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. 2016 Apr 17;139(5):1378–1393. doi: 10.1093/brain/aww079

Table 1.

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 | rs# dbsnp MAF ExAC MAF EVS6500 In HGMD
1 #8 CA plus chr6:152456368C>T c.25516-1G>A -NA- Splicing Het 7.62 29.1 0 0 0 Absent
2 #18 pCA chr6:152473139C>T c.24054G>A p.W8018* Stopgain SNV Het 7.625 61 0 0 0 Absent
3 #4 CA plus chr6:152473168G>A c.24025C>T p.Q8009* Stopgain SNV Het 5.634 60 0 0 0 Absent
4 #5, #23 CA plus chr6:152476161G>A c.23782C>T p.R7928* Stopgain SNV Het 1.316 59 0 ‖rs570 916267 0 0 Absent
5 #7 pCA chr6:152477125insCAC TCGGCATCAGTGGC ACAGGCGT c.23684_23685insACG CCTGTGCCACT GATGCCGAGTG p.C7895* Frameshift duplication | stopgain Het -NA- 54 0 0 0 Absent
6 #12 CA plus chr6:152542097G>T c.21528C>A p.Y7176* Stopgain SNV Het 0.153 58 0 0 0 Absent
7 #9 CA plus chr6:152542688G>A c.21316C>T p.Q7106* Stopgain SNV Het 9.038 60 0 0 0 Absent
8 #12 CA plus chr6:152551729G>A c.20935C>T p.R6979* Stopgain SNV Het 1.371 41 0 0 0 Absent
9 #14 CA plus chr6:152555035G>A c.20380C>T p.Q6794* Stopgain SNV Het 9.476 60 0 0 0 Absent
10 #23 CA plus chr6:152557241C>G c.G20183 + 1G>C -NA- Splicing Het 7.808 33 0 0 0 Absent
11 #11 CA plus chr6:152558041G>A c.19897C>T p.Q6633* Stopgain SNV Homo 7.646 59 0 0 0 Absent
12 #10 CA plus chr6:152558084C>G c.19855-1G>C -NA- Splicing Homo 7.304 28.1 0 0 0 Absent
13 #19 CA plus chr6:152605163G>A c.17944C>T p.R5982* Stopgain SNV Homo 1.582 50 0 0 0 Absent
14 #14 CA plus chr6:152615251insT c.17480dup p.Y5827* Frameshift insertion| stopgain Het -NA- 38 0 0 0 Absent
15 #18 pCA chr6:152639275- 152639281 delTCAGTTT c.16294_16300delA AACTGA p.K5432Lfs*25 Frameshift deletion Het -NA- 40 0 0 0 Absent
16 #3 pCA chr6:152642966G>A c.15760C>T p.R5254* Stopgain SNV Homo 5.373 53 0 0 0 Absent
17 #4 CA plus chr6:152644651- 152644652delGA c.15665_15666delTC p.L5222Hfs*21 Frameshift deletion Het -NA- 35 0 0 0 Absent
18 #7 pCA chr6:152646244T>C c.15419A>G p.D5140Gfs1* (Cryptic) splicing Het 3.931 19.05 0 8.2 × 10 −6 0 Absent
19 #2 CA plus chr6:152651038G>A c.14569C>T p.Q4857* Stopgain SNV Het 7.928 51 0 0 0 Absent
20 #21 CA plus chr6:152651345insA c.14261dup p.Q4755Profs*15 Frameshift insertion Het -NA- 36 0 0 0 Absent
21 #6 CA plus chr6:152651352- 152651352delC c.14255delG p.G4752Efs*10 Frameshift deletion Het -NA- 36 0 0 0 Absent
22 #1 pCA chr6:152652521- 152652521delG c.13086delC p.H4362Qfs*2 Frameshift deletion Homo -NA- 24.8 0 0 0 Absent
23 #15 CA plus chr6:152657975C>T c.12315 + 1G>A -NA- Splicing Homo 7.499 26.2 0 0 0 Absent
24 #9 CA plus chr6:152665320G>A c.11908C>T p.R3970* Stopgain SNV Het 6.313 51 0 0 0 Absent
25 #5 CA plus chr6:152706854insAT c.8627_8628insAT p.M2876Ifs*19 Frameshift insertion Het -NA- 34 0 0 0 Absent
26 #8 CA plus chr6:152711589T>C c.8026-2A>G -NA- Splicing Het 7.542 25.6 0 0 0 Absent
27 #16 pCA chr6:152722345C>T c.6978G>A p.W2326* Stopgain SNV Homo 5.118 20.3 0 0 0 Absent
28 #21 CA plus chr6:152737559G>A c.6034C>T p.R2012* Stopgain SNV Het 0.595 32 0.0002 | rs200119679 8.2 × 10 −6 0 Absent
29 #17 CA plus chr6:152765668C>A c.3736G>T p.E1246* Stopgain SNV Homo 5.495 39 0 0 0 Absent
30 #20 CA plus chr6:152776698T>A c.2776A>T p.K926* Stopgain SNV Het 3.905 36 0 0 0 Absent
31 #22 CA plus chr6:152826408G>A c.727C>T p.R243* Stopgain SNV Homo 0.771 35 0 0 0 Absent
32 #13 CA plus chr6:152826453G>A c.682C>T p.R228* Stopgain SNV Homo 4.534 36 0 8.2 × 10 −6 0 Absent
33 #20 CA plus chr6:152826476A>G c.659T>C p.F220S Missense Het 9.339 28.8 0 0 0 Absent
34 #6 CA plus chr6:152832174A>T c.395T>A p.L132* Stopgain SNV Het 9.14 38 0 1.6 × 10 −5 0 Absent
35 #2 CA plus chr6:152841593C>T c.309 + 1G>A -NA- Splicing Het 7.187 27.8 0 0 0 Absent

Genomic positions of the variants according to genome build hg19. DNA changes according to NM_033071.3. Variant type and protein changes according to GVS function based on NP_149062. pCA = pure cerebellar ataxia; CA plus = cerebellar ataxia plus clinical evidence for damage of at least one additional neurological system; 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.