TAF9B

protein-coding

TATA-box binding protein associated factor 9b

Gene summary

Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a protein that is similar to one of the small subunits of TFIID, TBP-associated factor 9, and is also a subunit of TFIID. TAF9 and TAF9b share some functions but also have distinct roles in the transcriptional regulatory process. [provided by RefSeq, Jul 2008]

Previous symbols:

TAF9L

MANE transcript

NM_015975.5

Inheritance

—

ClinVar variants

U:33B:2

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e 1.43

Max pathogenic AF

—

Genomic locus

chrX:78,129,748-78,139,650

External References & Databases

Ensembl (ENSG00000187325)

Transcript & Mutation Effects

hg38 • Region Span ~9.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TAF9B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 2

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015975.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	33	2	0	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015975.5	RefSeq	NP_057059.2	7	MANE Select
ENST00000341864.6	Ensembl	ENSP00000339917.5	7	MANE Select
ENST00000888658.1	Ensembl	ENSP00000558717.1	6	Standard
ENST00000888658.2	Ensembl	ENSP00000558717.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Basal transcription factors - Homo sapiens (human)
Herpes simplex infection - Homo sapiens (human)
miR-targeted genes in lymphocytes - TarBase
Disease
Gene expression (Transcription)

Biological Process

negative regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
transcription initiation from RNA polymerase II promoter
protein deubiquitination
positive regulation of cell growth

Molecular Function

transcription corepressor activity
histone acetyltransferase activity
protein binding
transcription factor binding
thiol-dependent ubiquitinyl hydrolase activity

Cellular Component

SAGA complex
nucleoplasm
transcription factor TFIID complex
transcription factor TFTC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341864
Coding exons: 7
Length: 9959
Individuals with no LoFs: 125698
Homozygous LoFs: 13
Heterozygous LoFs: 34
Defined: 125745
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.113	98	94.9	1.03	0.00000676	1636
Missense (PolyPhen)		29	18.155	1.5974		327
Synonymous	-1.61	48	35.7	1.34	0.00000276	501
Loss of Function	-1.20	13	9.08	1.43	7.42e-7	148

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00049	rare
Latino/Admixed American	0.00012	0.000087	rare
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0.00044	0.00033	rare
Finnish	0.00012	0.000092	rare
European (Non-Finnish)	0.00022	0.00016	rare
South Asian	0.00037	0.00023	rare
Other	0.00047	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription. {ECO:0000269|PubMed:15899866}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.751
RVIS EVS: -0.25
RVIS percentile EVS: 35.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.964

Gene Damage Prediction

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