ATAD3A ATPase family AAA domain containing 3A [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATAD3Aprovided by HGNC
Official Full Name: ATPase family AAA domain containing 3Aprovided by HGNC
Primary source: HGNC:HGNC:25567
See related: Ensembl:ENSG00000197785 MIM:612316; AllianceGenome:HGNC:25567
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HAYOS; PHRINL
Summary: This gene encodes a ubiquitously expressed mitochondrial membrane protein that contributes to mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. This gene is a member of the ATPase family AAA-domain containing 3 gene family which, in humans, includes two other paralogs. Naturally occurring mutations in this gene are associated with distinct neurological syndromes including Harel-Yoon syndrome. High-level expression of this gene is associated with poor survival in breast cancer patients. A homozygous knockout of the orthologous gene in mice results in embryonic lethality at day 7.5 due to growth retardation and defective development of the trophoblast lineage. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
Expression: Ubiquitous expression in bone marrow (RPKM 6.3), testis (RPKM 6.2) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 1p36.33

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (1512162..1534685)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (946666..969189)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (1447542..1470065)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PERK-ATAD3A interaction provides a subcellular safe haven for protein synthesis during ER stress.
Title: PERK-ATAD3A interaction provides a subcellular safe haven for protein synthesis during ER stress.
Identification of ATAD3A as a key regulator in non-small cell lung cancer by promoting STAT3-induced cell proliferation and tumor angiogenesis.
Title: Identification of ATAD3A as a key regulator in non-small cell lung cancer by promoting STAT3-induced cell proliferation and tumor angiogenesis.
The value of ATAD3A as a potential biomarker for bladder cancer.
Title: The value of ATAD3A as a potential biomarker for bladder cancer.
"ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
Title: "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
Title: ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
Targeting ATAD3A-PINK1-mitophagy axis overcomes chemoimmunotherapy resistance by redirecting PD-L1 to mitochondria.
Title: Targeting ATAD3A-PINK1-mitophagy axis overcomes chemoimmunotherapy resistance by redirecting PD-L1 to mitochondria.
The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
Title: The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.
Title: ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.
Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes.
Title: Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes.
Enhanced cGAS-STING-dependent interferon signaling associated with mutations in ATAD3A.
Title: Enhanced cGAS-STING-dependent interferon signaling associated with mutations in ATAD3A.

Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Harel-Yoon syndrome MedGen: C4310677 OMIM: 617183 GeneReviews: Not available	Compare labs
Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal MedGen: C5394137 OMIM: 618810 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpu	vpu	HIV-1 Vpu is identified to have a physical interaction with ATPase family, AAA domain containing 3A (ATAD3A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP hydrolysis activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine/threonine kinase inhibitor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of HRI-mediated signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in antiviral innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of PERK-mediated unfolded protein response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in mitochondria-associated endoplasmic reticulum membrane contact site	IDA Inferred from Direct Assay more info	PubMed
is_active_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial nucleoid	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HTP more info	PubMed
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ATPase family AAA domain-containing protein 3A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_053035.1 RefSeqGene

Range

5020..27543

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001170535.3 → NP_001164006.1 ATPase family AAA domain-containing protein 3A isoform 2

See identical proteins and their annotated locations for NP_001164006.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.

Source sequence(s)

AK001571, BC011814, BC014101, DA206969

Consensus CDS

CCDS53259.1

UniProtKB/TrEMBL

Q96T67

Related

ENSP00000368031.3, ENST00000378756.8

Conserved Domains (3) summary

smart00382
Location:346 → 476

AAA; ATPases associated with a variety of cellular activities

pfam00004
Location:348 → 475

AAA; ATPase family associated with various cellular activities (AAA)

pfam12037
Location:42 → 286

DUF3523; Domain of unknown function (DUF3523)
NM_001170536.3 → NP_001164007.1 ATPase family AAA domain-containing protein 3A isoform 3

See identical proteins and their annotated locations for NP_001164007.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences in the 5' UTR and 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AK001571, AK056099, BC011814, BC014101

Consensus CDS

CCDS53260.1

UniProtKB/TrEMBL

Q96T67

Related

ENSP00000439290.1, ENST00000536055.6

Conserved Domains (3) summary

smart00382
Location:267 → 397

AAA; ATPases associated with a variety of cellular activities

pfam00004
Location:269 → 396

AAA; ATPase family associated with various cellular activities (AAA)

pfam12037
Location:12 → 207

DUF3523; Domain of unknown function (DUF3523)
NM_018188.5 → NP_060658.3 ATPase family AAA domain-containing protein 3A isoform 1

See identical proteins and their annotated locations for NP_060658.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK001571, AK091144, BC011814, BC014101, DA206969

Consensus CDS

CCDS31.1

UniProtKB/Swiss-Prot

B3KPB3, D2K8Q1, G3V1I6, Q5SV23, Q8N275, Q96A50, Q9NVI7

UniProtKB/TrEMBL

Q96T67

Related

ENSP00000368030.5, ENST00000378755.9

Conserved Domains (3) summary

smart00382
Location:394 → 524

AAA; ATPases associated with a variety of cellular activities

pfam00004
Location:396 → 523

AAA; ATPase family associated with various cellular activities (AAA)

pfam12037
Location:42 → 334

DUF3523; Domain of unknown function (DUF3523)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

1512162..1534685

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047424288.1 → XP_047280244.1 ATPase family AAA domain-containing protein 3A isoform X1
XM_047424289.1 → XP_047280245.1 ATPase family AAA domain-containing protein 3A isoform X2
XM_047424290.1 → XP_047280246.1 ATPase family AAA domain-containing protein 3A isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

946666..969189

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054337419.1 → XP_054193394.1 ATPase family AAA domain-containing protein 3A isoform X1
XM_054337420.1 → XP_054193395.1 ATPase family AAA domain-containing protein 3A isoform X2
XM_054337421.1 → XP_054193396.1 ATPase family AAA domain-containing protein 3A isoform X3