Gene Gene information from NCBI Gene database.
Entrez ID 24
Gene name ATP binding cassette subfamily A member 4
Gene symbol ABCA4
Synonyms (NCBI Gene)
ABC10ABCRARMD2CORD3FFMRMPRP19STGDSTGD1
Chromosome 1
Chromosome location 1p22.1
Summary 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 s
SNPs SNP information provided by dbSNP.
427
SNP ID Visualize variation Clinical significance Consequence
rs1047376 A>G,T Likely-pathogenic Coding sequence variant, missense variant
rs1762111 A>G Likely-pathogenic, uncertain-significance, pathogenic Coding sequence variant, missense variant
rs1800548 C>T Likely-pathogenic, uncertain-significance Coding sequence variant, missense variant
rs1800552 C>T Likely-pathogenic, conflicting-interpretations-of-pathogenicity, uncertain-significance, pathogenic Coding sequence variant, missense variant
rs1800553 C>T Pathogenic-likely-pathogenic, likely-pathogenic, risk-factor, pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
10
miRTarBase ID miRNA Experiments Reference
MIRT017969 hsa-miR-335-5p Microarray 18185580
MIRT757923 hsa-miR-125a-3p CLIP-seq
MIRT757924 hsa-miR-1273e CLIP-seq
MIRT757925 hsa-miR-203 CLIP-seq
MIRT757926 hsa-miR-3934 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
54
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0001523 Process Retinoid metabolic process ISS
GO:0001523 Process Retinoid metabolic process TAS
GO:0001750 Component Photoreceptor outer segment IEA
GO:0001750 Component Photoreceptor outer segment ISS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601691 34 ENSG00000198691
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P78363
Protein name Retinal-specific phospholipid-transporting ATPase ABCA4 (EC 7.6.2.1) (ATP-binding cassette sub-family A member 4) (RIM ABC transporter) (RIM proteinv) (RmP) (Retinal-specific ATP-binding cassette transporter) (Stargardt disease protein)
Protein function Flippase that catalyzes in an ATP-dependent manner the transport of retinal-phosphatidylethanolamine conjugates like 11-cis and all-trans isomers of N-retinylidene-phosphatidylethanolamine (N-Ret-PE) from the lumen to the cytoplasmic leaflet of
PDB 7E7I , 7E7O , 7E7Q , 7LKP , 7LKZ , 7M1P , 7M1Q , 8F5B
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12698 ABC2_membrane_3 607 856 Family
PF00005 ABC_tran 946 1090 ABC transporter Domain
PF12698 ABC2_membrane_3 1595 1895 Family
PF00005 ABC_tran 1955 2099 ABC transporter Domain
Tissue specificity TISSUE SPECIFICITY: Retinal-specific. Seems to be exclusively found in the rims of rod photoreceptor cells.
Sequence
MGFVRQIQLLLWKNWTLRKRQKIRFVVELVWPLSLFLVLIWLRNANPLYSHHECHFPNKA
MPSAGMLPWLQGIFCNVNNPCFQSPTPGESPGIVSNYNNSILARVYRDFQELLMNAPESQ
HLGRIWTELHILSQFMDTLRTHPERIAGRGIRIRDILKDEETLTLFLIKNIGLSDSVVYL
LINSQVRPEQFAHGVPDLALKDIACSEALLERFIIFSQRRGAKTVRYALCSLSQGTLQWI
EDTLYANVDFFKLFRVLPTLLDSRSQGINLRSWGGILSDMSPRIQEFIHRPSMQDLLWVT
RPLMQNGGPETFTKLMGILSDLLCGYPEGGGSRVLSFNWYEDNNYKAFLGIDSTRKDPIY
SYDRRTTSFCNALIQSLESNPLTKIAWRAAKPLLMGKILYTPDSPAARRILKNANSTFEE
LEHVRKLVKAWEEVGPQIWYFFDNSTQMNMIRDTLGNPTVKDFLNRQLGEEGITAEAILN
FLYKGPRESQADDMANFDWRDIFNITDRTLRLVNQYLECLVLDKFESYNDETQLTQRALS
LLEENMFWAGVVFPDMYPWTSSLPPHVKYKIRMDIDVVEKTNKIKDRYWDSGPRADPVED
FRYIWGGFAYLQDMVEQGITRSQVQAEAPVGIYLQQMPYPCFVDDSFMIILNRCFPIFMV
LAWIYSVSMTVKSIVLEKELRLKETLKNQGVSNAVIWCTWFLDSFSIMSMSIFLLTIFIM
HGRILHYSDPFILFLFLLAFSTATIMLCFLLSTFFSKASLAAACSGVIYFTLYLPHILCF
AWQDRMTAELKKAVSLLSPVAFGFGTEYLVRFEEQGLGLQWSNIGNSPTEGDEFSFLLSM
QMMLLDAAVYGLLAWY
LDQVFPGDYGTPLPWYFLLQESYWLGGEGCSTREERALEKTEPL
TEETEDPEHPEGIHDSFFEREHPGWVPGVCVKNLVKIFEPCGRPAVDRLNITFYENQITA
FLGHNGAGKTTTLSILTGLLPPTSGTVLVGGRDIETSLDAVRQSLGMCPQHNILFHHLTV
AEHMLFYAQLKGKSQEEAQLEMEAMLEDTGLHHKRNEEAQDLSGGMQRKLSVAIAFVGDA
KVVILDEPTS
