ATAD2

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

Basic information

Region (hg38): 8:123319850-123416350

Links

ENSG00000156802

∙ NCBI:29028 ∙ OMIM:611941 ∙ HGNC:30123 ∙ Uniprot:Q6PL18 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATAD2 gene.

not_specified (132 variants)
not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATAD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014109.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			126 clinvar	7 clinvar		133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	7	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATAD2	protein_coding	protein_coding	ENST00000287394	28	96501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00180	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	589	714	0.825	0.0000370	9122
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000459	0.000456
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000375	0.000231
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000270	0.000229
Other	0.00	0.00

dbNSFP

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}.;
Pathway: 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;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors (Consensus)

Recessive Scores

pRec: 0.129

Intolerance Scores

loftool: 0.100
rvis_EVS: -0.93
rvis_percentile_EVS: 9.75

Haploinsufficiency Scores

pHI: 0.424
hipred: Y
hipred_score: 0.765
ghis: 0.678

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atad2
Phenotype

Gene ontology

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
Cellular component: nucleus;nucleoplasm;extracellular exosome
Molecular function: chromatin binding;protein binding;ATP binding;ATPase activity;histone binding