TAF1L

TATA-box binding protein associated factor 1 like, the group of Bromodomain containing

Basic information

Region (hg38): 9:32629454-32635669

Links

ENSG00000122728 ∙ NCBI:138474 ∙ OMIM:607798 ∙ HGNC:18056 ∙ Uniprot:Q8IZX4 ∙ 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 TAF1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1L 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				3		3
missense			93	4	1	98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	93	7	1

Variants in TAF1L

This is a list of pathogenic ClinVar variants found in the TAF1L region.

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

Position	Type	Phenotype	Significance	ClinVar
9-32630125-C-T		not specified	Uncertain significance (Feb 23, 2023)
9-32630243-G-A		not specified	Likely benign (Jan 03, 2024)
9-32630346-G-C		not specified	Uncertain significance (Oct 10, 2023)
9-32630351-A-C		not specified	Uncertain significance (Jun 09, 2022)
9-32630380-G-C		not specified	Uncertain significance (May 21, 2024)
9-32630389-T-C		not specified	Uncertain significance (May 14, 2024)
9-32630412-T-A		not specified	Uncertain significance (May 27, 2022)
9-32630424-T-A		not specified	Uncertain significance (Jan 23, 2024)
9-32630471-C-G		not specified	Uncertain significance (Jun 21, 2022)
9-32630550-G-A		not specified	Likely benign (Nov 16, 2021)
9-32630564-G-C		not specified	Uncertain significance (Jun 21, 2021)
9-32630605-C-G		not specified	Uncertain significance (Jul 08, 2022)
9-32630673-T-A		not specified	Uncertain significance (Apr 26, 2024)
9-32630728-T-C		not specified	Likely benign (Nov 10, 2022)
9-32630809-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-32630829-C-T		not specified	Uncertain significance (May 26, 2024)
9-32630838-T-C		not specified	Uncertain significance (Dec 18, 2023)
9-32630850-G-C		not specified	Uncertain significance (Jul 12, 2022)
9-32630901-T-C		not specified	Uncertain significance (Aug 28, 2023)
9-32630959-C-T		not specified	Uncertain significance (Dec 15, 2022)
9-32630995-T-G		not specified	Uncertain significance (Nov 09, 2021)
9-32631034-G-C		not specified	Uncertain significance (Aug 31, 2022)
9-32631220-G-A		not specified	Uncertain significance (Nov 28, 2023)
9-32631256-G-A		not specified	Uncertain significance (Oct 05, 2023)
9-32631286-C-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1L	protein_coding	protein_coding	ENST00000242310	1	6216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.962	0.0382	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.403	993	958	1.04	0.0000570	12102
Missense in Polyphen		283	308.72	0.91668		3956
Synonymous	-1.14	373	346	1.08	0.0000182	3525
Loss of Function	5.36	9	49.9	0.180	0.00000309	680

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a functional substitute for TAF1/TAFII250 during male meiosis, when sex chromosomes are transcriptionally silenced. {ECO:0000269|PubMed:12217962}.
• Pathway: Basal transcription factors - 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)

Intolerance Scores

• loftool: 0.582
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.732
• hipred: N
• hipred_score: 0.311
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein phosphorylation;male meiotic nuclear division;histone acetylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of signal transduction by p53 class mediator
• Cellular component: cellular_component;nucleoplasm;transcription factor TFIID complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;histone acetyltransferase activity;protein serine/threonine kinase activity;TBP-class protein binding;sequence-specific DNA binding;lysine-acetylated histone binding