TAF3

TATA-box binding protein associated factor 3, the group of General transcription factor IID complex subunits |Armadillo like helical domain containing|PHD finger proteins

Basic information

Region (hg38): 10:7818496-8016631

Links

ENSG00000165632 ∙ NCBI:83860 ∙ OMIM:606576 ∙ HGNC:17303 ∙ Uniprot:Q5VWG9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF3 gene.

• Inborn genetic diseases (29 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF3 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					2	2
missense			27	2	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	3

Variants in TAF3

This is a list of pathogenic ClinVar variants found in the TAF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-7818848-C-T		not specified	Uncertain significance (Feb 23, 2023)
10-7824524-C-T		not specified	Uncertain significance (May 11, 2022)
10-7824551-T-G		not specified	Uncertain significance (Oct 12, 2021)
10-7963996-T-G		not specified	Uncertain significance (May 13, 2022)
10-7964033-T-A		not specified	Uncertain significance (Jun 07, 2023)
10-7964111-A-G		not specified	Uncertain significance (Sep 01, 2021)
10-7964348-G-A		not specified	Uncertain significance (May 03, 2023)
10-7964375-G-A		not specified	Likely benign (Dec 13, 2023)
10-7964391-T-C		not specified	Uncertain significance (May 26, 2023)
10-7964451-G-A		not specified	Uncertain significance (Oct 25, 2022)
10-7964474-A-G		not specified	Uncertain significance (Jan 16, 2024)
10-7964490-C-T		not specified	Likely benign (Aug 02, 2021)
10-7964498-A-T			Benign (Mar 29, 2018)
10-7964581-C-T			Benign (Dec 31, 2019)
10-7964606-C-A		not specified	Uncertain significance (Oct 06, 2023)
10-7964636-C-G		not specified	Uncertain significance (Feb 09, 2023)
10-7964763-A-G		not specified	Uncertain significance (May 30, 2023)
10-7964829-C-T		not specified	Uncertain significance (Mar 08, 2024)
10-7964834-A-T		not specified	Uncertain significance (Jan 26, 2022)
10-7964912-G-A		not specified	Uncertain significance (Sep 06, 2022)
10-7964913-C-A		not specified	Uncertain significance (Jun 21, 2023)
10-7965137-G-C		not specified	Uncertain significance (Jan 23, 2023)
10-7965143-G-C		not specified	Uncertain significance (May 26, 2022)
10-7965199-G-C		not specified	Uncertain significance (Feb 05, 2024)
10-7965297-A-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF3	protein_coding	protein_coding	ENST00000344293	7	198124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000253	120057	0	1	120058	0.00000416

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	360	499	0.722	0.0000269	6042
Missense in Polyphen		63	115.82	0.54395		1511
Synonymous	-0.153	207	204	1.01	0.0000126	1803
Loss of Function	5.27	1	34.3	0.0292	0.00000200	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000120	0.0000591
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000120	0.0000591
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.
• Pathway: 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: 0.111

Intolerance Scores

• loftool: 0.0169
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.6

Haploinsufficiency Scores

• pHI: 0.899
• hipred: Y
• hipred_score: 0.752
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf3

Zebrafish Information Network

• Gene name: taf3
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;negative regulation of DNA-binding transcription factor activity;maintenance of protein location in nucleus;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;transcription factor TFIID complex;nuclear membrane
• Molecular function: p53 binding;protein binding;metal ion binding;protein heterodimerization activity