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Table 3 Rare variants observed in CMT-related genes from patients in the five Pakistani CMT families

From: Novel homozygous mutations in Pakistani families with Charcot–Marie–Tooth disease

Family

Gene

Variant

ClinVar

dbSNP151

Allele frequency

GERP

In silico analysisa

Note

Nucleotide

Amino acid

1000G

gnomAD

PP2

PRO

Fath

PaC2

KIF1B

c.3209C > T

p.A1070V

UR

rs768176241

UR

1.8E−05

4.82

0.02

− 0.01

− 0.77

Nonsegregation, LB

 

DST

[c.7252G > A + c.7765A > G]

[p.V2418I + p.I2589V]

UR

rs62621210

0.0400

0.0360

4.80

0.00

0.76

1.25

Cis, nonsegregation, LB

    

B,LB

rs150191284

0.0102

0.0249

4.45

0.02

0.07

− 0.74

 
 

MYH14

c.3748G > T

p.V1250L

LB

rs202242879

0.0006

0.0007

3.78

0.11

− 0.39

− 1.17

Nonsegregation, LB

 

SCN11A

c.1732 T > A

p.F578I

UR

rs772393665

UR

7.1E−05

5.58

0.98*

− 4.61*

− 4.30*

Nonsegregation, LB

PaC3

KIF1B

[c.2107 T > C] + [c.2455A > C]

[p.W703R] + [p.S819R]

B,LB

rs551543997

0.0054

0.0026

5.32

0.99*

− 10.0*

− 0.93

Trans, nonsegregation, LB

    

LB

rs140015591

0.0002

0.0003

− 2.96

0.02

− 2.19

− 1.03

 
 

NTRK1

[c.2339G > A + c.2360C > T]

[p.R780Q + p.A787V]

B,LB

rs35669708

0.0038

0.0046

4.10

0.87*

− 1.25

− 1.60*

Cis, nonsegregation, LB

    

UR

rs761207548

UR

5.0E−05

4.07

0.36

− 3.00*

− 1.13

 
 

NAGLU

c.2209C > A

p.R737S

B

rs86312

0.0116

0.0183

4.01

0.47*

− 0.19

− 5.34*

Nonsegregation, LB

 

SCN10A

c.3887G > T

p.S1296I

LB

rs779527264

UR

0.0002

4.88

1.00*

− 5.79*

− 4.55*

Nonsegregation, LB

PaC4

DST

[c.1933A > G] + [c.1933A > G]

[p.I645V] + [p.I645V]

UR

rs754692637

UR

8.0E−06

2.51

0.00

− 0.20

− 0.81

Homozygous, cosegregation, VUS

 

ARHGEF10

c.2566G > A

p.V856I

UR

rs773521162

UR

0.0003

4.25

0.87*

− 0.62

0.15

Nonsegregation, LB

PaC6

TFG

c.175A > G

p.K59E

UR

rs1232918261

UR

UR

5.90

1.00*

− 3.02*

− 3.02*

Nonsegregation, LB

PaC14

SETX

c.2385_2387delTTT

p.I795_K796delinsM

UR

rs755971927

UR

5.0E−05

–

–

–

–

Nonsegregation, LB

  1. 1000G: 1000 Genomes Project, B: benign, gnomAD: Genome Aggregation Database, LB: likely benign, VUS: variant of uncertain significance, trans: trans arrangement of variants in homologous chromosomes (bi-alleles), cis: cis arrangement of variants in a chromosome, UR: unreported
  2. aScores of PolyPhen-2 (PP2) ~ 1, PROVEAN (PRO) < − 2.5, and Fathmm (Fath) < − 1.5 indicate pathogenic prediction (* denotes a pathogenic prediction)
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BMC Medical Genomics

ISSN: 1755-8794

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