SNPs in ABCD1

August 15th, 2011 |

Single-nucleotide polymorphism in the ABCD1 gene

Allele frequencies obtained from combined sequence data from the Academic Medical Center and the Kennedy Krieger Institute

polymorphism exon SNP allele allele refSNP ID
p.Leu516Leu 6 c.1548G/A A (35/364) 9.6% G (329/364) 90.4% rs41314153
p.Phe673Phe 10 c.2019C/T T (7/158) 4.4% C (151/158) 95.6% www.x-ald.nl
3′UTR (stop+8) 10 c.2238+8C/G G (122/396) 30.8% C (274/396) 69.2% rs2229539
combination genotype N frequency reference
c.[1548G, c.2019C, c.2238+8C] (GCC) 102 59.0% www.x-ald.nl
c.[1548G, c.2019C, c.2238+8G] (GCG) 50 28.9% www.x-ald.nl
c.[1548G, c.2019T, c.2238+8C] (GTC) 8 4.6% www.x-ald.nl
c.[1548G, c.2019C, c.2238+8G] (GCG) 0 0% www.x-ald.nl
c.[1548A, c.2019C, c.2238+8G] (ACG) 0 0% www.x-ald.nl
c.[1548A, c.2019C, c.2238+8C] (ACC) 13 7.5% www.x-ald.nl
total 173

Unique polymorphisms

polymorphism exon SNP allele allele reference
p.Asn13Thr 1 c.38A/C C unique A >99.9% 48
p.His30His 1 c.90C>T T unique C >99.9% 72
p.Val86Val 1 c.258C/T T unique C >99.9% 33
p.Ile140Ile 1 c.420C/A A unique C >99.9% 71
p.Gln157Gln 1 c.471A/G G unique A >99.9% 33
p.Ala232Ala 1 c.696G/T T, <0.1% G >99.9% 32, 33
c.IVS1-5C/A IVS1 c.901-5c/a A unique C >99.9% 33
p.Ser633Ser 9 c.1899C/T T unique C >99.9% 33

Frequent polymorphisms

polymorphism exon SNP allele allele refSNP ID reference
5′UTR(-59) 1 c.-59C/T T (11/150) 7% C (139/150) 93% rs4148030 48
p.Leu516Leu 6 c.1548G/A A (32/322) 10% G (290/322) 90% rs41314153 6, 8, 10, 49
p.Phe673Phe 10 c.2019C/T T (2/150) 1% C (148/150) 99% 48
T (3/200) 1.5% C (198/200) 98.5% 49
3′UTR (stop+8) 10 c.2238+8C/G G (38/150) 25% C (112/150) 75% rs2229539 10, 49

Ethnic polymorphisms

polymorphism exon SNP reference
IVS5-6delC IVS5 c.1489-6delC 68 Taiwan: Identified in 9 out of 56 alleles (16%) Ref SNP ID: rs4148037

