The last four lines are missing from the legend for Table 3. Please see the complete legend and table here.
Table 3. List of variants of uncertain significance.
| Chr | Gene | Disorder | OMIM phenotype# | Individual identity | Genomic position (Hg19/GRCH 37) | Transcript | cDNA position | Amino acid position | LOVD variant ID | Zygosity | PhyloP score, in-silico pathogenicity predictions, CADD | Allele frequency in ExAC | Number of affected individuals carrying the variant in the respective family | Main phenotype—additional features |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | KCND3 a | SCA19 (AD) | 607346 | HCT-088 | g.112322852T>C | NM_004980.4 | c.1456A>G | p.(Thr486Ala) | 162993 | het | 4.40/m,p/19.2 | 0.001461 | 1 | comp AT–pyramidal and extrapyramidal signs |
| 3 | ITPR1 | SCA15/29 (AD) | 606658/117360 | HCT-029 | g.4735396G>A | NM_001168272.1 | c.4207G>A | p.(Val1403Met) | 162994 | het | 4.08/s,m,p/17.1 | 0.00004663 | 1 | pure HSP—none |
| 3 | ITPR1 b | SCA15/29 (AD) | 606658/117360 | HCT-077 | g.4810224G>A | NM_001168272.1 | c.5710G>A | p.(Glu1904Lys) | 162995 | het | 3.68/s,m/13.3 | 0.000008432 | 1# | comp AT—early onset, spastic AT |
| 11 | BSCL2 | SPG17 (AD) | 270685 | HCT-044 | g.62462158C>A | NM_001122955.3 | c.512G>T | p.(Arg171Leu) | 162996 | het | 2.14/s,m,p/19.3 | 0.000008322 | 1 | pure HSP—amyotrophy, neuropathy |
| 11 | SPTBN2 | SCA5 (AD) | 600224 | HCT-086 | g.66453485T>G | NM_00694.2 | c.7030A>C | p.(Ser2344Arg) | 162997 | het | 1.66/p/15.1 | 0.00001679 | 1# | comp AT—neuropathy |
| 11 | SPTBN2c | SCA5 (AD) | 600224 | HCT-071 | g.66453406C>T | NM_00694.2 | c.7109G>A | p.(Arg2370His) | 162998 | het | 5.86/s,m,p/33 | 0.0001252 | 1# | pure AT—none |
| 12 | KIF5A | SPG10 (AD) | 604187 | HCT-082 | g. 57970109C>T | NM_004984.2 | c.2146C>T | p.(Arg716Trp) | 162999 | het | 3.60/s,m,p/24.6 | 0.00005826 | 1# | comp AT—episodic |
| 15 | TTBK2 | SCA11 (AD) | 604432 | HCT-115 | g.43132604C>G | NM_173500.3 | c.245G>C | p.(Gly82Ala) | 163000 | het | 5.21/s,m,p/16 | 0.0002898 | 1 | comp AT—spastic AT |
| 16 | BEAN1 | SCA31 (AD) | 117210 | HCT-087 | g.66503607T>A | NM_001178020.2 | c.128T>A | p.(Ile43Lys) | 163001 | het | 3.35/s,m,p/25.3 | - | 2 | comp AT—lower limb paresis, neuropathy |
| 19 | RTN2 | SPG12 (AD) | 604805 | HCT-057 | g.45996535C>A | NM_005619.3 | c.916G>T | p.(Val306Phe) | 163002 | het | 2.71/p/15.6 | - | 3 | pure AT—none |
Abbreviations: Chr, chromosome; AD, autosomal dominant; AR, autosomal recessive; OMIM, online Mendelian inheritance in man; cDNA, complementary deoxyribonucleic acid; Zygosity, heterozygous (het), compound heterozygous (c.het), homozygous (hom); LOVD, Leiden open variation database; CADD, combined annotation dependent depletion score, also called as a PHRED score PhyloP, evolutionary conservation score at specific nucleotide position; s, damaging prediction by SIFT (http://sift.jcvi.org); m, damaging prediction by MutationTaster (http://www.mutationtaster.org); p, damaging prediction by PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/); ExAC, exome aggregation consortium (http://exac.broadinstitute.org); comp, complex; AT, ataxia; HSP, hereditary spastic paraplegia. OMIM gene identifiers: KCND3 (605411), ITPR1 (147265), BSCL2 (606158), SPTBN2 (604985), KIF5A (602821), TTBK2 (611695).
a Another variant, c.929G>A, p.(Arg310Gln) in CYP7B1 was found heterozygously in this individual.
b Another variant, c.2261C>T, p.(Pro754Leu) was found in SPG7 heterozygously in this individual.
c Another variant, c.2228T>C, p.(Ile743Thr) was found in SPG7 heterozygously in this individual.
#, No additional samples of affected and/or unaffected individuals were available for segregation analysis.
Reference
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