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Table 2 Rare non-synonymous CLU variants identified in Stage I Flanders-Belgium AD cohort.

From: Both common variations and rare non-synonymous substitutions and small insertion/deletions in CLU are associated with increased Alzheimer risk

Stage I: Flanders-Belgium AD cohort

      

Gene locationa

DNAb

Proteinc

dbSNP

Total number

MAF AD

MAF C

Protein location

PolyPhen (PSIC)

SIFT

Exon 5

c.924G > A

p.A309T

 

3

0.0018 (1)

 

β-chain

benign (1.07)

tolerated (0.65)

Exon 6

c.1012C > T

p.R338W

 

2

0.0012 (2)

 

β-chain

probable (2.37)

not tolerated (0.00)

Exon 6

c.1034C > T

p.T345M

 

1

0.0006 (2)

 

β-chain

possible (1.56)

tolerated (0.09)

Exon 7

c.1105A > C

p.N369H

rs9331936

2

0.0012

 

β-chain

possible (1.56)

tolerated (0.15)

Exon 7

c.1138G > A

p.D380N

rs9331938

1

0.0006

 

β-chain

benign (0.32)

tolerated (0.36)

Exon 7

c.1319C > T

p.T440M

 

1

0.0006

 

β-chain

possible (1.75)

not tolerated (0.01)

Exon 8

c.1333_1341del

p.T445_D447

del

 

3

0.0018 (1)

 

β-chain

  

Exon 8

c.1343C > T

p.S448L

rs13494

1

0.0006

 

β-chain

benign (0.73)

tolerated (0.23)

Exon 8

c.1349T > G

p.V450G

 

1

0.0006

 

β-chain

benign (1.42)

tolerated (0.15)

Exon 1

c.48C > A

p.S16R

 

11

0.0029

(5 AD)

0.0046

(6 C) (3)

extra AA isoform 2

benign (1.13)

not tolerated (0.00)

Exon 1

c.111C > A

p.H37Q

 

4

0.0012

(2 AD)

0.0015

(2 C)

extra AA isoform 2

possible (1.80)

not tolerated (0.00)

Exon 5

c.701G > A

p.R234H

 

3

0.0012

(2 AD)

0.0008

(1 C) (3)

α-chain

possible (1.64)

tolerated (0.15)

Exon 5

c.764C > T

p.T255I

rs4127629

11

0.0029

(5 AD)

0.0046

(6 C)

α-chain

benign (0.31)

tolerated (0.29)

Exon 5

c.965T > C

p.P322L

 

9

0.0029

(5 AD)

0.0030

(4 C)

β-chain

possible (1.96)

tolerated (0.25)

Exon 7

c.1153G > A

p.V385I

 

3

0.0006

(1 AD)

0.0015

(2 C)

β-chain

benign (0.15)

tolerated (0.40)

Exon 5

c.703G > A

p.A235T

 

1

 

0.0008

α-chain

benign (1.18)

tolerated (0.16)

Exon 5

c.797G > A

p.R266Q

 

1

 

0.0008

α-chain

benign (0.27)

tolerated (0.67)

Exon 6

c.994G > A

p.D332N

 

1

 

0.0008

β-chain

benign (0.04)

tolerated (0.1)

Exon 7

c.1268G > A

p.R423Q

 

1

 

0.0008

β-chain

benign (0.33)

tolerated (0.54)

Exon 7

c.1298A > C

p.Q433P

 

1

 

0.0008

β-chain

benign (0.41)

tolerated (0.13)

  1. aGene location position according to the longest CLU transcript with 9 coding exons [NM_001831.2], bNumbering according to CLU mRNA sequence starting at the A of the ATG translation initation codon in the reference sequence [GenBank accesion number NM_001831.2], cNumbering according to CLU protein sequence [GenPept accession number NP_001822.2]; MAF = Minor Allele Frequency, calculated upon the minimum number of successful sequences (1698 patient and 1318 control alleles); (1) 3 AD patients carry 2 different CLU variants (2) 1 AD patient with 2 CLU variants (3) 1 control individual with 2 CLU variants. Prediction of pathogenicity of missense mutations was performed using in silico programs PolyPhen (benign/possibly damaging/probably damaging) and SIFT (tolerated/not tolerated).