TAF6

TATA-box binding protein associated factor 6, the group of General transcription factor IID complex subunits |Armadillo like helical domain containing

Basic information

Region (hg38): 7:100106875-100119841

Previous symbols: [ "TAF2E" ]

Links

ENSG00000106290 ∙ NCBI:6878 ∙ OMIM:602955 ∙ HGNC:11540 ∙ Uniprot:P49848 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Alazami-Yuan syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Alazami-Yuan syndrome	AR	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; Dental; Musculoskeletal; Neurologic	25558065; 25574841

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF6 gene.

• not provided (85 variants)
• Inborn genetic diseases (19 variants)
• Alazami-Yuan syndrome (12 variants)
• not specified (3 variants)
• Hereditary spastic paraplegia (2 variants)
• Syndromic intellectual disability (1 variants)
• Abnormal facial shape;Global developmental delay (1 variants)
• Hereditary spastic paraplegia 50 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF6 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				23	10	33
missense		1	25	4	1	31
nonsense	1		1			2
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2				2
splice region				2	1	3
non coding			2	8	20	30
Total	1	3	31	35	31

Variants in TAF6

This is a list of pathogenic ClinVar variants found in the TAF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100106877-A-G		not specified • Hereditary spastic paraplegia 50 • Hereditary spastic paraplegia	Uncertain significance (Aug 07, 2022)
7-100106880-T-C		Hereditary spastic paraplegia 50	Uncertain significance (May 11, 2022)
7-100106905-C-T		Hereditary spastic paraplegia	Likely benign (Jan 24, 2017)
7-100107006-G-A		Hereditary spastic paraplegia	Uncertain significance (Jan 03, 2017)
7-100107101-G-T			Likely benign (Nov 13, 2019)
7-100107173-A-T			Benign (Jun 14, 2018)
7-100107204-A-G		Alazami-Yuan syndrome	Benign (Jul 15, 2021)
7-100107249-C-T			Likely benign (Dec 06, 2023)
7-100107269-C-T			Likely benign (Dec 01, 2023)
7-100107331-G-A			Uncertain significance (Feb 17, 2022)
7-100107359-T-C		Alazami-Yuan syndrome	Uncertain significance (Feb 13, 2018)
7-100107362-C-T		Inborn genetic diseases	Likely benign (Sep 08, 2023)
7-100107363-G-A			Benign (May 25, 2023)
7-100107375-C-T			Likely benign (Jul 01, 2022)
7-100107376-G-A		Alazami-Yuan syndrome	Benign (Oct 17, 2023)
7-100107381-C-T			Benign (Aug 08, 2018)
7-100107382-G-A		Inborn genetic diseases	Uncertain significance (Oct 30, 2023)
7-100107401-GAGA-G		Alazami-Yuan syndrome	Uncertain significance (Jan 01, 2018)
7-100107474-A-G			Benign (May 23, 2023)
7-100107509-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
7-100107510-G-A		TAF6-related disorder	Likely benign (Dec 21, 2023)
7-100107509-C-CGGTG		not specified	Uncertain significance (Nov 15, 2021)
7-100107511-G-T		Alazami-Yuan syndrome • Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
7-100107555-G-A			Likely benign (Jun 01, 2023)
7-100107557-C-T			Uncertain significance (Jul 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF6	protein_coding	protein_coding	ENST00000437822	15	12772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.27e-9	0.995	124054	50	1644	125748	0.00676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	333	450	0.739	0.0000279	4554
Missense in Polyphen		58	123.43	0.46992		1232
Synonymous	-1.64	224	195	1.15	0.0000134	1552
Loss of Function	2.58	19	35.6	0.534	0.00000195	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0969	0.0969
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.000218	0.000217
South Asian	0.000687	0.000686
Other	0.00424	0.00424

dbNSFP

Source: dbNSFP

• Function: FUNCTION: TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TIIFD is multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.
• Disease: DISEASE: Alazami-Yuan syndrome (ALYUS) [MIM:617126]: An autosomal recessive syndrome reminiscent of Cornelia de Lange syndrome and characterized by delayed psychomotor development with intellectual disability, hypotonia, microcephaly, short stature, poor speech, and dysmorphic features. {ECO:0000269|PubMed:25558065, ECO:0000269|PubMed:25574841}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Basal transcription factors - Homo sapiens (human);Herpes simplex infection - 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 transcribes snRNA genes;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: 0.138

Intolerance Scores

• loftool: 0.827
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.64

Haploinsufficiency Scores

• pHI: 0.740
• hipred: Y
• hipred_score: 0.715
• ghis: 0.588

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: taf6
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: chromatin organization;DNA-templated transcription, initiation;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;apoptotic process;snRNA transcription by RNA polymerase II;negative regulation of cell cycle;RNA polymerase II preinitiation complex assembly;regulation of signal transduction by p53 class mediator
• Cellular component: SAGA complex;nucleoplasm;transcription factor TFIID complex;cytosol;protein-containing complex;transcription factor TFTC complex;SLIK (SAGA-like) complex;MLL1 complex
• Molecular function: RNA polymerase II activating transcription factor binding;DNA binding;DNA-binding transcription factor activity;protein binding;aryl hydrocarbon receptor binding;protein heterodimerization activity