ATAD3A (ATPase family AAA domain containing 3A)

Gene

• Entrez ID: 55210
• Gene name: ATPase family AAA domain containing 3A
• Gene symbol: ATAD3A
• Synonyms (NCBI Gene): HAYOS, PHRINL
• Chromosome: 1
• Chromosome location: 1p36.33
• 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-domai

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200344678	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs760826883	C>A,G,T	Pathogenic	Stop gained, missense variant, coding sequence variant, non coding transcript variant
rs1057517686	C>T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057517687	C>T	Likely-pathogenic, uncertain-significance, pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant, non coding transcript variant
rs1557458134	C>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1570319915	T>G	Pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, missense variant
rs1570345942	T>G	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022238	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT030419	hsa-miR-24-3p	Microarray	19748357
MIRT048949	hsa-miR-92a-3p	CLASH	23622248
MIRT045393	hsa-miR-149-5p	CLASH	23622248
MIRT803878	hsa-miR-150	CLIP-seq
MIRT803879	hsa-miR-3620	CLIP-seq
MIRT803880	hsa-miR-4677-3p	CLIP-seq
MIRT803881	hsa-miR-4713-5p	CLIP-seq
MIRT803882	hsa-miR-516a-5p	CLIP-seq
MIRT803883	hsa-miR-532-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0001558	Process	Regulation of cell growth	IMP	20332122
GO:0005515	Function	Protein binding	IPI	22664726, 30914652, 31522117
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	IMP	20154147
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	20332122
GO:0005739	Component	Mitochondrion	IEA
GO:0005743	Component	Mitochondrial inner membrane	IDA	20154147
GO:0005743	Component	Mitochondrial inner membrane	IDA	20349121
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0006413	Process	Translational initiation	IDA	16289705
GO:0006974	Process	DNA damage response	IDA	37832546
GO:0007005	Process	Mitochondrion organization	IBA
GO:0007005	Process	Mitochondrion organization	IMP	20154147
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IMP	20154147, 39116259
GO:0030291	Function	Protein serine/threonine kinase inhibitor activity	IDA	39116259
GO:0036499	Process	PERK-mediated unfolded protein response	IDA	31023583, 39116259
GO:0042645	Component	Mitochondrial nucleoid	IEA
GO:0042802	Function	Identical protein binding	IPI	30914652
GO:0043066	Process	Negative regulation of apoptotic process	IMP	20332122
GO:0044233	Component	Mitochondria-associated endoplasmic reticulum membrane contact site	IDA	39116259
GO:0140374	Process	Antiviral innate immune response	IMP	31522117
GO:0140468	Process	HRI-mediated signaling	IDA	37832546
GO:1903898	Process	Negative regulation of PERK-mediated unfolded protein response	IDA	39116259

Other IDs

• MIM: 612316
• HGNC: 25567
• e!Ensembl: ENSG00000197785

Protein

• UniProt ID: Q9NVI7
• Protein name: ATPase family AAA domain-containing protein 3A (EC 3.6.1.-)
• Protein function: Essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organism and cellular level (PubMed:17210950, PubMed:20154147, PubMed:22453275, PubMed:31522117, PubMed:37832546, PubMed:39116259). May play an importa
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12037	DUF3523	29 → 104	Domain of unknown function (DUF3523)	Family
  PF12037	DUF3523	131 → 334	Domain of unknown function (DUF3523)	Family
  PF00004	AAA	396 → 523	ATPase family associated with various cellular activities (AAA)	Domain

• Tissue specificity: TISSUE SPECIFICITY: Overexpressed in lung adenocarcinomas (at protein level). {ECO:0000269|PubMed:20332122}.
• Sequence:

  MSWLFGINKGPKGEGAGPPPPLPPAQPGAEGGGDRGLGDRPAPKDKWSNFDPTGLERAAK
  AARELEHSRYAKDALNLAQMQEQTLQLEQQSKLKMRLEALSLLHTLVWAWSLCRAGAVQT
  QERLSGSASPEQVPAGECCALQEYEAAVEQLKSEQIRAQAEERRKTLSEETRQHQARAQY
  QDKLARQRYEDQLKQQQLLNEENLRKQEESVQKQEAMRRATVEREMELRHKNEMLRVEAE
  ARARAKAERENADIIREQIRLKAAEHRQTVLESIRTAGTLFGEGFRAFVTDWDKVTATVA
  GLTLLAVGVYSAKNATLVAGRFIEARLGKPSLVRETSRITVLEALRHPIQVSRRLLSRPQ
  DALEGVVLSPSLEARVRDIAIATRNTKKNRSLYRNILMYGPPGTGKTLFAKKLALHSGMD
  YAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRAT
  LNAFLYRTGQHSNKFMLVLASNQPEQFDWAINDRINEMVHFDLPGQEERERLVRMYFDKY
  VLKPATEGKQRLKLAQFDYGRKCSEVARLTEGMSGREIAQLAVSWQATAYASEDGVLTEA
  MMDTRVQDAVQQHQQKMCWLKAEGPGRGDEPSPS

