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Blood, Vol. 113, Issue 9, 1967-1976, February 26, 2009
Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes
Blood Salzer et al.
113: 1967
Supplemental materials for: Salzer et al
Files in this Data Supplement:
- Document 1. Supplemental methods (PDF, 108 KB)
- Document 1. Supplemental results (PDF, 14.2 KB)
- Table S1. Sequence analysis of TACI amino acid substitutions with ConSeq, ConSurf, PMut, PolyPhen, and SIFT, all of which evaluate the variant sequence in a multiple alignment (PDF, 24.5 KB) -
ConSeq and ConSurf both provide conservation scores, though ConSurf can only provide such scores for amino acids in the CRD2 domain. Positions in the CRD2 domain have ConSurf scores listed in parenthesis. For ConSeq or ConSurf, we consider an amino acid substitution to be deleterious if the conservation score is at least seven. PMut provides both a prediction of whether a substitution is pathological or neutral and a reliability score between zero and nine; the reliability score is the number in parenthesis. In the summary column, there are two “X” marks if at least two of the following four predictions are made: deleterious by ConSeq; pathological by PMut with a reliability score of five or higher; possibly or probably damaging by PolyPhen; and not tolerated (score < 0.05) by SIFT. There is a single “X,” if exactly one of the four predictions is made.
- Table S2. Locations that SCpred and SCide predict to be stability centers of wild-type TACI (PDF, 141 KB) -
The first column names an amino acid and its position in wild-type TACI. An “X” in the second column indicates that SCpred predicts the corresponding position to be a stabilization center. The “XX” in column three indicates that SCide predicts position 87 to be a stabilzation center for two of three chains of TACI in 1xu1. Note that SCide is only applicable to R72, Y79, and C104, as only those position are in the structure 1xu1.
- Table S3. Scores for intrinsic disorder reported by DisEMBL (PDF, 420 KB) -
Each row of the table contains the disorder scores at a particular position in both wild-type TACI and in TACI with the amino acid substitution named in the first column. Each pair of columns – two and three; four and five; or six and seven -- represents the scores generated by one of the rules used by DisEMBL. The score for wild-type TACI is on the left of each pair and the score for the corresponding substitution is on the right. Bold entries indicate positions predicted by DisEMBL to be disordered. The cutoffs used are above 0.516 for loops/coils, above 0.1204 for hot-loops, and above 0.6 for Remark465.
- Table S4. Scores for intrinsic disorder reported by DISOPRED2 (PDF, 237 KB) -
Each row of the table contains the disorder scores at a particular position in both wild-type TACI and in TACI with the amino acid substitution named in the first column. The score for wild-type TACI is in the second column and the score for TACI with the corresponding substitution is in the third column. Bold entries indicate positions predicted by DISOPRED2 to be disordered. The cutoff used is 0.086.
- Table S5. Scores for intrinsic disorder reported by DRIPPRED (PDF, 192 KB) -
Each row of the table contains the disorder scores at a particular position in both wild-type TACI and in TACI with the amino acid substitution named in the first column. The score for wild-type TACI is in the second column and the score for TACI with the corresponding substitution is in the third column. Bold entries indicate positions predicted by DRIPPRED to be disordered. The cutoff used is 0.5.
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