Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs Transcription factors Other IDs Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	21
Gene name Gene Name - the full gene name approved by the HGNC.	ATP binding cassette subfamily A member 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	ABCA3
Synonyms (NCBI Gene) Gene synonyms aliases	ABC-C, ABC3, EST111653, LBM180, SMDP3
Chromosome Chromosome number	16
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	16p13.3
Summary Summary of gene provided in NCBI Entrez Gene.	The membrane-associated 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 intracellular membranes. ABC genes are divided into seven distinct

Show/Hide all(20)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28936691	T>G	Pathogenic	Missense variant, coding sequence variant
rs45592239	G>A	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs45620539	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs121909181	C>T	Pathogenic	Coding sequence variant, stop gained
rs121909182	A>G	Pathogenic	Coding sequence variant, missense variant
rs121909183	A>G	Pathogenic	Coding sequence variant, missense variant
rs121909184	T>C	Pathogenic	Coding sequence variant, missense variant
rs121909185	A>C,G	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs141621969	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs143929832	G>A,C,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs149989682	T>A,C	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs201299260	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs754714105	C>T	Pathogenic	Missense variant, coding sequence variant
rs756855585	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs773223403	T>C	Likely-pathogenic	Splice acceptor variant
rs775903641	TGTAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs876657633	GCACCTT>TGG	Likely-pathogenic	Splice donor variant, intron variant, coding sequence variant
rs973835010	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1567335355	C>T	Pathogenic	Splice donor variant
rs1596842934	C>G	Likely-pathogenic	Splice acceptor variant

Show/Hide all(36)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016946	hsa-miR-335-5p	Microarray	18185580
MIRT050565	hsa-miR-20a-5p	CLASH	23622248
MIRT049276	hsa-miR-92a-3p	CLASH	23622248
MIRT049276	hsa-miR-92a-3p	CLASH	23622248
MIRT040559	hsa-miR-92b-3p	CLASH	23622248
MIRT441309	hsa-miR-409-5p	HITS-CLIP	24374217
MIRT441309	hsa-miR-409-5p	HITS-CLIP	24374217
MIRT757911	hsa-miR-1200	CLIP-seq
MIRT757912	hsa-miR-1343	CLIP-seq
MIRT757913	hsa-miR-3180	CLIP-seq
MIRT757914	hsa-miR-3180-3p	CLIP-seq
MIRT757915	hsa-miR-3193	CLIP-seq
MIRT757916	hsa-miR-3196	CLIP-seq
MIRT757917	hsa-miR-4324	CLIP-seq
MIRT757918	hsa-miR-4520a-5p	CLIP-seq
MIRT757919	hsa-miR-4520b-5p	CLIP-seq
MIRT757920	hsa-miR-4767	CLIP-seq
MIRT757921	hsa-miR-544b	CLIP-seq
MIRT757922	hsa-miR-617	CLIP-seq
MIRT757912	hsa-miR-1343	CLIP-seq
MIRT757913	hsa-miR-3180	CLIP-seq
MIRT757914	hsa-miR-3180-3p	CLIP-seq
MIRT757915	hsa-miR-3193	CLIP-seq
MIRT757916	hsa-miR-3196	CLIP-seq
MIRT757918	hsa-miR-4520a-5p	CLIP-seq
MIRT757919	hsa-miR-4520b-5p	CLIP-seq
MIRT1923558	hsa-miR-4708-5p	CLIP-seq
MIRT757920	hsa-miR-4767	CLIP-seq
MIRT1923559	hsa-miR-4771	CLIP-seq
MIRT757912	hsa-miR-1343	CLIP-seq
MIRT2165030	hsa-miR-3166	CLIP-seq
MIRT1923559	hsa-miR-4771	CLIP-seq
MIRT2165031	hsa-miR-4802-3p	CLIP-seq
MIRT2165032	hsa-miR-508-5p	CLIP-seq
MIRT2165033	hsa-miR-520a-5p	CLIP-seq
MIRT2165034	hsa-miR-525-5p	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
SALL4	Activation	21526180;23432194
SALL4A	Activation	21526180