GVDPYSRRSIWDLLLKYRSGRTIIMSTHHMDEADLLGDRIAIIAQGRLYC
SGTPLFLKNCFGTGLYLTLVRKMKNIQSQRKGSEGTCSCSSKGFSTTCPAHVDDLTPEQV
LDGDVNELMDVVLHHVPEAKLVECIGQELIFLLPNKNFKHRAYASLFRELEETLADLGLS
SFGISDTPLEEIFLKVTEDSDSGPLFAGGAQQKRENVNPRHPCLGPREKAGQTPQDSNVC
SPGAPAAHPEGQPPPEPECPGPQLNTGTQLVLQHVQALLVKRFQHTIRSHKDFLAQIVLP
ATFVFLALMLSIVIPPFGEYPALTLHPWIYGQQYTFFSMDEPGSEQFTVLADVLLNKPGF
GNRCLKEGWLPEYPCGNSTPWKTPSVSPNITQLFQKQKWTQVNPSPSCRCSTREKLTMLP
ECPEGAGGLPPPQRTQRSTEILQDLTDRNISDFLVKTYPALIRSSLKSKFWVNEQRYGGI
SIGGKLPVVPITGEALVGFLSDLGRIMNVSGGPITREASKEIPDFLKHLETEDNIKVWFN
NKGWHALVSFLNVAHNAILRASLPKDRSPEEYGITVISQPLNLTKEQLSEITVLTTSVDA
VVAICVIFSMSFVPASFVLYLIQERVNKSKHLQFISGVSPTTYWVTNFLWDIMNYSVSAG
LVVGIFIGFQKKAYTSPENLPALVALLLLYGWAVIPMMYPASFLFDVPSTAYVALSCANL
FIGINSSAITFILELFENNRTLLRFNAVLRKLLIVFPHFCLGRGLIDLALSQAVTDVYAR
FGEEHSANPFHWDLIGKNLFAMVVEGVVYFLLTLL
VQRHFFLSQWIAEPTKEPIVDEDDD
VAEERQRIITGGNKTDILRLHELTKIYPGTSSPAVDRLCVGVRPGECFGLLGVNGAGKTT
TFKMLTGDTTVTSGDATVAGKSILTNISEVHQNMGYCPQFDAIDELLTGREHLYLYARLR
GVPAEEIEKVANWSIKSLGLTVYADCLAGTYSGGNKRKLSTAIALIGCPPLVLLDEPTT
G
MDPQARRMLWNVIVSIIREGRAVVLTSHSMEECEALCTRLAIMVKGAFRCMGTIQHLKSK
FGDGYIVTMKIKSPKDDLLPDLNPVEQFFQGNFPGSVQRERHYNMLQFQVSSSSLARIFQ
LLLSHKDSLLIEEYSVTQTTLDQVFVNFAKQQTESHDLPLHPRAAGASRQAQD
Sequence length 2273
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  ABC transporters   Retinoid cycle disease events
The canonical retinoid cycle in rods (twilight vision)
ABC-family proteins mediated transport
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
89
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 Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
ABCA4-related disorder Likely pathogenic; Pathogenic rs150774447, rs61748558, rs61749409, rs61749410, rs61749420, rs62654397, rs61749423, rs61749429, rs61751395, rs61749433, rs61749446, rs61749451, rs61749459, rs61750065, rs61751398
View all (57 more)
RCV004529882
RCV000778263
RCV001849310
RCV000778262
RCV004732662
View all (68 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ABCA4-related retinopathy Pathogenic; Likely pathogenic rs61748550, rs61748559, rs61749409, rs61749412, rs61752401, rs61749420, rs201738997, rs62654397, rs61750202, rs62645946, rs1801269, rs61752428, rs61750145, rs62646861, rs61750152
View all (45 more)
RCV006272252
RCV006272253
RCV006272254
RCV006272255
RCV006272256
View all (57 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Abnormal macular morphology Pathogenic rs62654397, rs76157638 RCV000414796
RCV000415097
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Abnormal retinal morphology Pathogenic rs62654397 RCV000626666
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ATROPHIC RETINA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adrenoleukodystrophy Adrenoleukodystrophy BEFREE 10088993, 25592337, 29860501
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration BEFREE 10216065, 10396622, 10442900, 10458172, 10486215, 10509673, 10634626, 10662806, 10711710, 10852960, 10880298, 10913642, 10958763, 11097334, 11346402
View all (51 more)
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration LHGDN 11919200, 12592048, 15947798, 16604398
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration CTD_human_DG 16968212
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration HPO_DG
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration GENOMICS_ENGLAND_DG
★☆☆☆☆
Found in Text Mining only
Albinism Ocular Ocular albinism Pubtator 27367509 Associate
★☆☆☆☆
Found in Text Mining only
Albinism, Ocular Ocular albinism BEFREE 29847651
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 36521383 Associate
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease, Late Onset Alzheimer disease BEFREE 23571587, 27030769
★☆☆☆☆
Found in Text Mining only