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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			76	7		83
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			7			7
Total	0	0	83	8	0

Variants in ATAD2

This is a list of pathogenic ClinVar variants found in the ATAD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-123321149-G-C		not specified	Uncertain significance (Jul 30, 2024)
8-123321172-T-C		not specified	Uncertain significance (Jan 29, 2024)
8-123322970-G-A		not specified	Uncertain significance (Mar 08, 2025)
8-123322975-C-T		not specified	Likely benign (Aug 21, 2023)
8-123322986-T-A		not specified	Uncertain significance (Aug 27, 2024)
8-123323034-T-G		not specified	Uncertain significance (Oct 06, 2024)
8-123323050-A-G		not specified	Uncertain significance (May 24, 2023)
8-123323063-G-T		not specified	Uncertain significance (Dec 07, 2021)
8-123325906-T-G		not specified	Uncertain significance (Jul 14, 2024)
8-123325924-G-C		not specified	Uncertain significance (Oct 21, 2024)
8-123325986-C-A		not specified	Uncertain significance (Mar 16, 2024)
8-123328221-T-C		not specified	Uncertain significance (Apr 07, 2023)
8-123328223-T-A		not specified	Uncertain significance (Feb 06, 2023)
8-123328298-C-T		not specified	Uncertain significance (Feb 05, 2025)
8-123328300-T-C		not specified	Uncertain significance (Feb 13, 2025)
8-123328402-C-A		not specified	Uncertain significance (May 03, 2023)
8-123328437-G-C		not specified	Uncertain significance (Dec 21, 2023)
8-123328465-A-G		not specified	Uncertain significance (Jun 26, 2023)
8-123328474-T-A		not specified	Uncertain significance (Dec 21, 2023)
8-123328477-A-G		not specified	Likely benign (Jul 19, 2022)
8-123328495-T-C		not specified	Uncertain significance (Jan 23, 2024)
8-123328519-C-T		not specified	Uncertain significance (May 17, 2023)
8-123328558-C-T		not specified	Uncertain significance (Sep 12, 2023)
8-123328575-C-A		not specified	Uncertain significance (Nov 09, 2023)
8-123333881-G-A		not specified	Uncertain significance (Oct 04, 2024)

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

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