Show/Hide all(66)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005319	Function	Lipid transporter activity	IBA
GO:0005319	Function	Lipid transporter activity	IEA
GO:0005319	Function	Lipid transporter activity	TAS
GO:0005524	Function	ATP binding	IEA
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005737	Component	Cytoplasm	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005770	Component	Late endosome	IDA	27177387
GO:0005886	Component	Plasma membrane	IDA	11718719, 23137377
GO:0006855	Process	Xenobiotic transmembrane transport	IMP	26903515
GO:0006869	Process	Lipid transport	IBA
GO:0006869	Process	Lipid transport	IEA
GO:0006869	Process	Lipid transport	TAS
GO:0008559	Function	ABC-type xenobiotic transporter activity	IEA
GO:0008559	Function	ABC-type xenobiotic transporter activity	IMP	26903515
GO:0009410	Process	Response to xenobiotic stimulus	TAS	8706931
GO:0010875	Process	Positive regulation of cholesterol efflux	IMP	25817392
GO:0012505	Component	Endomembrane system	IEA
GO:0015914	Process	Phospholipid transport	IMP	28887056
GO:0016020	Component	Membrane	IEA
GO:0016887	Function	ATP hydrolysis activity	IDA	16959783
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030324	Process	Lung development	IEA
GO:0030324	Process	Lung development	ISS
GO:0030659	Component	Cytoplasmic vesicle membrane	IDA	16959783, 17574245, 20863830
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031902	Component	Late endosome membrane	IEA
GO:0032368	Process	Regulation of lipid transport	IEA
GO:0032464	Process	Positive regulation of protein homooligomerization	IDA	27352740
GO:0032585	Component	Multivesicular body membrane	IEA
GO:0034204	Process	Lipid translocation	IEA
GO:0042599	Component	Lamellar body	IDA	27177387
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA
GO:0042908	Process	Xenobiotic transport	IMP	26903515
GO:0043129	Process	Surfactant homeostasis	IEA
GO:0043129	Process	Surfactant homeostasis	ISS
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA
GO:0046470	Process	Phosphatidylcholine metabolic process	IEA
GO:0046470	Process	Phosphatidylcholine metabolic process	IMP	17574245, 28887056
GO:0046470	Process	Phosphatidylcholine metabolic process	ISS
GO:0046471	Process	Phosphatidylglycerol metabolic process	IEA
GO:0046471	Process	Phosphatidylglycerol metabolic process	ISS
GO:0046618	Process	Xenobiotic export from cell	IMP	26903515
GO:0046890	Process	Regulation of lipid biosynthetic process	IEA
GO:0051384	Process	Response to glucocorticoid	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0055091	Process	Phospholipid homeostasis	IEA
GO:0070925	Process	Organelle assembly	IEA
GO:0070925	Process	Organelle assembly	ISS
GO:0097208	Component	Alveolar lamellar body	IDA	11718719
GO:0097232	Component	Lamellar body membrane	IDA	20863830
GO:0097232	Component	Lamellar body membrane	TAS
GO:0097233	Component	Alveolar lamellar body membrane	IDA	11940594, 16959783
GO:0097233	Component	Alveolar lamellar body membrane	IEA
GO:0120009	Process	Intermembrane lipid transfer	IEA
GO:0120019	Function	Phosphatidylcholine transfer activity	IMP	28887056
GO:0140326	Function	ATPase-coupled intramembrane lipid transporter activity	IEA
GO:0140345	Function	Phosphatidylcholine flippase activity	IMP	27177387, 31473345
GO:0140359	Function	ABC-type transporter activity	IEA
GO:0150172	Process	Regulation of phosphatidylcholine metabolic process	IMP	25817392, 31473345
GO:1902995	Process	Positive regulation of phospholipid efflux	IMP	31473345
GO:2001140	Process	Positive regulation of phospholipid transport	IMP	27177387

MIM	HGNC	e!Ensembl
601615	33	ENSG00000167972

Protein

UniProt ID

Q99758

Protein name

Phospholipid-transporting ATPase ABCA3 (EC 7.6.2.1) (ABC-C transporter) (ATP-binding cassette sub-family A member 3) (ATP-binding cassette transporter 3) (ATP-binding cassette 3) (Xenobiotic-transporting ATPase ABCA3) (EC 7.6.2.2) [Cleaved into: 150 Kda m

Protein function

Catalyzes the ATP-dependent transport of phospholipids such as phosphatidylcholine and phosphoglycerol from the cytoplasm into the lumen side of lamellar bodies, in turn participates in the lamellar bodies biogenesis and homeostasis of pulmonary

PDB

7W01 , 7W02

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12698	ABC2_membrane_3	23 → 469		Family
PF00005	ABC_tran	549 → 693	ABC transporter	Domain
PF12698	ABC2_membrane_3	923 → 1323		Family
PF00005	ABC_tran	1399 → 1543	ABC transporter	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in brain, pancreas, skeletal muscle and heart (PubMed:8706931). Highly expressed in the lung in an AT2-cell-specific manner (PubMed:11718719, PubMed:8706931). Weakly expressed in placenta, kidney and liver (PubMed:8706931). A

