TAF5

protein-coding

TATA-box binding protein associated factor 5, the group of WD repeat domain containing|General transcription factor IID complex subunits

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 an integral subunit of TFIID associated with all transcriptionally competent forms of that complex. This subunit interacts strongly with two TFIID subunits that show similarity to histones H3 and H4, and it may participate in forming a nucleosome-like core in the TFIID complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

Previous symbols:

TAF2D

MANE transcript

NM_006951.5

Inheritance

—

ClinVar variants

U:85B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr10:103,367,966-103,389,065

External References & Databases

Ensembl (ENSG00000148835)

Transcript & Mutation Effects

hg38 • Region Span ~21.1 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 TAF5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 76

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006951.5. 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		1 clinvar	3
missense			80 clinvar	2 clinvar		82
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	85	2	1	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006951.5	RefSeq	NP_008882.2	11	MANE Select
ENST00000369839.4	Ensembl	ENSP00000358854.3	11	MANE Select
NM_139052.3	RefSeq	NP_620640.1	10	Standard
ENST00000684872.1	Ensembl	ENSP00000508463.1	2	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)
Eukaryotic Transcription Initiation
Disease
Gene expression (Transcription)

Biological Process

chromatin organization
DNA-templated transcription, initiation
regulation of transcription, DNA-templated
transcription by RNA polymerase II
transcription initiation from RNA polymerase II promoter

Molecular Function

DNA-binding transcription factor activity
histone acetyltransferase activity
protein binding
identical protein binding
transcription regulatory region DNA binding

Cellular Component

nuclear chromatin
nucleus
nucleoplasm
transcription factor TFIID complex
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369839
Coding exons: 11
Length: 21099
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.65	259	410	0.632	0.0000208	5133
Missense (PolyPhen)		43	113.86	0.37767		1419
Synonymous	0.638	146	156	0.935	0.00000824	1607
Loss of Function	5.16	3	36.7	0.0817	0.00000213	438

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TAFs components-TIIFD are essential for mediating regulation of RNA polymerase transcription. TAF5/TAFII100 interacts strongly with the histone H4-related TAF6/TAFII80 and the histone H3-related TAF9/TAFII31, as well as a stable complex comprised of both TAF5/TAFII80 and TAF6/TAFII31. Apparently weaker interactions of TAF5/TAFII100 with TBP, TAF1/TAFII250, TAF11/TAFII28, and TAF12/TAFII20, but not TAF7/TAFII55, also have been observed.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.180
RVIS EVS: -0.56
RVIS percentile EVS: 19.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.942

Gene Damage Prediction

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