Single nucleotides in and around the ABCD1 gene

SNP 5′ near sequence allele 3′ near sequence location chr position
rs4148029 CACACCAGTCCCAGGGCTAGGGCACA [A/G] GCACCCTCCTGCCTAACTCGCCTGC 5′ upstream 152988564
rs5987137 CAACGTGCAGGCCCCGCCGCAGCAAC [A/C] GAACTCTCCCACAGCAGCCCCGGCC 5′ upstream 152989830
rs5986926 GGAGCGGAGGGCCGGCGCTCCGAGCG [C/G] GAGAGGAAGAGGCGCCTCGGGCTCC 5′ upstream 152989989
rs45581532 CCTGACCTCAGGGGCCAGGGCACTGA [C/G] AGGACAGGAGAGCCAAGTTCCTCCA 5′UTR 152990468
rs4148030 AGAGCAACAATCCTTCCAGCCACCTG [C/T] CTCAACTGCTGCCCCAGGCACCAGC 5′UTR 152990663
rs12006790 AAGGTGTGGGCAGGCCATGGGAGAGC [C/G] GGGCTGGGGTGGGCAGGGCCTTTGG intron 1 152991758
rs4148031 GAGGAGGGGCACAATGGCATCCATCC [C/T] CCGAAGGCCTGTGTGTGCTCCCTGG intron 1 152992527
rs4148032 GAGTTTGAGACCTGGCCCCACCCAAT [C/T] GTAACCTCTGGCTCTCGGCCTTCTG intron 1 152994545
rs2269365 GCCAGGAAGCCTCTCTGTGTCTGTCA [C/T] CCCCCGCAGGTGGAGCTGGCCCTGC intron 1 152994677
rs6643780 GTGGGAGAATGTGCGGAGTACCTGGA [A/G] TGAGCCCCTTCATCACTCCAGCCTT intron 2 152995219
rs6571291 CTTCTGACTCTCTTCGTTGTGTCTTT [C/T] GGTTTCTGTTTACTGTTTCCCATCT intron 2 152997097
rs6571292 GTTCTATTTCATTCTATTTCAAATAG [A/G] AATTTGAAAATGGACATTTCCTTTT intron 2 152997277
rs7063261 AGCTTCAGTTCTTGGGAGTATCATTC [A/G] CCTGTCTTCTGTCTGCTGGTCTTCA intron 2 152997448
rs4148033 GCTCCCAGAAGTTTCCCTTGCTTTCC [A/G] TCAAGCTTGGCTCTGCTCGAAATAG intron 2 152997839
rs4148034 CAGCCCGCGAGACAGCACCTGCAGCC [A/G] CTTCGCTCCATGGCTGCCATTGGTC intron 2 152998125
rs12847119 GGGGCCTGTGCCAGGAGCACTCTTTC [C/T] TCTGCTGCCCCATGGCGCAGCCCCC intron 2 152998697
rs13440661 ACTGCTCTCCCAAGCACTCGACACCC [C/T] GTCAGTGGCGCTTTTCTCTCTCCCT intron 2 152998803
rs5987139 GGAGGGCTGTGTCCTTGAGAGCACCG [C/T] GGGAAGGAAGGTCCAAGGCCTTCGA intron 2 152999250
rs4148035 TCCTCGGGTCCTTCACAGGACATTCC [C/T] ACCACTTCAGCCACACCCCAGCACC intron 2 152999479
rs12559009 TTAAAAATCAACGTTATTGAGACGTA [A/G] TTAACATACTATACAATTCTTCCTT intron 2 153000235
rs5987140 GACGTAATTAACATACTATACAATTC [C/T] TCCTTTTCCATGTACAGTTTAAATT intron 2 153000255
rs6643781 AATGAGGGCGTGCAGCCAGGGGCACG [C/T] AGACTCCCCAGAATGCAGAGGGGTC intron 4 153002539
rs12836060 TGGGGGTGGGATGAAGCCTTGCCCAG [G/T] AGTTGCTGTGAGCGAGTGGGCAGGC intron 5 153003383
rs12836077 CTGTGAGCGAGTGGGCAGGCAGCTGA [A/G] GGTAGAGGAGTGAGGGGCCGTGGGC intron 5 153003415
rs7052985 GCGCAGGCAGGGCGGGCTTCTGCCAA [A/G] GACCGAGAAGGTGCCTCCGCTCGGG intron 5 153003875
rs12011661 CTGCCAAGGACCGAGAAGGTGCCTCC [A/G] CTCGGGGCCTCTGTCCCAGCTTCTG intron 5 153003894
rs7049648 GGATTAGGGTTCCCACATAGGAATTT [A/C] AGAGGACAGAGTTCCACCCATGACA intron 5 153004182
rs2266874 CCAGCCTGGGCAACAGAGCAAGGCCC [C/T] GTCTCAAAAAGAAAAGAAAGAAACT intron 5 153004815
rs2071120 ATCAAGAATGGCCTGCGTGCTGGCCT [C/T] GGGCATTGGGAGCCTCTCAAGGCTG intron 5 153005453
rs4148037 CTCTCTGGCGTCAGCGGCTGTTGCCC [-/C] TGCAGGTGGAGGAAGGCATGCATCT intron 5 153005540
rs41314153 CCCAATGGCTGCGGCAAGAGCTCCCT [A/G] TTCCGGATCCTGGGTGGGCTCTGGCC exon 6 153005605
rs7059198 CTTCCTGCCTGTGCGCTCACACATGG [C/T] TTCCTGCAGAGGCCCAGGAAGTGGT intron 6 153005749
rs4148036 TTTTGGATCTGTGTGGGGTGTGTGCA [C/T] GGGCGGCGATGTGAGCGTGTGGATG intron 6 153005903
rs62594789 AGGGATGTGCACCTCACTGGGGGACC [A/C] AGGATACCCTCTCCCAGAGAAAAGA intron 7 153006391
rs11156606 GGGGCAGCAGGGCGGAGTGCGTTCCG [A/C] AGGCTTGGTGGTGCGAGAGGCTGGC intron 7 153006495
rs6643643 CATGTGTGCAGTGATGGCTACTGTCA [A/G] GAGGTTTGTGCAGACGCTTGGAGGG intron 7 153006659
rs2266875 AGGTGCCAGCAGGGTGGGCTCCTTCC [A/G] GGTGCCATGACAGAAGGATGTGTTC intron 7 153008001
rs2266876 CACTTCTCCCTGTATATCTTCACCTC [A/G] TGTTCCCCTGTGCATGTCTTCTGCC intron 7 153008083
rs4898368 GCGGCTGTCATCAGCAGCCCCCGTGC [C/T] GTGCCCCTGACCCTGTCCCTCTCCT intron 9 153008911
rs2229539 CCAGGGTGCCTCCACCTGACACAACC [C/G] TCCCCGGCCCCTGCCCCGCCCCCAA exon 10 153009197
rs1055842 TGCCAGCAGCGGGGGCGGCCCAGCCT [C/T] TGAGTCCCGTGGGGCCCCGGCTCCC 3′downstream 153009903
rs11803 CGCTGGCTCCGCAGACAGCTCCCCCT [A/G] GTGACCCCTCTTTGGCACTGAGCTG 3′downstream 153010066
rs1055847 AGGGGTCACTAGGGGGAGCTGTCTGC [A/G] GAGCCAGCGCCTGCCCGAGAGAGAC 3′downstream 153010083
s1055848 GCCAGCGCCTGCCCGAGAGAGACCCC [A/C] CCGCCACCGTGTGCCTTTCCCGGGC 3′downstream 153010112

