UCSF Pharmacogenetics of Membrane Transporters
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Common Name:ABC1
HGNC Symbol:ABCA1
HGNC Description:ATP-binding cassette, sub-family A (ABC1), member 1
HGNC ID:29
Chromosome:Chr.9(-): 106583104-106730257
Location:9q31.1
OMIM:600046
OMIM Phenotype:Tangier disease; High density lipoprotein deficiency, type 2; Tangier disease, variant; High density lipoprotein deficiency; Coronary heart disease in familial hypercholesterolema, protection aganist
Accessions:NM_005502
Nucleotide RefSeq:NM_005502
Protein RefSeq:NP_005493
Entrez:19
Isoforms:1
Evidence:Substrate In Vitro Evidence: 1. Free Cholesterol Efflux - Using J774 macrophages - Kellner-Weibel G, Atherosclerosis 2003: 235-243 2. Phospholipid efflux - Oram JF, Current Opinion in Lipidology 2002, 373-381 3. Interleukin 1-beta transport in Macrophages, but not monocytes from normal and TD patients- Xiaoqin Zhou et al, Biochemical and Biophysical Research Communications, 2002: 598-604 4. Apolipoprotein E secretion from monocyte-derived macrophages- Von Eckardstein A et al, FASEB, 2001: 1555-1561 Substrate In Vivo Evidence: 1. Atherogenesis, Tangier's Disease, Familial Hypoalphalipopreteinemia (FHA) - Singaraja RR et al, Ateriosclerosis Thrombosis and Vascular Biology 2003: 1322-1332 2. Apoptotic cell Engulfment by macrophages - Broccando C et al, Biochimica et Biophysica Acta, 1999: 395-404 3. ABCA1 modulates the development of aortic atherosclerosis in C57BL/6 and apoE-knockout mice, Joyce CW et al, PNAS 2002: 407-412 4. Glyburide inhibits ApoE secretion - Von Eckardstein A et al, FASEB, 2001: 1555-1561 Tissue Distribution Evidence: 1. Macrophages 2. Liver 3. Lymph node 4. Adrenals 5. Uterus 6. Low in Brain and Lung By Northern Blot Reference: C. Broccardo et al, Biochimia et Biophysica Acta 1461 (1999) 395-404
Tissues:Macrophages, liver, lymph nodes, adrenals, uterus
Type:protein coding
Sets:IV
PharmGKB ID:PA24373
HPRD ID:02501
Substrates:Free cholesterol, phospholipids, ApoE
Trivial Names:TGD, ABC1, CERP, ABC-1, HDLDT1, FLJ14958, MGC164864, MGC165011
Transcripts:NM_005502 [Chr.9(-): 106583104-106730257]
View on UCSC Genome Browser or Ensembl Genome Browser
ABCA1 Resequencing
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Study Name:ABCA1 Resequencing
Experiments:
SNP impact: P - Public  D - Discovered  E - Exclusive  (dbSNP build 130)
SNP array availability: I - found on Illumina Human1M-Duo BeadChip  A - found on Affymetrix Genome-Wide SNP Array 6.0  
FeaturePMT SNP IDdbSNP/ PubMedSNP Array AvailabilityGenomic PositionTranscript PositionCoding PositionNucleotide ChangeStrand, '+' or '-'Amino Acid PositionAmino Acid ChangeStatisticsAA FreqCA FreqAS FreqME FreqSample Set
 
2987
PDE
rs2246298
3 pubs		 106730554-297-24773
CCAGCGCTTCCCGCGCGTCTTAGGC C → T GGCGGGCCCGGGCGGGGGAAGGGGA
- 
 
n=
C/C=
C/T=
T/T=
T=
134
60
7
0
0.052
136
40
23
5
0.243
132
30
31
5
0.311
124
42
18
2
0.177
PMT-272
 
2988
PDE
rs1800976
9 pubs		 106730530-273-24749
CCGGCGGGCCCGGGCGGGGGAAGGG G → C ACGCAGACCGCGGACCCTAAGACAC
- 
 
n=
G/G=
G/C=
C/C=
C=
134
24
29
14
0.425
136
13
36
19
0.544
132
20
31
15
0.462
124
12
37
13
0.508
PMT-272
Promoter
3177
 106730476-219-24695
CTGTACCCTCCACCCCCACCCCACC C → CCACCC ACCTCCCCCCAACTCCCTAGATGTG
- 
 
n=
C/C=
C/CCACCC=
CCACCC/CCACCC=
CCACCC=
134
60
7
0
0.052
136
45
23
0
0.169
132
35
31
0
0.235
124
44
18
0
0.145
PMT-272
Promoter
2990
PDE
rs56064613
1 pub		 106730362-105-24581
GTGACTGAACTACATAAACAGAGGC C → T GGGAAGGGGGCGGGGAGGAGGGAGA
- 
 
n=
C/C=
C/T=
T/T=
T=
120
57
3
0
0.025
90
45
0
0
0.000
70
35
0
0
0.000
88
43
1
0
0.011
PMT-272
Promoter
2991
PDE
rs2740483
8 pubs		I106730356-99-24575
GAACTACATAAACAGAGGCCGGGAA G → C GGGGCGGGGAGGAGGGAGAGCACAG
- 
 
