ABCA7 (ATP binding cassette subfamily A member 7)

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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 10347
• Gene name: ATP binding cassette subfamily A member 7
• Gene symbol: ABCA7
• Synonyms (NCBI Gene): ABCA-SSN, ABCX, AD9
• Chromosome: 19
• Chromosome location: 19p13.3
• Summary: The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, M

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs115536223	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, intron variant, synonymous variant, non coding transcript variant, 3 prime UTR variant, downstream transcript variant, genic downstream transcript variant
rs189260652	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs201060968	G>A	Risk-factor, likely-benign, uncertain-significance	Coding sequence variant, stop gained, non coding transcript variant
rs538591288	T>-	Conflicting-interpretations-of-pathogenicity	Frameshift variant, coding sequence variant, non coding transcript variant
rs547447016	AGCAGGG>-	Conflicting-interpretations-of-pathogenicity, risk-factor	Coding sequence variant, upstream transcript variant, non coding transcript variant, frameshift variant, genic upstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017401	hsa-miR-335-5p	Microarray	18185580

Gene ontology (GO) Show/Hide all (74)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0001891	Component	Phagocytic cup	IEA
GO:0001891	Component	Phagocytic cup	ISS
GO:0005524	Function	ATP binding	IEA
GO:0005548	Function	Phospholipid transporter activity	IEA
GO:0005548	Function	Phospholipid transporter activity	IGI	28373057
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IDA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	IDA	14570867, 28373057
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006869	Process	Lipid transport	IEA
GO:0006909	Process	Phagocytosis	IEA
GO:0007613	Process	Memory	ISS
GO:0008542	Process	Visual learning	ISS
GO:0009986	Component	Cell surface	ISS
GO:0010875	Process	Positive regulation of cholesterol efflux	ISS
GO:0016020	Component	Membrane	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0019216	Process	Regulation of lipid metabolic process	ISS
GO:0030054	Component	Cell junction	IDA
GO:0031901	Component	Early endosome membrane	IEA
GO:0032587	Component	Ruffle membrane	IEA
GO:0032587	Component	Ruffle membrane	ISS
GO:0033344	Process	Cholesterol efflux	IBA
GO:0033344	Process	Cholesterol efflux	IDA	14570867
GO:0033344	Process	Cholesterol efflux	IEA
GO:0033700	Process	Phospholipid efflux	IBA
GO:0033700	Process	Phospholipid efflux	IDA	14570867
GO:0033700	Process	Phospholipid efflux	IEA
GO:0033700	Process	Phospholipid efflux	IGI	28373057
GO:0034188	Function	Apolipoprotein A-I receptor activity	IBA
GO:0034188	Function	Apolipoprotein A-I receptor activity	IDA	14570867
GO:0034188	Function	Apolipoprotein A-I receptor activity	IEA
GO:0034205	Process	Amyloid-beta formation	IEA
GO:0034205	Process	Amyloid-beta formation	IMP	26260791
GO:0034380	Process	High-density lipoprotein particle assembly	IDA	14570867
GO:0034504	Process	Protein localization to nucleus	ISS
GO:0038027	Process	Apolipoprotein A-I-mediated signaling pathway	IDA	14570867
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA
GO:0042985	Process	Negative regulation of amyloid precursor protein biosynthetic process	ISS
GO:0042995	Component	Cell projection	IEA
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA
GO:0043409	Process	Negative regulation of MAPK cascade	ISS
GO:0044857	Process	Plasma membrane raft organization	ISS
GO:0045332	Process	Phospholipid translocation	IDA	24097981
GO:0045806	Process	Negative regulation of endocytosis	ISS
GO:0050766	Process	Positive regulation of phagocytosis	ISS
GO:0055085	Process	Transmembrane transport	IEA
GO:0070374	Process	Positive regulation of ERK1 and ERK2 cascade	ISS
GO:0090554	Function	Phosphatidylcholine floppase activity	IBA
GO:0090554	Function	Phosphatidylcholine floppase activity	IDA	24097981
GO:0090554	Function	Phosphatidylcholine floppase activity	IEA
GO:0090556	Function	Phosphatidylserine floppase activity	IBA
GO:0090556	Function	Phosphatidylserine floppase activity	IDA	24097981
GO:0090556	Function	Phosphatidylserine floppase activity	IEA
GO:0097386	Component	Glial cell projection	ISS
GO:0140326	Function	ATPase-coupled intramembrane lipid transporter activity	IEA
GO:0140328	Function	Floppase activity	IDA	24097981
GO:0140328	Function	Floppase activity	IEA
GO:0140359	Function	ABC-type transporter activity	IEA
GO:0150094	Process	Amyloid-beta clearance by cellular catabolic process	ISS
GO:1900223	Process	Positive regulation of amyloid-beta clearance	ISS
GO:1901076	Process	Positive regulation of engulfment of apoptotic cell	ISS
GO:1902430	Process	Negative regulation of amyloid-beta formation	ISS
GO:1902991	Process	Regulation of amyloid precursor protein catabolic process	IEA
GO:1902991	Process	Regulation of amyloid precursor protein catabolic process	IMP	26260791
GO:1902995	Process	Positive regulation of phospholipid efflux	ISS
GO:1903898	Process	Negative regulation of PERK-mediated unfolded protein response	ISS
GO:2000010	Process	Positive regulation of protein localization to cell surface	ISS

