ATAD2

protein-coding

ATPase family AAA domain containing 2, the group of Bromodomain containing|MicroRNA protein coding host genes|AAA ATPases

Gene summary

A large family of ATPases has been described, whose key feature is that they share a conserved region of about 220 amino acids that contains an ATP-binding site. The proteins that belong to this family either contain one or two AAA (ATPases Associated with diverse cellular Activities) domains. AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. The protein encoded by this gene contains two AAA domains, as well as a bromodomain. [provided by RefSeq, Jul 2008]

MANE transcript

NM_014109.4

Inheritance

—

ClinVar variants

U:158B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr8:123,319,850-123,416,350

External References & Databases

Ensembl (ENSG00000156802)

Transcript & Mutation Effects

hg38 • Region Span ~96.5 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 ATAD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 147

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014109.4. 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			1 clinvar			1
missense			146 clinvar	7 clinvar		153
nonsense			5 clinvar			5
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	158	7	0	165

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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_014109.4	RefSeq	NP_054828.2	28	MANE Select
ENST00000287394.10	Ensembl	ENSP00000287394.5	28	MANE Select
ENST00000517666.5	Ensembl	ENSP00000429331.1	2	Standard
ENST00000519124.5	Ensembl	ENSP00000429617.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric Cancer Network 2
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors

Biological Process

chromatin organization
regulation of transcription by RNA polymerase II
negative regulation of chromatin silencing
positive regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Molecular Function

chromatin binding
protein binding
ATP binding
ATPase activity
histone binding

Cellular Component

nucleus
nucleoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000287394
Coding exons: 28
Length: 96501
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125747
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	589	714	0.825	0.0000370	9122
Missense (PolyPhen)		83	179.63	0.46206		2188
Synonymous	-0.511	258	248	1.04	0.0000121	2587
Loss of Function	6.68	13	75.8	0.172	0.00000482	908

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00037	0.00023	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00027	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.;

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.100
RVIS EVS: -0.93
RVIS percentile EVS: 9.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.959

Gene Damage Prediction

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