TAF6L

TATA-box binding protein associated factor 6 like, the group of SAGA complex

Basic information

Region (hg38): 11:62771356-62787342

Links

ENSG00000162227 ∙ NCBI:10629 ∙ OMIM:602946 ∙ HGNC:17305 ∙ Uniprot:Q9Y6J9 ∙ 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 TAF6L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF6L 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						0
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in TAF6L

This is a list of pathogenic ClinVar variants found in the TAF6L region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62775884-C-T		not specified	Uncertain significance (Oct 02, 2023)
11-62778000-A-T		not specified	Uncertain significance (Sep 30, 2022)
11-62778032-G-A		not specified	Uncertain significance (Oct 27, 2021)
11-62778053-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-62778922-G-A		not specified	Uncertain significance (Feb 13, 2023)
11-62781928-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-62781934-C-T		not specified	Uncertain significance (May 04, 2022)
11-62781939-C-G		not specified	Uncertain significance (Jun 22, 2023)
11-62782180-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-62782183-A-C		not specified	Uncertain significance (Apr 01, 2024)
11-62782213-G-A		not specified	Uncertain significance (Nov 14, 2023)
11-62782270-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-62782321-G-A		not specified	Uncertain significance (May 09, 2023)
11-62782713-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-62782724-C-A		not specified	Uncertain significance (Jan 04, 2022)
11-62782796-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-62786623-G-A		not specified	Uncertain significance (May 09, 2023)
11-62786623-G-C		not specified	Uncertain significance (Oct 06, 2022)
11-62786653-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-62786722-C-T		not specified	Uncertain significance (Jun 02, 2024)
11-62786811-G-T		not specified	Uncertain significance (Dec 01, 2022)
11-62786829-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-62786875-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-62786922-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-62786922-G-C		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF6L	protein_coding	protein_coding	ENST00000294168	10	16040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0701	0.930	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.846	308	353	0.873	0.0000195	3903
Missense in Polyphen		60	77.558	0.77361		793
Synonymous	-0.968	171	156	1.10	0.00000849	1379
Loss of Function	3.40	7	25.5	0.274	0.00000133	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000636	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000112	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a component of the PCAF complex. The PCAF complex is capable of efficiently acetylating histones in a nucleosomal context. The PCAF complex could be considered as the human version of the yeast SAGA complex.
• Pathway: Basal transcription factors - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0909

Intolerance Scores

• loftool: 0.333
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.771
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf6l

Gene ontology

• Biological process: chromatin organization;chromatin remodeling;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;histone H3 acetylation;positive regulation of nucleic acid-templated transcription
• Cellular component: histone deacetylase complex;SAGA complex;nucleus;nucleoplasm;transcription factor TFIID complex;STAGA complex;SLIK (SAGA-like) complex;extracellular exosome
• Molecular function: RNA polymerase II activating transcription factor binding;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;histone acetyltransferase activity;protein binding;protein heterodimerization activity