Returns structural disruption classification of a variant Query by DNA    (Search by chromosome position with alternative nucleotide)
Chromosome		Coordinate (hg19)		Alternate nucleotide	select A C G T	or
or     Query by protein   (Search by gene or protein position with alternative amino acid)
Gene name	select ABCB1 ACE ADH1A ADH1B ADH1C ADRB1 ADRB2 AHR ALDH1A1 ALOX5 BRCA1 COMT CYP1A2 CYP2A6 CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2J2 CYP3A4 CYP3A5 DPYD DRD2 F5 G6PD GSTP1 GSTT1 HMGCR KCNH2 KCNJ11 MTHFR NQO1 NR1I2 P2RY1 P2RY12 PTGIS PTGS2 SCN5A SLC19A1 SLCO1B1 SULT1A1 TPMT TYMS UGT1A1 VDR VKORC1	Amino acid position		Alternate amino acid	select A C D E F G H I K L M N P Q R S T V W Y	or
or
Uniprot accession	select B2RC52 O75469 P00325 P00326 P00352 P04035 P04818 P05177 P05181 P07327 P07550 P08183 P08588 P08684 P09211 P09917 P10632 P10635 P11413 P11473 P11509 P11712 P12259 P12821 P14416 P15559 P20813 P20815 P21964 P22309 P30711 P33261 P35354 P35869 P38398 P41440 P42898 P47900 P50225 P51580 P51589 Q12809 Q12882 Q14524 Q16647 Q9BQB6 Q9H244 Q9Y6L6

Search for variants with selected SDS within a gene or protein
Gene name	select ABCB1 ACE ADH1A ADH1B ADH1C ADRB1 ADRB2 AHR ALDH1A1 ALOX5 BRCA1 COMT CYP1A2 CYP2A6 CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2J2 CYP3A4 CYP3A5 DPYD DRD2 F5 G6PD GSTP1 GSTT1 HMGCR KCNH2 KCNJ11 MTHFR NQO1 NR1I2 P2RY1 P2RY12 PTGIS PTGS2 SCN5A SLC19A1 SLCO1B1 SULT1A1 TPMT TYMS UGT1A1 VDR VKORC1	SDS [0-5]	select 0 1 2 3 4 5	or
or
Uniprot accession	select B2RC52 O75469 P00325 P00326 P00352 P04035 P04818 P05177 P05181 P07327 P07550 P08183 P08588 P08684 P09211 P09917 P10632 P10635 P11413 P11473 P11509 P11712 P12259 P12821 P14416 P15559 P20813 P20815 P21964 P22309 P30711 P33261 P35354 P35869 P38398 P41440 P42898 P47900 P50225 P51580 P51589 Q12809 Q12882 Q14524 Q16647 Q9BQB6 Q9H244 Q9Y6L6

 

 

Algorithm description
“SDS Pharmacogenes” is a score that represents the number of structural disturbances caused by an amino acid variant in a pharmacogene. The structural changes are examined in the context of 3-dimensional (3D) protein structures. Five strongest indicators that can discriminate pharmacogenomic variants from neutral mutations are incorporated into a five-feature “Structural Disruption Index” (SDI). The scores of five selected components in SDI determines the “Structural Disruption Score for Pharmacogenes” (SDS Pharmacogenes).

Our study examines all amino acid mutations within the 45 Very Important Pharmacogenes (VIPs)*. The algorithm can be used to infer structural significance of their amino acid changes based on the consensus prediction of structural disturbance (SDI positive/negative) and the magnitude of structural impact (SDS 0-5).

 

List of 45 Very Important Pharmacogenes (VIPs)
ACE, ADH1A, ADH1B, ADH1C, ADRB1, ADRB2, AHR, ALDH1A1, ALOX5, BRCA1, COMT, CYP1A2, CYP2A6, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP2J2, CYP3A4, CYP3A5, DPYD, DRD2, F5, G6PD, GSTP1, GSTT1, HMGCR, KCNH2, KCNJ11, MTHFR, NQO1, NR1I2, P2RY1, P2RY12, PTGIS, PTGS2, SCN5A, SLC19A1, SULT1A1, TPMT, TYMS, UGT1A1, VDR