ATAD3B

protein-coding

ATPase family AAA domain containing 3B, the group of AAA ATPases

Gene summary

The protein encoded by this gene is localized to the mitochondrial inner membrane, where it can bind to a highly-related protein, ATAD3A. ATAD3A appears to interact with matrix nucleoid complexes, and the encoded protein negatively regulates that interaction. This gene is expressed almost exclusively in pluripotent embryonic stem cells and some cancer cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

MANE transcript

NM_031921.6

Inheritance

—

ClinVar variants

U:211B:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr1:1,471,765-1,497,848

External References & Databases

Ensembl (ENSG00000160072)

Transcript & Mutation Effects

hg38 • Region Span ~26.1 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 ATAD3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 200

not providedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031921.6. 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			3 clinvar	3 clinvar	1 clinvar	7
missense			195 clinvar	16 clinvar	2 clinvar	213
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	211	19	3	233

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031921.6	RefSeq	NP_114127.3	16	MANE Select
ENST00000673477.1	Ensembl	ENSP00000500094.1	16	MANE Select
NM_001317238.2	RefSeq	NP_001304167.1	14	Standard
ENST00000308647.8	Ensembl	ENSP00000311766.8	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Neutrophil degranulation
Innate Immune System

Biological Process

mitochondrion organization
neutrophil degranulation

Molecular Function

ATP binding
zinc ion binding

Cellular Component

mitochondrion
mitochondrial inner membrane
plasma membrane
secretory granule membrane
ficolin-1-rich granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308647
Coding exons: 16
Length: 26086
Individuals with no LoFs: 125564
Homozygous LoFs: 4
Heterozygous LoFs: 160
Defined: 125728
p: 0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.79	557	400	1.39	0.0000285	4099
Missense (PolyPhen)		168	125.08	1.3432		1313
Synonymous	-3.46	233	175	1.33	0.0000128	1328
Loss of Function	-0.497	32	29.1	1.10	0.00000164	336

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.0016	0.0014	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00082	0.00082	rare
Finnish	0.00019	0.00014	rare
European (Non-Finnish)	0.00068	0.00066	rare
South Asian	0.00033	0.00033	rare
Other	0.00099	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in a mitochondrial network organization typical for stem cells, characterized by reduced mitochondrial metabolism, low mtDNA copies and fragmentated mitochondrial network. may act by suppressing ATAD3A function, interfering with ATAD3A interaction with matrix nucleoid complexes. {ECO:0000269|PubMed:22664726}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.167
RVIS EVS: 2.17
RVIS percentile EVS: 98.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.936

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High