Table 5 Single variant association and functional prediction for variants contributing to the gene-level significance.

From: Deleterious variants in LTBP4 are associated with severe pediatric sepsis

Gene

Variant

SNP Informationa

Amino acid changeb

CADD scorec

GERP scored

SIFT scoree

Polyphen2 scoref

LTBP4

rs370696272

19:41105311:C:T

Leu27Leu

17.55

1.63

-

-

rs573310430

19:41122842:C:T

Arg984Cys

34

4.63

0.044 (D)

1.0 (D)

-

19:41132970:C:T

Pro1388Leu

25.8

4.58

0.68 (T)

0.998 (D)

rs200607327

19:41133005:G:A

Gly1437Arg

27

4.58

0.38 (T)

1.0 (D)

PLA2G4E

-

15:42276733:T:G

Lys387Gln

23

4.48

0.275 (T)

0.26 (B)

rs764494895

15:42278161:G:A

Ala693Val

11.04

0.591

0.25 (T)

0.004 (B)

rs143966595

15:42293394:C:T

Val212Ile

23.1

5.34

0.099 (T)

0.05 (B)

rs776016335

15:42298270:T:C

Asp148Gly

27.1

5.66

0.002 (D)

1.0 (D)

CCDC157

rs9606721

22:30762035:A:G

Thr16Ala

12.47

1.76

0.28 (T)

0.001 (B)

rs540507025

22:30762080:C:T

Arg31Cys

23.1

2.89

0.002 (D)

1.0 (D)

rs143249037

22:30766366:G:A

Glu158Lys

14.06

1.36

0.282 (T)

0.035 (B)

-

22:30766438:C:A

Gln182Lys

8.248

2.89

0.931 (T)

0.009 (B)

rs139609945

22:30766496:C:T

Thr201Met

8.755

2.19

0.107 (T)

0.155 (B)

rs1235664314

22:30766672:G:T

Asp260Tyr

28.4

5.29

0.008 (D)

1.0 (D)

rs148283823

22:30766868:G:A

Arg325Gln

6.266

0.566

0.712 (T)

0.093 (B)

rs202178544

22:30772567:T:C

Ser698Pro

0.246

−2.83

0.339 (T)

0.0 (B)

  1. aSNPs are listed as chromosome: position (hg19): reference allele: alternative allele.
  2. bAmino acid substitutions caused by SNPs.
  3. cCADD (Combined Annotation-Dependent Depletion) score measures the predicted variant effect rank, higher value implies a greater damaging effect throughout the human genome reference assembly. A score of 10 indicates that the SNP is predicted to be in the top 10% most deleterious substitutions in the human genome, a score 0f 20 indicates that the SNP is predicted to be in the top 1% most deleterious substitutions, a score of 30 indicates that the SNP is predicted to be in the top 0.1% most deleterious substitutions and so forth.
  4. dGERP (Genomic Evolutionary Rate Profiling) score indicates position-specific estimates of evolutionary constraint. A positive score scale with the level of constraint, a greater score suggests a greater level of evolutionary constraint. A negative score indicates that a site is probably evolving neutrally.
  5. eSIFT (Sorting Intolerant from tolerant) score ranges from 0 to 1. A value less than 0.05 is classified as damaging (D), whereas a higher score is classified as tolerated (T).
  6. fPolyphen2 (Polymorphism Phenotyping v2) score ranges from 0 to 1. Value implies probably damaging” (“D”) for scores in [0.957, 1]; “possibly damaging” (“D”) for scores in [0.453, 0.956]; “benign” (“B”) for scores in [0, 0.452].
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