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Table 1 Rare variants of SPTLC1 and SPTLC2 identified in patients with amyotrophic lateral sclerosis

From: Mutation screening of SPTLC1 and SPTLC2 in amyotrophic lateral sclerosis

Genomic position

Rsid

Annotation

hgvs_c

hgvs_p

gnomAD as control (N = 9977)

Normal control (N = 3298)

Dam

Control MAF

P

OR (95% CI)

Control MAF

P

OR (95% CI)

9:94794611

rs1288792833

Missense

c.A1526G

p.Y509C

0 (0/12136)

0.249

Inf (0.08-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

9:94794623

rs189582528

Missense

c.A1514C

p.K505T

7.70E-5 (1/12980)

0.417

3.23 (0.04–252.87)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

9:94794633

n.a

Missense

c.A1504G

p.I502V

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

9:94800568

rs750753414

Missense

c.G1216A

p.E406K

1.09E-4 (2/18394)

0.447

2.29 (0.04–43.94)

1.52E-4 (1/6596)

1.000

1.64 (0.02–128.64)

D

9:94800570

rs567541925

Missense

c.G1214A

p.R405H

0 (0/19952)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94800579

rs576468489

Missense

c.C1205G

p.T402S

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

9:94800586

n.a

Stopgain

c.G1198T

p.E400X

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94809456

rs1587914537

Missense

c.C1079T

p.P360L

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94809510

n.a

Frameshift substitution

c.1025delins

TCGTTACC

p.P342Lfs*12

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94809544

n.a

Missense

c.T991A

p.S331T

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94817751

rs773121449

Missense

c.G716A

p.R239Q

0 (0/18384)

0.180

Inf (0.12-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94821465

rs1236408812

Missense

c.A686G

p.Q229R

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94821469

rs1290542896

Missense

c.G682A

p.D228N

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

9:94821511

rs781435924

Missense

c.A640G

p.M214V

5.45E-5 (1/18360)

0.327

4.57 (0.06–357.35)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

9:94830356

rs45461899

Missense

c.G452A

p.R151H

2.46E-3 (49/19904)

0.476

0.71 (0.27–1.57)

4.09E-3 (27/6596)

0.050

0.42 (0.16–1.00)

D

9:94841727

rs181424155

Missense

c.C50T

p.P17L

6.41E-4 (1/1560)

1.000

0.78 (0.04–45.79)

0 (0/6596)

0.143

Inf (0.31-Inf)

 

9:94843164

rs752029386

Missense

c.C342A

p.N114K

0 (0/18392)

0.032

Inf (0.86-Inf)

0 (0/6596)

0.143

Inf (0.31-Inf)

D

14:77978635

rs1484082947

Missense

c.G1681A

p.E561K

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:77978695

rs746495804

Missense

c.C1621T

p.R541C

0 (0/18392)

0.179

Inf (0.12-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:77984475

n.a

Missense

c.G1475A

p.G492D

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:77987811

n.a

Missense

c.C1417G

p.L473V

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:77987924

rs879253951

Missense

c.G1304T

p.G435V

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78018481

rs557959879

Missense

c.A1261G

p.T421A

5.44E-5 (1/18384)

0.327

4.57 (0.06–357.82)

1.52E-4 (1/6596)

1.000

1.64 (0.02–128.64)

D

14:78018516

rs368357970

Missense

c.C1226T

p.T409M

0 (0/19936)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78023441

rs375502150

Missense

c.A899G

p.Q300R

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78036791

n.a

Missense

c.C692G

p.A231G

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78045345

rs749262868

Missense

c.G435T

p.R145S

8.15E-4 (15/18394)

0.753

0.61 (0.07–2.62)

1.67E-3 (11/6596)

0.150

0.30 (0.03–1.37)

 

14:78045373

rs760762454

Missense

c.G407A

p.R136Q

0 (0/18392)

0.179

Inf (0.12-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78063530

n.a

Missense

c.A326G

p.K109R

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

 

14:78063569

rs2079852183

Missense

c.T287C

p.I96T

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78063573

n.a

Frameshift substitution

c.283delinsGA

p.R95Efs*3

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78063717

n.a

Missense

c.C139T

p.H47Y

0 (0/19954)

0.168

Inf (0.13-Inf)

0 (0/6596)

0.379

Inf (0.04-Inf)

D

14:78082850

rs1017782894

Missense

c.G73C

p.V25L

1.92E-3 (23/11960)

0.271

0.52 (0.13–1.51)

7.58E-4 (5/6596)

0.738

1.31 (0.26–6.10)

 
  1. MAF Minor allele frequency; n.a. Not available; Variants with MAF < 0.01 were considered rare; P and OR values were obtained using Fisher’s exact test implemented in R 3.6.2 with default parameters; RefSeq accession numbers: SPTLC1, NM_001281303; SPTLC2, NM_004863. Genomic position was based on GRCh37. Dam denotes whether the variant is protein-truncating variant or missense variant which is predicted as damaging by at least five out of ten prediction tools, with D indicating that the variant is damaging
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Human Genomics

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