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Table 2 Pathogenicity prediction for 20 unreported missense variants in COL4A5

From: X-linked Alport syndrome: pathogenic variant features and further auditory genotype-phenotype correlations in males

Gene

Variant

Polyphen-2 score

SIFT3

GERP++RS4

phyloP100waye

vertebrate

PhyloP20way6

mammalian

 

Polyphen-2 HDIV1

Polyphen-2 HVAR2

 

COL4A5

c.395 G > A,

p.Gly132Glu

1

1

0

6.13

8.383000

1.048000

COL4A5

c.3383G > A,

p.Gly1128Asp

1

1

0.01

5.45

7.901000

1.048000

COL4A5

c.892G > C,

p.Gly298Arg

1

1

0

5.5

8.333000

1.048000

COL4A5

c.2858G > T,

p.Gly953Val

1

1

0

5.97

7.247000

1.048000

COL4A5

c.1175G>A,

p.Gly325Arg

1

1

0

unknown

unknown

unknown

COL4A5

c.2858G > T,

p.Gly953Val

1

1

0

5.97

7.247000

1.048000

COL4A5

c.3418G>C,

p.Gly1140Arg

1

1

0

5.45

6.217000

1.048000

COL4A5

c.4688G > A,

p.Arg1563Gln

1

1

0

unknown

unknown

unknown

COL4A5

c.3713G > A,

p. Ala1238Thr

0.996

0.885

0

5.97

7.155000

1.048000

COL4A5

c.1121G > T,

p.Gly374Val

1

1

0.13

5.2

7.122000

0.998000

COL4A5

c.4862 T > C,

p.Leu1621Ser

1

1

0

unknown

unknown

unknown

COL4A5

c.3446G > T,

Gly1149Val

unknown

unknown

0

Unknown

unknown

unknown

COL4A5

c.3704G > C,

p.Gly1235Ala

0.969

0.69

0.1

5.97

9.459000

1.048000

COL4A5

c.4427G>T,

p.Cys1476Phe

1

1

0

unknown

unknown

unknown

COL4A5*

c.1410G > T,

p.Gly403Val

1

1

0

unknown

unknown

unknown

COL4A5

c.4186C > T,

p.Pro1396Ser

unknown

unknown

0.23

4.14

1.857000

0.935000

COL4A5*

c.4787G>A,

p.Gly1596Asp

1

1

0

5.57

10.003000

1.048000

COL4A5*

c.3704G>A,

p.Gly1235Asp

0.999

0.986

0

5.97

9.459000

1.048000

COL4A5

c.1984G>A,

p.Ser992Asn

1

1

0.01

unknown

unknown

unknown

COL4A5*

c.3170G > A,

p.Gly1057Glu

1

1

0

5.76

7.136000

1.048000

  1. The accession number for the reference isoform of the COL4A5 gene is NM_033380.2
  2. The COL4A5 is marked by“*“indicates the Gly substitutions that result in severe disease
  3. Note:
  4. 1Scores of 0.0–0.446 (benign), 0.447–0.909 (possibly damaging), and 0.909–1 (probably damaging)
  5. 2Scores of 0.0–0.446 (benign), 0.447–0.909 (possibly damaging), and 0.909–1 (probably damaging)
  6. 3Scores of 0.00–0.05 = D (damaging), 0.06–1.0 = T (tolerated)
  7. 4The larger the score, the more conserved the site. Scores ranged from −12.3 to 6.17
  8. 5Phylop (phylogenetic p-values) conservation score based on multiple alignments of 100 vertebrate genomes (including human). Scores ranged from −20.0 to 10.003 in dbNSFP
  9. 6Phylop (phylogenetic p-values) conservation score based on multiple alignments of 20 mammalian genomes (including human). Scores ranged from −13.282 to 1.199 in dbNSFP
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172