rs2066714 Rat Genome Database

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Variant: rs2066714 -  Homo sapiens

RGD ID: 11611664
RS ID: rs2066714
ClinVar ID: CV315998
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: ABCA1  
Reference Nucleotide: T
Variant Nucleotide: C
Position
Assembly Chr Position
GRCh37 9 107,586,753
GRCh38 9 104,824,472
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Age of Onset Prevalence Trait Synonyms
NG_007981.1:g.108684A>G
NC_000009.12:g.104824472T>C
NC_000009.11:g.107586753T>C
NP_005493.2:p.Ile883Met
More... 		12/04/2020 missense variant benign childhood <1 / 1 000 000 A-alphalipoprotein neuropathy; AllHighlyPenetrant; Alpha high density lipoprotein deficiency disease; Analphalipo-proteinemia; Cholesterol thesaurismosis; Familial high density lipoprotein deficiency disease; Familial Hypoalphalipo-proteinemia; Hdl lipoprotein deficiency disease; High density lipoprotein deficiency, Tangier type; High density lipoprotein deficiency, type 1; none provided
Disease Annotations     Click to see Annotation Detail View

GWAS Catalog Data
GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG SNP Passing QC Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GCST010245 LDL cholesterol levels 440,546 European ancestry individuals T 0.871227 2E-11 10.698970004336019 Affymetrix [NR] (imputed) 0.0209673 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:32203549
GCST010242 HDL cholesterol levels 403,943 European ancestry individuals T 0.87138 4E-60 59.39794000867204 Affymetrix [NR] (imputed) 0.0465057 high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:32203549
GCST010241 Apolipoprotein A1 levels 393,193 European ancestry individuals T 0.87145 1E-76 76.0 Affymetrix [NR] (imputed) 0.0542774 apolipoprotein A 1 measurement (EFO:0004614)
 PMID:32203549

