TADA1

protein-coding

transcriptional adaptor 1, the group of SAGA complex

Gene summary

TADA1L is a protein subunit of the human STAGA complex (SPT3; (MIM 602947)/TAF9 (MIM 600822)/GCN5 (MIM 602301) acetyltransferase complex), which is a chromatin-modifying multiprotein complex (Martinez et al., 2001 [PubMed 11564863]).[supplied by OMIM, Apr 2009]

Previous symbols:

TADA1L

MANE transcript

NM_053053.4

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr1:166,856,510-166,876,264

External References & Databases

Ensembl (ENSG00000152382)

Transcript & Mutation Effects

hg38 • Region Span ~19.8 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 TADA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_053053.4. 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			51 clinvar	1 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	55	1	1	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_053053.4	RefSeq	NP_444281.1	8	MANE Select
ENST00000367874.5	Ensembl	ENSP00000356848.4	8	MANE Select
ENST00000910858.1	Ensembl	ENSP00000580917.1	8	Standard
ENST00000910859.1	Ensembl	ENSP00000580918.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

regulation of transcription by RNA polymerase II
histone H3 acetylation
positive regulation of nucleic acid-templated transcription

Molecular Function

transcription coactivator activity
histone acetyltransferase activity

Cellular Component

SAGA complex
nucleus
nucleoplasm
cytosol
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367874
Coding exons: 8
Length: 19818
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.800	156	187	0.835	0.00000977	2190
Missense (PolyPhen)		31	47.615	0.65105		577
Synonymous	1.25	59	72.5	0.814	0.00000410	660
Loss of Function	2.76	5	17.4	0.287	9.04e-7	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00043	0.00043	rare
South Asian	0.000099	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably involved in transcriptional regulation.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.775
RVIS EVS: -0.23
RVIS percentile EVS: 37.11

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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