n=
G/G=
G/C=
C/C=
C=
120
45
14
1
0.133
90
24
14
7
0.311
70
18
15
2
0.271
88
20
18
6
0.341
PMT-272
Promoter
2992
PDE
rs1800977
16 pubs		I106730271-14-24490
GCCGAATCTATAAAAGGAACTAGTC C → T CGGCAAAAACCCCGTAATTGCGAGC
- 
 
n=
C/C=
C/T=
T/T=
T=
120
41
16
3
0.183
90
24
14
7
0.311
70
28
2
5
0.171
88
24
16
4
0.273
PMT-272
Exon: Coding
6141
rs34879708
 10658647470426729
GTAGAAAAGATGTGAGAACTGCAAC G → T TCCACTACTGTCTGGTTTTTGTGTA
+2243
Asp → Glu
n=
G/G=
G/T=
T/T=
T=
136
63
5
0
0.037
136
68
0
0
0.000
132
66
0
0
0.000
134
67
0
0
0.000
PMT-272
Exon: 3UTR
6140
 1065863217195 
CAGTATCCAGTTTACTTCTTCCCAC A → G TCAACTTCTGGCTCTTTTCTCCACA
+ 
 
n=
A/A=
A/G=
G/G=
G=
136
66
2
0
0.015
136
68
0
0
0.000
132
66
0
0
0.000
134
67
0
0
0.000
PMT-272
Exon: 3UTR
6139
rs13306080
 1065860497467 
TTTGATCAATAATCGCTGGCCATGA T → C TACTTGATGAATTATTGTTGCAACC
+ 
 
n=
T/T=
T/C=
C/C=
C=
136
68
0
0
0.000
136
68
0
0
0.000
136
67
1
0
0.007
136
68
0
0
0.000
PMT-272
Exon: 3UTR
6138
rs73517870
 1065860227494 
GAATGAGGATGTGCATTACCTTTTG A → T TTTTGATCAATAATCGCTGGCCATG
+ 
 
n=
A/A=
A/T=
T/T=
T=
136
51
16
1
0.132
136
67
1
0
0.007
136
65
3
0
0.022
136
67
1
0
0.007
PMT-272
Exon: 3UTR
6137
rs73517867
 1065860017515 
CTGGGCATGGCATGGCTTAGTGAAT G → A AGGATGTGCATTACCTTTTGATTTT
+ 
 
n=
G/G=
G/A=
A/A=
A=
136
67
1
0
0.007
136
68
0
0
0.000
136
68
0
0
0.000
136
68
0
0
0.000
PMT-272
Exon: 3UTR
6125
rs4149338
I1065857247792 
CAATGGAACCAAGTTTCCCGTGCCT G → A GAGACACCCACATTTTTGTTGCATG
+ 
 
n=
G/G=
G/A=
A/A=
A=
134
25
29
13
0.410
136
28
36
4
0.324
136
2
22
44
0.809
136
20
34
14
0.456
PMT-272
Exon: 3UTR
6076
 1065837129804 
AGTCACAAAGCATTTGCTTTCAGTA C → T AGATAATGAAATACAGTAGTGTGAG
+ 
 
n=
C/C=
C/T=
T/T=
T=
98
45
4
0
0.041
104
52
0
0
0.000
88
44
0
0
0.000
92
46
0
0
0.000
PMT-272
Exon: 3UTR
6075
 1065835209996 
TTACATTATTACTAGTAGATAATAA CAA → - GGGTACAAATTAATGTCTCAATA
+ 
 
n=
CAA/CAA=
CAA/-=
-/-=
-=
128
48
15
1
0.133
132
52
14
0
0.106
134
42
23
2
0.201
136
43
22
3
0.206
PMT-272
Exon: 3UTR
6074
 1065835179999 
GTATTACATTATTACTAGTAGATAA T → C AACAAGGGTACAAATTAATGTCTCA
+ 
 
n=
T/T=
T/C=
C/C=
C=
128
63
1
0
0.008
132
66
0
0
0.000
134
67
0
0
0.000
136
68
0
0
0.000
PMT-272
Exon: 3UTR
6073
 10658333410182 
ATAGATCCCATTACAGACAGCGTAA A → G GTGCTTGGAATGAGGGCCAATGATG
+ 
 
n=
A/A=
A/G=
G/G=
G=
128
61
3
0
0.023
132
66
0
0
0.000
134
67
0
0
0.000
136
68
0
0
0.000
PMT-272
Exon: 3UTR
6072
rs10991377
 10658319710319 
CATTTTAATACTTCATATAAAGTTA T → C TGACATACAAAATTTTTTTTCTTTT
+ 
 
n=
T/T=
T/C=
C/C=
C=
128
62
2
0
0.016
132
60
6
0
0.045
134
67
0
0
0.000
136
66
2
0
0.015
PMT-272
Exon: 3UTR
6071
 10658316310353 
TTTGTGACTCATTATATTACAACAT A → G GAAATATGCATTTTAATACTTCATA
+ 
 
n=
A/A=
A/G=
G/G=
G=
128
64
0
0
0.000
132
66
0
0
0.000
134
66
1
0
0.007
136
68
0
0
0.000
PMT-272

Transmembrane prediction:

Non-synonymous amino acid changes shown in red, indels (insertions and deletions) in blue, and synonymous changes in green. Exon(s) indicated by black outlines.
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