Variant Details
Variant Transcripts
Gene Symbol:ABCA1
Accession:NM_005502
Location:EXON
Amino Acid Prediction: I to M (nonsynonymous)
Amino Acid Position: 883
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKAMPSAGTLPWVQGIICNANNP
CFRYPTPGEAPGVVGNFNKSIVARLFSDARRLLLYSQKDTSMKDMRKVLRTLQQIKKSSSNLKLQDFLVDNETFSGFLYH
NLSLPKSTVDKMLRADVILHKVFLQGYQLHLTSLCNGSKSEEMIQLGDQEVSELCGLPREKLAAAERVLRSNMDILKPIL
RTLNSTSPFPSKELAEATKTLLHSLGTLAQELFSMRSWSDMRQEVMFLTNVNSSSSSTQIYQAVSRIVCGHPEGGGLKIK
SLNWYEDNNYKALFGGNGTEEDAETFYDNSTTPYCNDLMKNLESSPLSRIIWKALKPLLVGKILYTPDTPATRQVMAEVN
KTFQELAVFHDLEGMWEELSPKIWTFMENSQEMDLVRMLLDSRDNDHFWEQQLDGLDWTAQDIVAFLAKHPEDVQSSNGS
VYTWREAFNETNQAIRTISRFMECVNLNKLEPIATEVWLINKSMELLDERKFWAGIVFTGITPGSIELPHHVKYKIRMDI
DNVERTNKIKDGYWDPGPRADPFEDMRYVWGGFAYLQDVVEQAIIRVLTGTEKKTGVYMQQMPYPCYVDDIFLRVMSRSM
PLFMTLAWIYSVAVIIKGIVYEKEARLKETMRIMGLDNSILWFSWFISSLIPLLVSAGLLVVILKLGNLLPYSDPSVVFV
FLSVFAVVTILQCFLISTLFSRANLAAACGGIIYFTLYLPYVLCVAWQDYVGFTLKIFASLLSPVAFGFGCEYFALFEEQ
GIGVQWDNLFESPVEEDGFNLTTSVSMMLFDTFLYGVMTWYIEAVFPGQYGIPRPWYFPCTKSYWFGEESDEKSHPGSNQ
KRMSEICMEEEPTHLKLGVSIQNLVKVYRDGMKVAVDGLALNFYEGQITSFLGHNGAGKTTTMSILTGLFPPTSGTAYIL
GKDIRSEMSTIRQNLGVCPQHNVLFDMLTVEEHIWFYARLKGLSEKHVKAEMEQMALDVGLPSSKLKSKTSQLSGGMQRK
LSVALAFVGGSKVVILDEPTAGVDPYSRRGIWELLLKYRQGRTIILSTHHMDEADVLGDRIAIISHGKLCCVGSSLFLKN
QLGTGYYLTLVKKDVESSLSSCRNSSSTVSYLKKEDSVSQSSSDAGLGSDHESDTLTIDVSAISNLIRKHVSEARLVEDI
GHELTYVLPYEAAKEGAFVELFHEIDDRLSDLGISSYGISETTLEEIFLKVAEESGVDAETSDGTLPARRNRRAFGDKQS
CLRPFTEDDAADPNDSDIDPESRETDLLSGMDGKGSYQVKGWKLTQQQFVALLWKRLLIARRSRKGFFAQIVLPAVFVCI
ALVFSLIVPPFGKYPSLELQPWMYNEQYTFVSNDAPEDTGTLELLNALTKDPGFGTRCMEGNPIPDTPCQAGEEEWTTAP
VPQTIMDLFQNGNWTMQNPSPACQCSSDKIKKMLPVCPPGAGGLPPPQRKQNTADILQDLTGRNISDYLVKTYVQIIAKS
LKNKIWVNEFRYGGFSLGVSNTQALPPSQEVNDAIKQMKKHLKLAKDSSADRFLNSLGRFMTGLDTKNNVKVWFNNKGWH
AISSFLNVINNAILRANLQKGENPSHYGITAFNHPLNLTKQQLSEVALMTTSVDVLVSICVIFAMSFVPASFVVFLIQER
VSKAKHLQFISGVKPVIYWLSNFVWDMCNYVVPATLVIIIFICFQQKSYVSSTNLPVLALLLLLYGWSITPLMYPASFVF
KIPSTAYVVLTSVNLFIGINGSVATFVLELFTDNKLNNINDILKSVFLIFPHFCLGRGLIDMVKNQAMADALERFGENRF
VSPLSWDLVGRNLFAMAVEGVVFFLITVLIQYRFFIRPRPVNAKLSPLNDEDEDVRRERQRILDGGGQNDILEIKELTKI
YRRKRKPAVDRICVGIPPGECFGLLGVNGAGKSSTFKMLTGDTTVTRGDAFLNKNSILSNIHEVHQNMGYCPQFDAITEL
LTGREHVEFFALLRGVPEKEVGKVGEWAIRKLGLVKYGEKYAGNYSGGNKRKLSTAMALIGGPPVVFLDEPTTGMDPKAR
RFLWNCALSVVKEGRSVVLTSHSMEECEALCTRMAIMVNGRFRCLGSVQHLKNRFGDGYTIVVRIAGSNPDLKPVQDFFG
LAFPGSVLKEKHRNMLQYQLPSSLSSLARIFSILSQSKKRLHIEDYSVSQTTLDQVFVNFAKDQSDDDHLKDLSLHKNQT
VVDVAVLTSFLQDEKVKESYV*
Variant Samples
Additional References at PubMed
PMID:10431237   PMID:16429166   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000310886 CLINVAR
  RCV000398007 CLINVAR
  RCV001509913 CLINVAR
  RCV001700360 CLINVAR
  RCV002450939 CLINVAR
dbSNP (RS) rs2066714 CLINVAR
GWAS Catalog GCST90269744 GWAS Catalog
MedGen C0039292 CLINVAR
  C3661900 CLINVAR
  C5231558 CLINVAR
  CN169374 CLINVAR
  CN230736 CLINVAR
NCBI Gene ABCA1 CLINVAR
OMIM 205400 CLINVAR
  600046 CLINVAR
  604091 CLINVAR