Sequence

MAVLRQLALLLWKNYTLQKRKVLVTVLELFLPLLFSGILIWLRLKIQSENVPNATIYPGQ
SIQELPLFFTFPPPGDTWELAYIPSHSDAAKTVTETVRRALVINMRVRGFPSEKDFEDYI
RYDNCSSSVLAAVVFEHPFNHSKEPLPLAVKYHLRFSYTRRNYMWTQTGSFFLKETEGWH
TTSLFPLFPNPGPREPTSPDGGEPGYIREGFLAVQHAVDRAIMEYHADAATRQLFQRLTV
TIKRFPYPPFIADPFLVAIQYQLPLLLLLSFTYTALTIARAVVQEKERRLKEYMRMMGLS
SWLHWSAWFLLFFLFLLIAASFMTLLFCVKVKPNVAVLSRSDPSLVLAFLLCFAISTISF
SFMVSTFFSKANMAAAFGGFLYFFTYIPYFFVAPRYNWMTLSQKLCSCLLSNVAMAMGAQ
LIGKFEAKGMGIQWRDLLSPVNVDDDFCFGQVLGMLLLDSVLYGLVTWYMEAVFPGQFGV
PQPWYFFIMPSYWCGKPRAVAGKEEEDSDPEKALRNEYFEAEPEDLVAGIKIKHLSKVFR
VGNKDRAAVRDLNLNLYEGQITVLLGHNGAGKTTTLSMLTGLFPPTSGRAYISGYEISQD
MVQIRKSLGLCPQHDILFDNLTVAEHLYFYAQLKGLSRQKCPEEVKQMLHIIGLEDKWNS
RSRFLSGGMRRKLSIGIALIAGSKVLILDEPTSGMDAISRRAIWDLLQRQKSDRTIVLTT
HFMDEADLLGDRIAIMAKGELQCCGSSLFLKQKYGAGYHMTLVKEPHCNPEDISQLVHHH
VPNATLESSAGAELSFILPRESTHRFEGLFAKLEKKQKELGIASFGASITTMEEVFLRVG
KLVDSSMDIQAIQLPALQYQHERRASDWAVDSNLCGAMDPSDGIGALIEEERTAVKLNTG
LALHCQQFWAMFLKKAAYSWREWKMVAAQVLVPLTCVTLALLAINYSSELFDDPMLRLTL
GEYGRTVVPFSVPGTSQLGQQLSEHLKDALQAEGQEPREVLGDLEEFLIFRASVEGGGFN
ERCLVAASFRDVGERTVVNALFNNQAYHSPATALAVVDNLLFKLLCGPHASIVVSNFPQP
RSALQAAKDQFNEGRKGFDIALNLLFAMAFLASTFSILAVSERAVQAKHVQFVSGVHVAS
FWLSALLWDLISFLIPSLLLLVVFKAFDVRAFTRDGHMADTLLLLLLYGWAIIPLMYLMN
FFFLGAATAYTRLTIFNILSGIATFLMVTIMRIPAVKLEELSKTLDHVFLVLPNHCLGMA
VSSFYENYETRRYCTSSEVAAHYCKKYNIQYQENFYAWSAPGVGRFVASMAASGCAYLIL
LFLIETNLLQRLRGILCALRRRRTLTELYTRMPVLPEDQDVADERTRILAPSPDSLLHTP
LIIKELSKVYEQRVPLLAVDRLSLAVQKGECFGLLGFNGAGKTTTFKMLTGEESLTSGDA
FVGGHRISSDVGKVRQRIGYCPQFDALLDHMTGREMLVMYARLRGIPERHIGACVENTLR
GLLLEPHANKLVRTYSGGNKRKLSTGIALIGEPAVIFLDEPSTGMDPVARRLLWDTVARA
RESGKAIIITSHSMEECEALCTRLAIMVQGQFKCLGSPQHLKSKFGSGYSLRAKVQSEGQ
QEALEEFKAFVDLTFPGSVLEDEHQGMVHYHLPGRDLSWAKVFGILEKAKEKYGVDDYSV
SQISLEQVFLSFAHLQPPTAEEGR

