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Table 2 Pathogenic variants identified in disease causing genes

From: A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects

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
  1. 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