ATAD2B

ATPase family AAA domain containing 2B, the group of Bromodomain containing|AAA ATPases

Basic information

Region (hg38): 2:23748664-23927123

Links

ENSG00000119778 ∙ NCBI:54454 ∙ OMIM:615347 ∙ HGNC:29230 ∙ Uniprot:Q9ULI0 ∙ 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 ATAD2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATAD2B 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					1	1
missense			41	2		43
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	1

Variants in ATAD2B

This is a list of pathogenic ClinVar variants found in the ATAD2B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-23752065-A-G		not specified	Uncertain significance (Apr 19, 2023)
2-23754682-C-G		not specified	Uncertain significance (Jan 16, 2024)
2-23754751-G-A		not specified	Uncertain significance (Jul 12, 2023)
2-23757442-T-C		not specified	Uncertain significance (Sep 15, 2021)
2-23757462-G-A		not specified	Uncertain significance (Nov 15, 2023)
2-23757531-G-A		not specified	Likely benign (Jan 09, 2024)
2-23757532-T-C		not specified	Uncertain significance (Mar 15, 2024)
2-23757534-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-23757585-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-23757699-T-C		not specified	Likely benign (May 09, 2022)
2-23757802-C-G		not specified	Uncertain significance (Jun 14, 2022)
2-23757883-T-G		not specified	Uncertain significance (Apr 07, 2023)
2-23757889-T-C		not specified	Uncertain significance (Mar 06, 2023)
2-23758006-T-A		not specified	Uncertain significance (Oct 25, 2022)
2-23762214-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-23762272-C-G		not specified	Uncertain significance (Apr 18, 2023)
2-23762278-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-23762316-G-T		not specified	Uncertain significance (Aug 03, 2022)
2-23765509-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-23765527-T-C		not specified	Uncertain significance (Aug 30, 2021)
2-23782986-A-C		not specified	Uncertain significance (Dec 08, 2023)
2-23786077-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-23786121-A-G		not specified	Uncertain significance (Jul 15, 2021)
2-23788529-G-C		not specified	Uncertain significance (Apr 09, 2024)
2-23788563-C-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATAD2B	protein_coding	protein_coding	ENST00000238789	28	178451

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.53e-8	124644	0	13	124657	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.96	411	708	0.581	0.0000361	9512
Missense in Polyphen		62	199.87	0.3102		2663
Synonymous	1.18	220	243	0.904	0.0000116	2716
Loss of Function	7.07	5	67.8	0.0737	0.00000379	951

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000300	0.0000300
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000113	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000642	0.0000619
Middle Eastern	0.000113	0.000111
South Asian	0.0000327	0.0000327
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.57

Haploinsufficiency Scores

• pHI: 0.903
• hipred: Y
• hipred_score: 0.662
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atad2b
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype

Gene ontology

• Biological process: negative regulation of chromatin silencing;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: chromatin binding;ATP binding;ATPase activity;histone binding;lysine-acetylated histone binding