation;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;midbrain development;positive regulation of protein binding;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;cellular response to UV;transcription factor catabolic process;negative regulation of DNA-binding transcription factor activity;positive regulation of transcription by RNA polymerase I;positive regulation of transcription by RNA polymerase II;protein autophosphorylation;protein stabilization;RNA polymerase II preinitiation complex assembly;regulation of transcription initiation from RNA polymerase II promoter;positive regulation of transcription initiation from RNA polymerase II promoter;cellular response to ATP;regulation of signal transduction by p53 class mediator;regulation of cell cycle G1/S phase transition;negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding;negative regulation of protein autoubiquitination;negative regulation of ubiquitin-dependent protein catabolic process;positive regulation of androgen receptor activity
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;transcription factor TFIID complex;nucleolus;MLL1 complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;p53 binding;transcription coactivator activity;histone acetyltransferase activity;protein serine/threonine kinase activity;protein binding;ATP binding;transcription factor binding;RNA polymerase II general transcription initiation factor activity;kinase activity;TBP-class protein binding;nuclear hormone receptor binding;sequence-specific DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity;H3K27me3 modified histone binding;RNA polymerase II-specific DNA-binding transcription factor binding;ubiquitin conjugating enzyme activity;lysine-acetylated histone binding;acetyl-CoA binding