Legend: All mutations are arranged according to their amino acid positions. All mutations are indicated conform to the nomenclature recommended by the Human Genome Variation Society.
Note: unpublished mutations (unpublished data) may not be used for publication purposes without prior approval from the editor of the database and the laboratories/investigators that have identified these mutations.

References

6 Fanen et al. J Clin Invest 1994;94(2):516-20
8 Fuchs et al. Hum Mol Genet 1994;3(10):1903-5
10 Kemp et al. Biochem Biophys Res Commun 1994;202(2):647-53
32 J. Haasjes & P.A.W. Mooijer. Lab. Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands. Contact person: Dr. H.R. Waterham (e-mail h.r.waterham [at_symbol] amc.uva.nl). Unpublished data
33 The Peroxisomal Diseases Laboratory, The Kennedy Krieger Institute, Baltimore, MD, USA. Contact person: Dr. S.J.S. Steinberg (e-mail steinbergs [at_symbol] kennedykrieger.org). Unpublished data
48 Dvorakova et al., (2001) Hum Mutat 18(1):52-60
49 Kemp et al., (2001) Hum Mutat 18(6):499-515
68 Chiu HC, et al., (2006) Pediatr Neurol 35(4):250-6
71 All India Institute of Medical Sciences (AIIMS), Department Pediatrics, Genetic Unit, Old Ot Block, New Delhi, India. Contact person: Pallavi Shukla (e-mail pallavi15july [at_symbol] rediffmail.com). Unpublished data
72 Department of Biochemistry, Vallabhbhai Patel Chest Institute (VPCI), University of Delhi & Institute of Genomics and Integrative Biology (IGIB), Mall Road, Delhi University Campus. Delhi-110007, India. Contact person: Neeraj Kumar (e-mail nirwal_niraj [at_symbol] yahoo.co.in). Unpublished data

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