Other IDs

• MIM: 605414
• HGNC: 37
• e!Ensembl: ENSG00000064687

Protein

• UniProt ID: Q8IZY2
• Protein name: Phospholipid-transporting ATPase ABCA7 (EC 7.6.2.1) (ABCA-SSN) (ATP-binding cassette sub-family A member 7) (Autoantigen SS-N) (Macrophage ABC transporter)
• Protein function: Catalyzes the translocation of specific phospholipids from the cytoplasmic to the extracellular/lumenal leaflet of membrane coupled to the hydrolysis of ATP (PubMed:24097981). Transports preferentially phosphatidylserine over phosphatidylcholine
• PDB: 8EDW , 8EE6 , 8EEB , 8EOP , 8Y1O , 8Y1P
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12698	ABC2_membrane_3	1433 → 1750		Family
  PF12698	ABC2_membrane_3	530 → 750		Family
  PF00005	ABC_tran	824 → 968	ABC transporter	Domain
  PF00005	ABC_tran	1810 → 1954	ABC transporter	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in leukocytes (at protein level) (PubMed:10873640). Widely expressed (PubMed:10873640). Highly expressed in myelo-lymphatic tissues including peripheral leukocytes, thymus, spleen and bone marrow (PubMed:10873640, PubMed:1143
• Sequence:

  MAFWTQLMLLLWKNFMYRRRQPVQLLVELLWPLFLFFILVAVRHSHPPLEHHECHFPNKP
  LPSAGTVPWLQGLICNVNNTCFPQLTPGEEPGRLSNFNDSLVSRLLADARTVLGGASAHR
  TLAGLGKLIATLRAARSTAQPQPTKQSPLEPPMLDVAELLTSLLRTESLGLALGQAQEPL
  HSLLEAAEDLAQELLALRSLVELRALLQRPRGTSGPLELLSEALCSVRGPSSTVGPSLNW
  YEASDLMELVGQEPESALPDSSLSPACSELIGALDSHPLSRLLWRRLKPLILGKLLFAPD
  TPFTRKLMAQVNRTFEELTLLRDVREVWEMLGPRIFTFMNDSSNVAMLQRLLQMQDEGRR
  QPRPGGRDHMEALRSFLDPGSGGYSWQDAHADVGHLVGTLGRVTECLSLDKLEAAPSEAA
  LVSRALQLLAEHRFWAGVVFLGPEDSSDPTEHPTPDLGPGHVRIKIRMDIDVVTRTNKIR
  DRFWDPGPAADPLTDLRYVWGGFVYLQDLVERAAVRVLSGANPRAGLYLQQMPYPCYVDD
  VFLRVLSRSLPLFLTLAWIYSVTLTVKAVVREKETRLRDTMRAMGLSRAVLWLGWFLSCL
  GPFLLSAALLVLVLKLGDILPYSHPGVVFLFLAAFAVATVTQSFLLSAFFSRANLAAACG
  GLAYFSLYLPYVLCVAWRDRLPAGGRVAASLLSPVAFGFGCESLALLEEQGEGAQWHNVG
  TRPTADVFSLAQVSGLLLLDAALYGLATWYLEAVCPGQYGIPEPWNFPFRRSYWCGPRPP
  KSPAPCPTPLDPKVLVEEAPPGLSPGVSVRSLEKRFPGSPQPALRGLSLDFYQGHITAFL
  GHNGAGKTTTLSILSGLFPPSGGSAFILGHDVRSSMAAIRPHLGVCPQYNVLFDMLTVDE
  HVWFYGRLKGLSAAVVGPEQDRLLQDVGLVSKQSVQTRHLSGGMQRKLSVAIAFVGGSQV
  VILDEPTAGVDPASRRGIWELLLKYREGRTLILSTHHLDEAELLGDRVAVVAGGRLCCCG
  SPLFLRRHLGSGYYLTLVKARLPLTTNEKADTDMEGSVDTRQEKKNGSQGSRVGTPQLLA
  LVQHWVPGARLVEELPHELVLVLPYTGAHDGSFATLFRELDTRLAELRLTGYGISDTSLE
  EIFLKVVEECAADTDMEDGSCGQHLCTGIAGLDVTLRLKMPPQETALENGEPAGSAPETD
  QGSGPDAVGRVQGWALTRQQLQALLLKRFLLARRSRRGLFAQIVLPALFVGLALVFSLIV
  PPFGHYPALRLSPTMYGAQVSFFSEDAPGDPGRARLLEALLQEAGLEEPPVQHSSHRFSA
  PEVPAEVAKVLASGNWTPESPSPACQCSRPGARRLLPDCPAAAGGPPPPQAVTGSGEVVQ
  NLTGRNLSDFLVKTYPRLVRQGLKTKKWVNEVRYGGFSLGGRDPGLPSGQELGRSVEELW
  ALLSPLPGGALDRVLKNLTAWAHSLDAQDSLKIWFNNKGWHSMVAFVNRASNAILRAHLP
  PGPARHAHSITTLNHPLNLTKEQLSEGALMASSVDVLVSICVVFAMSFVPASFTLVLIEE
  RVTRAKHLQLMGGLSPTLYWLGNFLWDMCNYLVPACIVVLIFLAFQQRAYVAPANLPALL
  LLLLLYGWSITPLMYPASFFFSVPSTAYVVLTCINLFIGINGSMATFVLELFSDQKLQEV
  SRILKQVFLIFPHFCLGRGLIDMVRNQAMADAFERLGDRQFQSPLRWEVVGKNLLAMVIQ
  GPLFLLFTLLLQHRSQLLPQPRVRSLPLLGEEDEDVARERERVVQGATQGDVLVLRNLTK
  VYRGQRMPAVDRLCLGIPPGECFGLLGVNGAGKTSTFRMVTGDTLASRGEAVLAGHSVAR
  EPSAAHLSMGYCPQSDAIFELLTGREHLELLARLRGVPEAQVAQTAGSGLARLGLSWYAD
  RPAGTYSGGNKRKLATALALVGDPAVVFLDEPTTGMDPSARRFLWNSLLAVVREGRSVML
  TSHSMEECEALCSRLAIMVNGRFRCLGSPQHLKGRFAAGHTLTLRVPAARSQPAAAFVAA
  EFPGAELREAHGGRLRFQLPPGGRCALARVFGELAVHGAEHGVEDFSVSQTMLEEVFLYF
  SKDQGKDEDTEEQKEAGVGVDPAPGLQHPKRVSQFLDDPSTAETVL

• Sequence length: 2146

Pathways

KEGG Pathway:

ABC transporters

Reactome Pathway:

ABC transporters in lipid homeostasis

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
ABCA7-related disorder	Likely pathogenic; Pathogenic	rs2041967070, rs1302770627, rs2512353998, rs765531464, rs769207938	RCV003416716 RCV003412008 RCV003402755 RCV003399840 RCV003893740	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alzheimer disease 9	Likely pathogenic	rs780510608, rs770510230	RCV003991794 RCV005410921	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (17)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Acute myeloid leukemia	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	21460840, 21460841, 23571587, 24162737, 30617256, 31473137, 33074286, 33589840, 34493870, 34743297, 35379992, 35589863, 35770850, 37198259, 37985413, 39129223, 39537608, 40676597	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMERS DISEASE	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Amyotrophic lateral sclerosis	Uncertain significance	ClinVar Disgenet	—	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	39046104, 39129223	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Flexion contracture	Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LATE-ONSET ALZHEIMER'S DISEASE	—	GWAS catalog	21460841, 23571587, 24162737, 30617256, 34493870, 38958117	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	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
Neuromuscular disease	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROMUSCULAR DISEASES	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary degenerative dementia of the Alzheimer type, presenile onset	Conflicting classifications of pathogenicity; risk factor	ClinVar Disgenet	—	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (71)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute Confusional Senile Dementia	Senile Dementia	CTD_human_DG	21460840, 25807283		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	24439028		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	22445811, 23226438, 23360175, 23419238, 23669301, 23836404, 23954108, 24141082, 24743338, 25129075, 25189118, 25365775, 25706306, 26004081, 26092349, 26101835, 26654793, 27037232, 27289440, 27770636, 28005991, 28084078, 28199971, 28447221, 28650998, 28655137, 28789839, 29340569, 29589097, 29750252, 30318785, 30448613, 30478411, 31405128, 31585107, 31727106, 31745181, 31831047, 32039842, 32740652, 32941707, 32991610, 34090711, 34092785, 34151536, 34958020, 35001095, 35307406, 36094096, 36189598, 36421824, 36521383, 36573011, 37101235, 37212111, 37658429, 37681876, 37762058, 37827850, 37946268, 38232788, 38241287, 38422817, 40157320, 40528303	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Alzheimer Disease	Alzheimer disease	Pubtator	36982820	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Alzheimer Disease	Alzheimer disease	Pubtator	40708016	Stimulate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Alzheimer Disease 9	Alzheimer disease	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Alzheimer Disease Familial 3 with Spastic Paraparesis and Apraxia	Alzheimer disease	Pubtator	37212111	Associate	★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	CTD_human_DG	21460840, 25807283		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	BEFREE	28447221, 31381512		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Late Onset	Alzheimer disease	CTD_human_DG	21460840, 25807283		★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

ABCA10 2 shared pathwaysABC transporters, ABC transporters in lipid homeostasis Related via 2 shared pathways including ABC transporters, ABC transporters in lipid homeostasis. ABCA9 2 shared pathwaysABC transporters, ABC transporters in lipid homeostasis Related via 2 shared pathways including ABC transporters, ABC transporters in lipid homeostasis. ABCA5 2 shared pathwaysABC transporters, ABC transporters in lipid homeostasis Related via 2 shared pathways including ABC transporters, ABC transporters in lipid homeostasis. ABCG4 2 shared pathwaysABC transporters, ABC transporters in lipid homeostasis Related via 2 shared pathways including ABC transporters, ABC transporters in lipid homeostasis. ABCA2 2 shared pathwaysABC transporters, ABC transporters in lipid homeostasis Related via 2 shared pathways including ABC transporters, ABC transporters in lipid homeostasis.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
ABCA10	0	[]	2	["ABC transporters","ABC transporters in lipid homeostasis"]	0	[]
ABCA9	0	[]	2	["ABC transporters","ABC transporters in lipid homeostasis"]	0	[]
ABCA5	0	[]	2	["ABC transporters","ABC transporters in lipid homeostasis"]	0	[]
ABCG4	0	[]	2	["ABC transporters","ABC transporters in lipid homeostasis"]	0	[]
ABCA2	0	[]	2	["ABC transporters","ABC transporters in lipid homeostasis"]	0	[]

Diseases Linked via Similar Genes

Colorectal neoplasms Linked via 3 of 5 related genesABCA10, ABCA9, ABCA5 Ovarian cancer Linked via 1 of 5 related genesABCA10 Scoliosis Linked via 1 of 5 related genesABCA9 Ventricular tachycardia Linked via 1 of 5 related genesABCA5 Gingival diseases Linked via 1 of 5 related genesABCA5

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Colorectal neoplasms	3	["ABCA10","ABCA9","ABCA5"]
Ovarian cancer	1	["ABCA10"]
Scoliosis	1	["ABCA9"]
Ventricular tachycardia	1	["ABCA5"]
Gingival diseases	1	["ABCA5"]