• Sequence length: 634

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Congenital cerebellar hypoplasia	Pathogenic	rs1570345942	RCV000991277	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Harel-Yoon syndrome	Likely pathogenic; Pathogenic	rs902213391, rs1057517686, rs2524212771, rs2524128308, rs1557458134, rs1641698007, rs1641722871, rs1172676832	RCV002227839 RCV000412539 RCV003236238 RCV004555171 RCV000723303 RCV001270778 RCV001293245 RCV001293246	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal	Likely pathogenic; Pathogenic	rs1464547304, rs2524128308, rs1557458134, rs1570345942, rs760826883, rs1570319915	RCV003223544 RCV004555171 RCV003989590 RCV001171378 RCV001027873 RCV001027874	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
1P36.33 DUPLICATION SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia	Conflicting classifications of pathogenicity; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATAD3A-related condition	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEREBELLAR HYPOPLASIA/ATROPHY, EPILEPSY, AND GLOBAL DEVELOPMENTAL DELAY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Disorder of development or morphogenesis	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing impairment	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR ANOMALIES, AXONAL NEUROPATHY, DEVELOPMENTAL DELAY SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR ANOMALIES-AXONAL NEUROPATHY-DEVELOPMENTAL DELAY SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATIC NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	20332122		★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	28549128	Associate	★☆☆☆☆ Found in Text Mining only
Athetoid cerebral palsy	Athetoid cerebral palsy	BEFREE	28158749		★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	28549128	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	25823022		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	38134103	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	CLINVAR_DG	27640307		★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	Pubtator	37095554, 38105692	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	28158749, 38105692	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	Pubtator	32933822	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	BEFREE	28549128		★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Cerebellar diseases	Pubtator	28549128	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	GENOMICS_ENGLAND_DG	27640307		★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	BEFREE	31727539		★☆☆☆☆ Found in Text Mining only
Cerebral Palsy	Cerebral palsy	Pubtator	28158749	Associate	★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	21743956		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Class III malocclusion	Malocclusion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	38551450	Associate	★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pontocerebellar hypoplasia	Pontoneocerebellar hypoplasia	BEFREE	28549128		★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	28158749	Associate	★☆☆☆☆ Found in Text Mining only
Distal amyotrophy	Distal amyotrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dyssomnias	Dyssomnia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dystonia	Dystonia	Pubtator	28549128	Associate	★☆☆☆☆ Found in Text Mining only
Dystonia Disorders	Dystonia	BEFREE	28549128		★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	28549128		★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	BEFREE	22276910		★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	24057885		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	27640307, 28158749		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG	27640307		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
HAREL-YOON SYNDROME	Harel-Yoon Syndrome	GENOMICS_ENGLAND_DG	25529582, 27640307, 28327206, 29898916		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HAREL-YOON SYNDROME	Harel-Yoon Syndrome	ORPHANET_DG	27640307		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HAREL-YOON SYNDROME	Harel-Yoon Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HAREL-YOON SYNDROME	Harel-Yoon Syndrome	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Henoch-Schoenlein Purpura	Henoch-Schonlein Nephritis	BEFREE	28158749		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	BEFREE	30914652		★☆☆☆☆ Found in Text Mining only
Hypersensitivity Immediate	Hypersensitivity	Pubtator	34387651	Associate	★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	27640307, 28158749		★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	GENOMICS_ENGLAND_DG	27640307		★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophic obstructive cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	27640307, 28158749		★☆☆☆☆ Found in Text Mining only
Hypoplasia of the optic nerve	Hypoplasia Of The Optic Nerve	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	38018291	Stimulate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25823022		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	21584487		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	CTD_human_DG	21584487		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	22318359, 25823022, 30919342		★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	32004445, 32933822	Associate	★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25823022, 30919342		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ocular anomalies-axonal neuropathy-developmental delay syndrome	Ocular Anomalies-Axonal Neuropathy-Developmental Delay Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
oligodendroglioma	Oligodendroglioma	LHGDN	18639545		★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	CLINVAR_DG	27640307		★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	GENOMICS_ENGLAND_DG	27640307		★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic atrophy	Pubtator	28158749	Associate	★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peripheral axonal neuropathy	Peripheral axonal neuropathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Peripheral nervous system disease	Pubtator	32933822	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Neuropathy	Peripheral Neuropathy	CLINVAR_DG	27640307		★☆☆☆☆ Found in Text Mining only
Pontocerebellar Hypoplasia	Pontocerebellar hypoplasia	Pubtator	28549128, 37095554	Associate	★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	21584487		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	CTD_human_DG	21584487		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Scoliosis, unspecified	Scoliosis	GENOMICS_ENGLAND_DG	27640307		★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sleep Disorders	Sleep Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia Hereditary	Hereditary spastic paraplegia	Pubtator	28158749	Associate	★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	BEFREE	28158749		★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	GENOMICS_ENGLAND_DG	27640307		★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	38018291	Stimulate	★☆☆☆☆ Found in Text Mining only