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.

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.

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				6	4	10
missense			52	5	7	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	52	11	11

Variants in TAF4B

This is a list of pathogenic ClinVar variants found in the TAF4B region.

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

Position	Type	Phenotype	Significance	ClinVar
18-26226950-C-T		not specified	Uncertain significance (Mar 18, 2024)
18-26226980-C-T		not specified	Uncertain significance (Mar 17, 2023)
18-26227039-G-A		not specified	Uncertain significance (Aug 01, 2022)
18-26227061-G-A		not specified	Uncertain significance (Dec 19, 2022)
18-26227063-G-C			Benign (Jul 16, 2018)
18-26227080-T-C		TAF4B-related disorder	Benign (Dec 31, 2019)
18-26227102-A-G		not specified	Uncertain significance (May 21, 2024)
18-26227124-C-A		not specified	Uncertain significance (Feb 13, 2024)
18-26227129-G-A		not specified	Uncertain significance (Apr 06, 2022)
18-26227181-G-T		not specified	Uncertain significance (May 11, 2022)
18-26227198-C-T		not specified	Uncertain significance (Apr 08, 2024)
18-26227215-C-T			Likely benign (Apr 20, 2018)
18-26227252-C-G		not specified	Uncertain significance (Mar 06, 2023)
18-26227271-C-T		not specified	Uncertain significance (Jan 27, 2022)
18-26265280-G-A			Benign (Sep 11, 2018)
18-26265281-C-T			Benign (Sep 11, 2018)
18-26265314-C-T		not specified	Uncertain significance (Aug 30, 2022)
18-26267520-C-G		not specified	Uncertain significance (Sep 06, 2022)
18-26267574-A-T		not specified	Uncertain significance (Nov 17, 2023)
18-26267611-T-G		TAF4B-related disorder	Benign (Aug 23, 2018)
18-26267615-T-G		not specified	Uncertain significance (Oct 05, 2023)
18-26267618-G-A		not specified	Uncertain significance (Jan 09, 2023)
18-26274687-G-A		not specified	Uncertain significance (Sep 22, 2023)
18-26274700-C-T		not specified	Uncertain significance (Dec 07, 2023)
18-26274719-T-C			Likely benign (Sep 11, 2018)

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