TAF4B

TATA-box binding protein associated factor 4b

Basic information

Region (hg38): 18:26226445-26391685

Previous symbols: [ "TAF2C2" ]

Links

ENSG00000141384

∙ NCBI:6875 ∙ OMIM:601689 ∙ HGNC:11538 ∙ Uniprot:Q92750 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spermatogenic failure 13 (Limited), mode of inheritance: AR
male infertility with azoospermia or oligozoospermia due to single gene mutation (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 13	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	Genitourinary	24431330

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF4B gene.

not_specified (112 variants)
not_provided (17 variants)
TAF4B-related_disorder (8 variants)
Spermatogenic_failure_13 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF4B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005640.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	5 clinvar	10
missense			109 clinvar	5 clinvar	6 clinvar	120
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	109	10	11

Highest pathogenic variant AF is 0.000005767911

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF4B	protein_coding	protein_coding	ENST00000269142	15	165750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.234	0.766	124776	0	18	124794	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.353	417	438	0.952	0.0000210	5450
Missense in Polyphen		108	134.22	0.80463		1773
Synonymous	-1.26	188	167	1.12	0.00000823	1879
Loss of Function	4.37	9	38.1	0.236	0.00000205	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000129
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.000187	0.000186
European (Non-Finnish)	0.0000890	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cell type-specific subunit of the general transcription factor TFIID that may function as a gene-selective coactivator in certain cells. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TAF4B is a transcriptional coactivator of the p65/RELA NF-kappa-B subunit. Involved in the activation of a subset of antiapoptotic genes including TNFAIP3. May be involved in regulating folliculogenesis. Through interaction with OCBA/POU2AF1, acts as a coactivator of B-cell-specific transcription. Plays a role in spermiogenesis and oogenesis. {ECO:0000250|UniProtKB:G5E8Z2, ECO:0000269|PubMed:10828057, ECO:0000269|PubMed:10849440, ECO:0000269|PubMed:16088961, ECO:0000303|PubMed:24431330}.;
Disease: DISEASE: Spermatogenic failure 13 (SPGF13) [MIM:615841]: A disorder resulting in the absence (azoospermia) or reduction (oligozoospermia) of sperm in the semen, leading to male infertility. {ECO:0000269|PubMed:24431330}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Huntington,s disease - Homo sapiens (human);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;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

pRec: 0.109

Intolerance Scores

loftool: 0.448
rvis_EVS: 0.58
rvis_percentile_EVS: 82.31

Haploinsufficiency Scores

pHI: 0.756
hipred: Y
hipred_score: 0.583
ghis: 0.493

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Taf4b
Phenotype: reproductive system phenotype; 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); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;spermatogenesis;positive regulation of transcription by RNA polymerase II;oogenesis;regulation of signal transduction by p53 class mediator
Cellular component: fibrillar center;nucleoplasm;transcription factor TFIID complex;cytoplasm
Molecular function: DNA binding;DNA-binding transcription factor activity;transcription factor binding;protein heterodimerization activity;NF-kappaB binding