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Table 1 Recessive LoF variants

From: Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing

WES results

Variant characteristics

Functional information

Validation

     

ExAC (EU)

      

Gene

Type

Chr:bp (hg19)

Ref/Alt all

dbSNP137

MAF

n HZ (freq.)

Variant type

AA change

AA length

CADD

Functional

Genetic

ANKRD30A

CH

10:37438759

G/T

x

x

x

stopgain

NM_052997:p.E487X

1341

35.0

  
  

10:37508648

A/AT

x

0.0031%

0

fs insertion

NM_052997:p.Q1280fs

1341

24.2

  

ARSB

HZ

5:78281383

T/TA

rs138279020

x

x

splicing

NM_198709:c.190-2insT

533

2.2

S

neuroX

c11orf21

HZ

11:2321829

C/T

rs74048215

0.037%

0

stopgain

NM_001142946:p.W69X

178

35.0

  

CALML4

HZ

15:68497597

G/A

rs11071990

0.75%

1 (0.00003%)

stopgain

NM_001031733:p.R40X

120

25.9

  

CAPS2

HZ

12:75687045

C/CTATTTGAT

x

0.68%

4 (0.00012%)

stopgain

NM_001286547:p.L321X

382

33.0

  

CD36

CH

7:80285955

C/T

x

0.0075%

0

stopgain

NM_001127444:p.Q74X

472

26.5

 

GRIP

  

7:80302705

C/T

x

0.011%

0

missense

NM_001127444:p.P412S

472

25.9

  

COL6A5

CH

3:130132401

C/T

rs190283135

0.12%

0

stopgain

NM_001278298:p.Q1559X

2611

38.0

  
  

3:130107827

G/A

x

0.32%

0

missense

NM_001278298:p.V756M

2611

23.0

  

DIS3

CH

13:73355096

G/A

rs201493043

0.0045%

0

stopgain

NM_014953:p.Q92X

958

37.0

Mm

 
  

13:73333935

A/G

rs141067458

0.22%

0

stoploss

NM_014953:p.X959Q

958

14.1

  

FAM71A

HZ

1:212799882

A/T

rs143861665

0.80%

2 (0.00006%)

stopgain

NM_153606:p.K555X

594

36.0

Mm

 

FAM83A

CH

8:124195352

G/T

rs148011353

0.23%

2 (0.00006%)

stopgain

NM_032899:p.G86X

434

26.2

 

PPMI

  

8:124195506

T/G

x

x

x

missense

NM_032899:p.V137G

434

25.6

  

GH2

HZ

17:61957946

C/T

rs150668018

0.33%

1 (0.00003%)

stopgain

NM_022557:p.W214X

256

26.8

  

GPATCH2L

HZ

14:76644266

C/T

rs117516637

0.53%

1 (0.00003%)

stopgain

NM_017972:p.R362X

482

18.8

Mp,Mm

PPMI

KALRN

HZ

3:124303696

C/T

rs56407180

0.39%

0

stopgain

NM_007064:p.R10X

1289

37.0

Mp

 

KCNK16

HZ

6:39282816

G/A

rs138573996

0.44%

2 (0.00006%)

stopgain

NM_001135107:p.Q251X

322

9.5

Mm

 

MNS1

CH

15:56736045

G/A

x

x

x

stopgain

NM_018365:p.Q232X

495

38.0

Mm

 
  

15:56748680

G/A

x

0.003%

0

stopgain

NM_018365:c.C265T:p.Q89X

495

37.0

  

OR7G3

HZ

19:9236969

G/A

rs61751875

0.15%

1 (0.00003%)

stopgain

NM_001001958:p.R220X

312

35.0

Mm

 

PCDHA9

HZ

5:140229907

C/G

x

0.0046%

0

stopgain

NM_014005:p.Y609X

950

34.0

Mm

 

PTCHD3

HZ

10:27688101

G/A

rs142646098

0.97%

6 (0.00018%)

stopgain

NM_001034842:p.R476X

767

34.0

Mp,Mm

 

PTPRH

CH

19:55697712

G/A

rs147881000

0.39%

1 (0.00003%)

stopgain

NM_002842:p.Q887X

1115

36.0

S,Mm

neuroX

  

19:55716715

C/A

rs201517965

0.0030%

0

stopgain

NM_002842:p.E200X

1115

26.0

  

PZP

CH

12:9321534

G/A

rs145240281

0.85%

4 (0.00012%)

stopgain

NM_002864:p.R680X

1482

32.0

  
  

12:9333626

G/A

rs117889746

0.021%

0

stopgain

NM_002864:p.Q598X

1482

36.0

  

SSPO

HZ

7:149493519

C/T

rs57595625

0.011%

0

stopgain

NM_198455:p.Q2199X

5150

10.4

  

SVOPL

HZ

7:138341219

G/A

rs117871806

0.35%

0

stopgain

NM_174959:p.R18X

492

38.0

Mp,Mm

 

TCHHL1

HZ

1:152058192

G/A

rs150014958

0.037%

0

stopgain

NM_001008536:p.Q656X

904

35.0

Mp

 

TMEM134

HZ

11:67235051

G/A

rs143199541

0.70%

3 (0.00009%)

stopgain

NM_001078650:p.R84X

195

34.0

S

 

UHRF1BP1L

HZ

12:100433523

T/A

x

x

x

stopgain

NM_015054:p.K1376X

1464

35.0

Mm

neuroX

VPS13C

CH

15:62174851

C/A

x

x

x

stopgain

NM_017684:p.E3147X

3628

55.0

S,Mm

neuroX,GWAS

  

15:62305257

C/CTCTG

x

x

x

fs insertion

NM_017684:p.R226fs

3628

27.4

  

ZNF543

HZ

19:57838058

G/A

rs150392165

0.60%

1 (0.00003%)

stopgain

NM_213598:p.W68X

600

25.0

Mp,Mm

 
  1. The current designation of rs138279020 is rs11424557
  2. Type type of affecting 2 alleles, CH putative compound heterozygote, HZ homozygote, Chr:bp chromosome and base-pair position, hg19 reference build, Ref reference, Alt alternative, ExAC Exome Aggregation consortium, EU European, fs frameshift, AA change amino acid change for specified RefSeq transcript, MAF minor allele frequency, n HZ number of individuals with homozygous variant, AA length length of specified transcript in amino acids, PPMI Parkinson Progression Markers Initiative, CADD functional algorithm prediction (>20 = belongs to 1% most damaging variants of total genome), Mp mitochondrial Parkin translocation assay, Mm mitochondrial morphology assay, S α-synuclein assay