TAF2

TATA-box binding protein associated factor 2, the group of General transcription factor IID complex subunits |M1 metallopeptidases

Basic information

Region (hg38): 8:119730773-119832863

Previous symbols: [ "TAF2B" ]

Links

ENSG00000064313 ∙ NCBI:6873 ∙ OMIM:604912 ∙ HGNC:11536 ∙ Uniprot:Q6P1X5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly-thin corpus callosum-intellectual disability syndrome (Supportive), mode of inheritance: AR
• microcephaly-thin corpus callosum-intellectual disability syndrome (Moderate), mode of inheritance: AR
• microcephaly-thin corpus callosum-intellectual disability syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity	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	Musculoskeletal; Neurologic	21937992; 24084144

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF2 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				47	10	57
missense			94	2	7	103
nonsense			1			1
start loss						0
frameshift		1	2			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)			2			2
splice region			5	8	4	17
non coding			3	32	8	43
Total	0	1	103	81	25

Variants in TAF2

This is a list of pathogenic ClinVar variants found in the TAF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-119731946-C-T		Inborn genetic diseases	Uncertain significance (Aug 07, 2023)
8-119731947-G-A		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
8-119731954-C-T			Benign (Jan 08, 2024)
8-119731974-A-C		Inborn genetic diseases	Uncertain significance (Jul 23, 2021)
8-119731990-C-T			Likely benign (Jan 02, 2024)
8-119731990-C-CT			Uncertain significance (Sep 01, 2022)
8-119732008-G-A			Likely benign (Jan 24, 2024)
8-119732010-C-A		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
8-119732035-A-C		Inborn genetic diseases	Uncertain significance (Feb 22, 2021)
8-119732043-GCTT-G			Uncertain significance (Dec 02, 2021)
8-119732046-T-G		not specified • Inborn genetic diseases	Uncertain significance (Mar 16, 2022)
8-119732053-C-T		Microcephaly-thin corpus callosum-intellectual disability syndrome	Benign (Jan 30, 2024)
8-119732063-T-G			Uncertain significance (Apr 04, 2022)
8-119732076-G-A		Inborn genetic diseases	Uncertain significance (Apr 09, 2024)
8-119732084-T-C			Uncertain significance (Jul 15, 2022)
8-119732088-G-T			Uncertain significance (Dec 03, 2021)
8-119732109-T-C		TAF2-related disorder	Benign (Jan 26, 2024)
8-119732110-A-G			Likely benign (Sep 08, 2022)
8-119732131-G-A			Likely benign (Oct 20, 2021)
8-119732136-G-A		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
8-119732140-G-A			Likely benign (Nov 08, 2022)
8-119732146-C-T			Likely benign (Dec 06, 2023)
8-119732159-C-T		TAF2-related disorder	Benign (Jan 25, 2024)
8-119732175-C-T			Uncertain significance (May 16, 2022)
8-119732190-C-G		Inborn genetic diseases	Uncertain significance (Sep 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF2	protein_coding	protein_coding	ENST00000378164	26	102089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00260	0.997	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.78	427	622	0.686	0.0000300	7993
Missense in Polyphen		89	163.78	0.54341		2142
Synonymous	-0.0383	212	211	1.00	0.0000103	2142
Loss of Function	5.19	17	60.6	0.281	0.00000293	788

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.00114	0.000978

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. It requires core promoter-specific cofactors for productive transcription stimulation. TAF2 stabilizes TFIID binding to core promoter. {ECO:0000269|PubMed:9418870, ECO:0000269|PubMed:9774672}.
• 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)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.712
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.5

Haploinsufficiency Scores

• pHI: 0.414
• hipred: Y
• hipred_score: 0.738
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.477

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf2

Zebrafish Information Network

• Gene name: taf2
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;response to organic cyclic compound;positive regulation of transcription by RNA polymerase II;regulation of signal transduction by p53 class mediator
• Cellular component: nucleoplasm;transcription factor TFIID complex;transcription factor TFTC complex
• Molecular function: TFIID-class transcription factor complex binding;chromatin binding;protein binding;transcription regulatory region DNA binding