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. 2016 May 19;139(8):e46. doi: 10.1093/brain/aww115

Table 2.

SYNE1 mutations identified in this study

Variant ID Family ID Phenotype Genomic variant cDNA variant Protein change Variant type Zygosity PhyloP CADD score MAF 1000 genomes MAF ExAC MAF EVS6500 in HGMD
1 #1 Ataxia MND chr6:152590412G > A c.18583C > T p.Q6195* Stopgain SNV Homo 8.90 56 0 0 0 absent
2 #2 Ataxia MND chr6:152485320_ 152485321delTG c.23767_23768delCA p.Q7923Efs*4 Frameshift deletion Het NA 43 0 0 0 absent
3 #2 Ataxia MND chr6:152751303G > A c.4732C > T p.P1578S Missense Het 6.03 24.2 0 2.26 × 10−4 7.70 × 10−5 absent
4 #3 Ataxia MND chr6:152469342G > A c.24814C > T p.R8272* Stopgain SNV Het 1.93 53 0 8.25 × 10−6 0 absent
5 #3 Ataxia MND chr6:152652250_ 152652253delCTTC c.13567_13570delGAAG p.E4523Sfs*34 Frameshift Het NA 35 0 0 0 absent
6 #4 Ataxia cognition chr6:152647692_ 152647695delTCCT c.15029_15032delAGGA p.E5010Vfs*13 Frameshift Het NA 37 0 0 0 absent
7 #4 Ataxia cognition chr6:152647091A > T c.15438 + 2T > A ? Splice donor Het 5.79 24.1 0 0 0 absent
8 #5 Ataxia MND chr6:152680513_ 152680514delAT c.10379_10380delAT p.Y3460Cfs*28 Frameshift Het NA 36 0 0 0 absent
9 #5 Ataxia MND chr6:152674803_ 152674810del TCGTCCAG c.10996_11003delCT GGACGA p.L3666Efs*51 Frameshift Het NA 37 0 0 0 absent
10 #6 Ataxia MND chr6:152786422dup c.1903dupA p.M635Nfs*35 Frameshift Homo NA 33 0 0 0 absent
11 #7 Ataxia MND chr6:152457757delC c.25655delG p.C8552Sfs*7 Frameshift Het NA 46 0 0 0 absent
12 #7 Ataxia MND chr6:152540211G > T c.21971C > A p.S7324* Stopgain SNV Het 7.44 59 0 8.24 × 10−6 0 absent

Genomic positions of the variants according to genome build hg19.

DNA changes according to NM_182961.3. Variant type and protein changes according to GVS function based on NP_149062. MND = motor neuron disease; zygosity = homozygous (homo) or heterozygous (het); PhyloP = PhyloP conservation score based on base-wise conservation across 100 vertebrates; CADD score = scaled Combined Annotation Dependent Depletion score, integrating many diverse annotations into a single measure (C score) for each variant. The predicted pathogenicity of each variant is scored and ranked relative to all ∼8.6 billion single nucleotide variants of the GRCh37/hg19 reference. A scaled CADD score of 20 indicates variants at the top 1%, a CADD score of 30 indicates variants at the top 0.1%, etc. (Kircher et al., 2014). MAF = minor allele frequency; ExAC = Exome Aggregation Consortium; EVS = Exome Variant Server 6500 exomes all from the NHLBI GO Exome Sequencing Project; HGMD = Human Gene Mutation Database; NA = not available.