Table 2 Pathogenic variants identified in disease causing genes

Gene

Coding change

dbSNP/ClinVar

ExAC

SIFT

Polyphen

CADD

Local ancestry

APP

g.(26253828_30011000)dup

SCV001751549

.

–

–

–

European

PSEN1

c.349C>G (p.Pro117Ala)

rs63750550

.

D

P

26.9

European

c.356C>T (p.Thr119Ile)

rs1566630791

.

T

P

24.4

European

c.428T>C (p.Ile143Thr)

rs63750004

.

D

D

26.8

European

c.485T>G (p.Ile162Ser)

rs1898533739

.

D

D

32

Native American

c.488A>G (p.His163Arg)

rs63750590

.

T

B

23.4

European

c.667C>A (p.Gln223Lys)

rs1898776259

.

D

D

33

Native American

c.782T>C (p.Val261Ala)

SCV001751539

.

D

P

25.9

Undetermined

c.791C>T (p.Pro264Leu)

rs63750301

.

D

D

35

Native American

c.839A>C (p.Glu280Ala)

rs63750231

.

D

D

29.3

European

c.851C>T (p.Pro284Leu)

rs63750863

.

D

D

33

European

c.1247T>C (p.Ile416Thr)

SCV001751540

.

D

P

25.9

African

PSEN2

c.487C>T (p.Arg163Cys)

rs200931244

.

D

D

35

African

Gene

Coding change

dbSNP

ExAC

SIFT

Polyphen

CADD

Local ancestry

C9ORF72

(GGGGCC)n Repeat Expansion

rs143561967

.

.

.

European

GRN

c.709-2A>G (p.Ala237fs)

rs63750548

.

.

.

23.1

European

MAPT

c.902C>T (p.Pro301Leu)

rs63751273

.

D

D

34

European

c.1189C>T (p.Pro397Ser)

rs1295855402

.

D

D

25

European

TARDBP

c.881G>T (p.Gly294Val)

rs80356721

0.00000824

T

P

18.89

European

c.1147A>G (p.Ile383Val)

rs80356740

0.00000865

T

B

0.308

European

TBK1

c.1257_1258del (p.Val421Cfs*26)

rs1392685429

.

.

.

.

European

c.1717C>T (p.Arg573Cys)⁺

rs772820487

0.00003329

T

D

29.6

European

Gene

Coding change

dbSNP

ExAC

SIFT

Polyphen

CADD

Local ancestry

ANXA11

c.904C>T (p.Arg302Cys)

rs142183550

0.0000412

D

D

31

Native American

FIG4

c.122T>C (p.Ile41Thr) ⁺

rs121908287

0.001

D

D

26.5

European

HNRNPA2B1

c.965G>A (p.Gly322Glu)

SCV001751542

.

D

D

23.6

Native American

SOD1

c.63C>G (p.Phe21Leu)

rs1555836170

.

T

D

22.9

Native American

SQSTM1

c.1175C>T(p.Pro392Leu)

rs104893941

0.0009

D

B

34

European

TUBA4A

c.820C>G (p.Pro274Ala)

rs1241875438

.

.

D

23.8

Native American

TUBB4A

c.811G>A (p.Ala271Thr)

rs587777074

0.000003992

.

P

22.8

Native American

UBQLN2

c.724G>A (p.Ala242Thr)

SCV001751543

.

D

D

25.9

Undetermined

Gene

Coding change

dbSNP

ExAC

SIFT

Polyphen

CADD

Local ancestry

CSF1R

c.2068G>A (p.Gly690Ser)

rs141866247

0.0000165

T

D

23.1

Native American

DNAJC5

c.347T>G (p.Leu116Arg)

SCV001751544

.

D

P

27.2

African

LRRK2

c.4334C>G (p.Ser1445Cys)

rs1945001552

.

T

P

24.3

European