Table 2.
Pathogenic variants identified in disease causing genes
| Alzheimer disease 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 |
| FTLD genes | |||||||
| 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 | |
| ALS genes | |||||||
| 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 |
| Other neurodegeneration associated genes | |||||||
| 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 |
ExAC ExAC database minor allelic frequency. SIFT scores are D, deleterious, and T, tolerated. PolyPhen-2 scores are D, probably damaging, P, possibly damaging, and B, benign. CADD corresponds to the Phred score. Variants with + were identified in homozygous states. GenBank transcripts for each gene can be found in Additional file 4: Table S3