Table 2 Rare and novel variant identified

From: Surfactant proteins gene variants in premature newborn infants with severe respiratory distress syndrome

Gene

Region

Variant

rs

Frequency

Protein prediction

Splicing prediction

  

Coding DNA

Putative protein

 

1000 G

ExAC/ gnomAD

n. of homoz.

PP2

SIFT

Grantham distance

Align GVGD

MaxEnt, NNSPLICE, GeneSplicer, HSF, SSPNN

ABCA3

Coding

c.745 C > A

p.(Pro249Thr)

Novel

0

0

0

Benign (0.063)

Deleterious (0.03)

38

C0

–

  

c.863 G > A

p.(Arg288Lys) [13, 25]

rs117603931

0.002

0.0059

10

Benign (0.002)

Tolerated (1)

26

C0

–

  

c.1502 C > A

p.(Ala501Glu) [12]

rs141621969

0.0034

0.0038

17

Benign (0.001)

Tolerated (1)

107

C0

–

  

c.1982G > A

p.(Arg661Gln)

rs376672600

0

0.00003

0

Benign (0.054)

Tolerated (0.4)

43

C0

–

  

c.2108 T > C

p.(Ile703Thr)

novel

0

0

0

Benign (0.001)

Tolerated (0.37)

89

C0

–

  

c.2268 C > T

p.(Ala756 = )

rs143552557

0.0006

0.0017

1

–

–

–

–

No difference

  

c.3231 C > A

p.(Phe1077Leu)

rs143240655

0

0.0003

0

Benign (0.003)

Tolerated (0.34)

22

C0

–

  

c.4122 C > G

p.(Asp1374Glu)

–

0

0.00001

0

Benign (0.001)

Tolerated (1)

45

C0

–

  

c.4170 C > T

p.(Tyr1390 = )

rs532847219

0.0002

0.00001

0

–

–

–

–

IVS27-1 new donor

 

INTRONIC

c.613 + 11 C > T

p.?

rs370890203

0

0.00006

0

–

–

–

–

No difference

  

c.613 + 18 G > T

p.?

rs201364163

0

0.0019

2

–

–

-

–

IVS7 + 12 new donor

  

c.991-94 G > C

p.?

Novel

0

0

0

–

–

–

–

No difference

  

c.2053-65 G > A

p.?

rs147395547

0.0034

0

0

–

–

–

–

No difference

  

c.2513 + 23_2513 + 24insGT

p.?

Novel

0

0

0

–

–

–

–

No difference

  

c.2513 + 28 T > A

p.?

Novel

0

0

0

–

–

–

–

No difference

  

c.3279-39 G > A

p.?

rs374377819

0

0.00001

0

–

–

–

–

No difference

  

c.3483 + 26 G > A

p.?

rs183047748

0.0002

0.00015

0

–

–

–

–

No difference

  

c.3483 + 133 G > A

p.?

Novel

0

0

0

–

–

–

–

IVS23 + 135 new acceptor

  

c.3704-5 C > A

p.?

Novel

0

0

0

–

–

–

–

Affecting splice at exon 25 acceptor

  

c.3862 + 40 T > C

p.?

rs369424856

0.0006

0.003

5

–

–

–

–

No difference

SFTPB

Coding

c.327 G > A

p.(Glu109 = )

rs34682912

0.0028

0.0036

11

–

–

-

–

No difference

  

c.394 T > C

p. (Phe132Leu)

rs138729391

0

0.00006

0

Benign (0.018)

Tolerated (1)

22

C0

–

  

c.541_552del12

p.Pro181_Leu184del

–

0

0.0004

0

–

–

–

–

Affecting splice at exon 5 donor

  

c.883 G > A

p.(Ala295Thr)

rs36210375

0.0034

0.0016

1

Benign (0.000)

Tolerated (0.43)

58

C0

–

  

c.918 G > A

p.(Pro306 = )

rs750280427

0

0.00002

0

–

–

–

–

No difference

 

3′-UTR

c*9 C > T

p.?

rs771704983

0

0.000017

0

–

–

–

–

No difference

SFTPC

INTRONIC

c.43-7 G > A [14]

p.?

rs79440568

0.0086

0.0027

12

–

–

–

–

No difference

 

3′-UTR

c*12 T > A

p.?

rs200469074

0.0004

0.00008

0

–

–

–

–

No difference

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