Table 2.
List of variants in SPG11
| Genomic location (GRCh38) | dbSNP/ClinVar | HGVS | 1000G MAF | Variant interpretation | CADD | MutationTaster | I:2 | I:1 | II:1 | II:2 |
|---|---|---|---|---|---|---|---|---|---|---|
| Chr15: 44565997 | rs312262785/41353 | ENST00000261866:c.6856C>T; p.Arg2286* | 0.0002 | Pathogenic (PVS1, PM1, PM2, PP3, PP4) | Pathogenic (47) | Disease causing (1) | N/A | 0/1 | 0/1 | 0/1 |
| Chr15: 44622723 | rs879255274/252959 | ENST00000261866:c.2316+5G>A ENST00000559193:c.2321G>A; p.Gly774Asp |
N/A | Likely pathogenic (PM2, PM3, PP1, PP3, PP4) | Pathogenic (19.36) | Disease causing (1) | 0/1 | N/A | 0/1 | 0/1 |
| Chr15: 44651599 | rs3759873/130364 | ENST00000261866:c.1348A>G; p.Ile450Val | 0.0389 | Benign (BA1, BS1, BS4, BP4) | Neutral (0.002) | Polymorphism (0.994) | N/A | 0/1 | N/A | N/A |
Genotypes for each family member are shown in the right-most columns, in which 0/1 represents heterozygous. Parenthetical codes in the Variant interpretation column denote the pathogenic criteria in the ACMG (American College of Genetics and Genomics) guidelines 2015 (Richards et al. 2015). Predicted functional impact on the transcript and protein was calculated by SnpEff, CADD, and MutationTaster. Numbers in the CADD column denote the degree of pathogenicity in Phred scale. Numbers in the MutationTaster column denote the confidence of pathogenicity classification, in which 1 is the most confident and 0 is the least confident.
dbSNP, Database for Short Genetic Variations; HGVS, Human Genome Variation Society; 1000G, 1000 Genomes; MAF minor allele frequency; CADD, Combined Annotation-Dependent Depletion; N/A, not applicable.