Table 3 Genes with high deleterious and loss-of-function mutations in SCA patients from Tanzania. Details of mutation on SNPs below can be found in Supplementary File: Table S2

chr19

ZBTB7A

2; 1

Nonsynonymous

MutationTaster, FATHMM, fathmm-MKL, RadialSVM, LR, PROVEAN, MetaSVM, MetaLR, CADD, GERP++, DANN, M-CAP, Eigen, GenoCanyon, Polyphen2 HVAR, Polyphen2 HDIV, PhyloP and SiPhy

chr12

CHD4

11; 4

Nonsynonymous

SIFT, LRT, MutationTaster, MutationAssessor, FATHMM, fathmm-MKL, RadialSVM, LR, PROVEAN, MetaSVM, MetaLR, CADD, GERP++, DANN, M-CAP, GenoCanyon, Polyphen2 HVAR, Polyphen2 HDIV

chr11

HBB

3; 2

Nonsynonymous

SIFT, LRT, MutationAssessor, FATHMM, fathmm-MKL, RadialSVM, LR, ROVEAN, MetaSVM, MetaLR, CADD, DANN, Polyphen2 HVAR, Polyphen2 HDIV, PhyloP and SiPhy

chr19

PGLYRP1

4; 4

Nonsynonymous

SIFT, LRT, MutationAssessor, FATHMM, fathmm-MKL, RadialSVM, LR, PROVEAN, MetaSVM, DANN, M-CAP, GenoCanyon, Polyphen2 HVAR, Polyphen2 HDIV, PhyloP and SiPhy

chr19

MBD3

1; 2

Stop-gain

SIFT, LRT, MutationTaster, MutationAssessor, LR, PROVEAN, MetaSVM, MetaLR, CADD, GERP++, DANN, M-CAP, Eigen, GenoCanyon, Polyphen2 HVAR, Polyphen2 HDIV, PhyloP and SiPhy

chr6

MYB

1; 1

Nonsynonymous

SIFT, LRT, MutationTaster, MutationAssessor, FATHMM, fathmm-MKL, RadialSVM, LR, PROVEAN, MetaSVM, MetaLR, CADD, GERP++, DANN, M-CAP, GenoCanyon, Polyphen2 HVAR, Polyphen2 HDIV, PhyloP