TAF4

TATA-box binding protein associated factor 4, the group of General transcription factor IID complex subunits

Basic information

Region (hg38): 20:61953469-62065881

Previous symbols: [ "TAF4A", "TAF2C1", "TAF2C" ]

Links

ENSG00000130699 ∙ NCBI:6874 ∙ OMIM:601796 ∙ HGNC:11537 ∙ Uniprot:O00268 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the TAF4 gene.

• Inborn genetic diseases (2 variants)
• Intellectual developmental disorder, autosomal dominant 73 (1 variants)
• not provided (1 variants)
• 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				4	2	6
missense			126	7	2	135
nonsense	3					3
start loss						0
frameshift	1	3	8			12
inframe indel			3		1	4
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	4	3	137	11	5

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)
20-61976225-TA-T			Uncertain significance (Apr 06, 2023)
20-61976286-G-A		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
20-61976291-T-TC		Inborn genetic diseases	Uncertain significance (Jan 18, 2024)
20-61976301-G-A		not specified	Uncertain significance (Sep 13, 2024)
20-61976323-CGG-C		not specified	Uncertain significance (Jan 01, 2020)
20-61976327-G-A			Benign (Jul 20, 2018)
20-61997566-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
20-61997586-CCT-C		Intellectual developmental disorder, autosomal dominant 73	Uncertain significance (May 03, 2024)
20-61999051-G-A		Intellectual developmental disorder, autosomal dominant 73	Pathogenic (Jun 18, 2024)
20-61999095-T-A		Neurodevelopmental disorder	Uncertain significance (Jul 17, 2023)
20-61999102-C-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
20-62000192-G-A		Inborn genetic diseases	Pathogenic (Jan 18, 2024)
20-62000246-GT-G		Intellectual developmental disorder, autosomal dominant 73	Pathogenic (Jun 18, 2024)
20-62000251-T-C		Inborn genetic diseases	Uncertain significance (Oct 20, 2024)
20-62000581-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
20-62000600-C-T			Uncertain significance (Nov 27, 2023)
20-62000665-T-C			Uncertain significance (Jan 09, 2024)
20-62000709-G-GTCA			Uncertain significance (Apr 27, 2023)
20-62003184-T-C		not specified	Uncertain significance (May 03, 2024)
20-62003192-A-AT		Intellectual developmental disorder, autosomal dominant 73	Pathogenic (Jun 18, 2024)
20-62003258-G-A		Inborn genetic diseases	Likely benign (Nov 09, 2024)
20-62003739-A-G		not specified	Uncertain significance (Jun 27, 2024)
20-62003781-C-T		Inborn genetic diseases • not specified	Uncertain significance (Jun 13, 2024)
20-62003839-G-T		not specified	Uncertain significance (Jul 17, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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