ATAD2B

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the AAA ATPase family. This family member includes an N-terminal bromodomain. It has been found to be localized to the nucleus, partly to replication sites, consistent with a chromatin-related function. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MANE transcript

NM_017552.4

Inheritance

ClinVar variants

U:137B:7

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr2:23,748,664-23,927,123

External References & Databases

Ensembl (ENSG00000119778)

Transcript & Mutation Effects

hg38 • Region Span ~178.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATAD2B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 125

not providedTotal: 5

See casesTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017552.4. 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			4 clinvar	2 clinvar		6
missense			128 clinvar	5 clinvar		133
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	137	7	0	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017552.4	RefSeq	NP_060022.2	28	MANE Select
ENST00000238789.10	Ensembl	ENSP00000238789.5	28	MANE Select
NM_001242338.3	RefSeq	NP_001229267.2	28	Standard
NM_001354107.2	RefSeq	NP_001341036.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of chromatin silencing
positive regulation of transcription by RNA polymerase II

Molecular Function

chromatin binding
ATP binding
ATPase activity
histone binding
lysine-acetylated histone binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000238789
Coding exons: 28
Length: 178451
Individuals with no LoFs: 124644
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 124657
p: 0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.96	411	708	0.581	0.0000361	9512
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000064	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.25
RVIS percentile EVS: 69.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.251

Gene Damage Prediction

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