Sequence length

1704

Interactions

View interactions

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hereditary Pulmonary Alveolar Proteinosis	hereditary pulmonary alveolar proteinosis	rs754714105, rs775903641, rs1596842934, rs756855585	N/A
Interstitial Lung Disease	interstitial lung disease due to abca3 deficiency, Interstitial lung disease 2	rs149989682, rs754714105, rs775903641, rs121909181, rs121909182, rs121909183, rs756855585, rs28936691, rs121909184, rs1567335355	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Surfactant Metabolism Dysfunction, Pulmonary	Pulmonary Surfactant Metabolism Dysfunction, Recessive, surfactant metabolism dysfunction, pulmonary, 1	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (55)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma Bronchiolo Alveolar	Associate	38226623
Adrenal Cortex Diseases	Associate	18603241
Allan Herndon Dudley syndrome	Associate	18603241
Brachydactyly type A3	Inhibit	32532878
Brain Diseases	Associate	18603241
Breast Neoplasms	Associate	31146704, 32977823, 38019257
Bronchopulmonary Dysplasia	Associate	18603241, 34465876
Congenital Deficiency of Pulmonary Surfactant Protein B	Associate	23814005, 34449154
COVID 19	Associate	37795896
Critical Illness	Associate	38275610
Death	Associate	17660803, 22068586, 29255193, 34449154
Fibrosis	Associate	36324278
Genetic Diseases Inborn	Associate	22707629, 36376106
Hepatitis B	Associate	19647838
Hyaline Membrane Disease	Associate	33040033
Hypertension Pulmonary	Associate	17885266
Idiopathic Pulmonary Fibrosis	Associate	24730976, 28642621
Inflammation	Associate	36324278
Interstitial Pneumonitis Desquamative Familial	Associate	15976379
Leukemia	Associate	19880777
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	19880777, 25056761
Lung Diseases	Associate	15044640, 15976379, 17660803, 21867529, 22068586, 22337229, 22866751, 24024739, 24871971, 27031696, 28887056, 34638622, 36135709, 36376106, 36808083, 39789505 View all (1 more)
Lung Diseases Interstitial	Associate	15976379, 17660803, 18676873, 20371530, 20863830, 21214890, 22068586, 22337229, 23814005, 24730976, 24871971, 27031696, 28642621, 31210424, 31331098 View all (11 more)
Lung Injury	Associate	22866751
Lung Neoplasms	Associate	38575158
Meconium Aspiration Syndrome	Associate	39789505
Mental Disorders	Associate	22866751
Myasthenia Gravis	Associate	25246735
Mycoplasma Infections	Associate	39789505
Neoplasm Residual	Stimulate	24145140
Neoplasms	Associate	21873242, 40641097
Neoplasms Glandular and Epithelial	Associate	38226623
Neuroma Acoustic	Associate	31146115
Osteopetrosis lethal	Associate	34715861
Pediatric Obesity	Associate	26522252, 29255193
Pneumonia Mycoplasma	Associate	39789505
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	24145140
Premature Birth	Associate	26522252
Pseudoxanthoma Elasticum	Associate	18936737
Pulmonary Alveolar Proteinosis	Associate	17660803, 24859540
Pulmonary Disease Chronic Obstructive	Associate	22866751
Pulmonary Fibrosis	Associate	18603241, 24730976
Respiratory Distress Syndrome	Associate	16415354, 22707629, 23166334, 25031143, 26522252, 27031696, 28642621, 29255193, 31210424, 31331098, 33040033, 33526094, 34449154, 34715861, 36376106, 39789505 View all (1 more)
Respiratory Distress Syndrome In Premature Infants	Associate	29255193
Respiratory Distress Syndrome Newborn	Associate	22068586, 23166334, 26522252, 31331098, 33526094, 34638622, 35170262, 36324278
Respiratory Insufficiency	Associate	17660803, 19647838, 21867529, 22337229, 24871971, 25031143, 31331098, 32532878, 32692933, 33526094, 34715861, 36376106, 36808083
Respiratory Tract Diseases	Associate	22337229
Severe Acute Respiratory Syndrome	Associate	35170262
Surfactant Dysfunction	Associate	15044640, 15976379, 16959783, 18603241, 18676873, 19647838, 20863830, 21214890, 21867529, 24024739, 25031143, 28215425, 29255193, 31210424, 32532878 View all (5 more)
Surfactant Metabolism Dysfunction Pulmonary 3	Associate	22337229, 35170262
Surfactant Metabolism Dysfunction Pulmonary 3	Inhibit	33504532
Syndrome	Associate	18603241
Synovitis	Associate	20371530
Tuberculosis Multidrug Resistant	Associate	24145140
Uniparental Disomy	Associate	19647838

ABCA3 (ATP binding cassette subfamily A member 3)