BTAF1

protein-coding

B-TFIID TATA-box binding protein associated factor 1, the group of Armadillo like helical domain containing

Gene summary

This gene encodes a TAF (TATA box-binding protein-associated factor), which associates with TBP (TATA box-binding protein) to form the B-TFIID complex that is required for transcription initiation of genes by RNA polymerase II. This TAF has DNA-dependent ATPase activity, which drives the dissociation of TBP from DNA, freeing the TBP to associate with other TATA boxes or TATA-less promoters. [provided by RefSeq, Sep 2011]

MANE transcript

NM_003972.3

Inheritance

—

ClinVar variants

U:179B:7

Top phenotype

BTAF1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr10:91,923,770-92,031,437

External References & Databases

Ensembl (ENSG00000095564)

Transcript & Mutation Effects

hg38 • Region Span ~107.7 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 BTAF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 159

not providedTotal: 16

BTAF1-related disorderTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003972.3. 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	3 clinvar	2 clinvar	7
missense			169 clinvar	2 clinvar		171
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	179	5	2	186

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003972.3	RefSeq	NP_003963.1	38	MANE Select
ENST00000265990.12	Ensembl	ENSP00000265990.6	38	MANE Select
ENST00000928669.1	Ensembl	ENSP00000598728.1	37	Standard
ENST00000928669.2	Ensembl	ENSP00000598728.1	37	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of chromatin binding
negative regulation of transcription, DNA-templated

Molecular Function

DNA binding
DNA-binding transcription factor activity
helicase activity
ATP binding

Cellular Component

nucleoplasm
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265990
Coding exons: 38
Length: 106557
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.38	578	960	0.602	0.0000485	12125
Missense (PolyPhen)		106	300.08	0.35323		3663
Synonymous	-0.308	343	336	1.02	0.0000172	3524
Loss of Function	8.75	7	103	0.0681	0.00000566	1221

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates transcription in association with TATA binding protein (TBP). Removes TBP from the TATA box in an ATP-dependent manner.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.0233
RVIS EVS: -1.72
RVIS percentile EVS: 2.47

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.876

Gene Damage Prediction

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