Table 3.
Novel sequence variants in IPN genes inplicated in disease
| Family ID | Disease Classification | Gene | cDNA change | Amino acid change | Vertebrate conservation | GERP | SIFT | Polyphen-2 | Likely to cause disease |
|---|---|---|---|---|---|---|---|---|---|
| J | HMNP | SETX | c.1504C>T | p.R502W | 2.15 | 3.86 | nt | 0.999 | + |
| K | CMT2 | SETX | c.4273A>G | p.K1425E | 0.04 | 1.35 | pt | 0.001 | − |
| L | CMT2 | SETX | c.4225A>T | p.N1409Y | 0.61 | 0.0559 | nt | 0.124 | − |
| M | CMT2 | NEFL | c.803T>G | p.L268R | 4.33 | 5.62 | nt | 0.998 | + |
| N | CMT2 | NEFL | c.794A>G | p.Y265C | 3.35 | 5.62 | pt | 1.00 | + |
| O | CMT2 | NEFL | c.1007T>C | p.L336P | 5.90 | 5.1 | nt | 0.956 | + |
| P | CMT2 | NEFL | c.1319C>T | p.P440L | 6.55 | 5.04 | nt | 0.551 | + |
| Q | HMN | TRPV4 | c.549G>C | p.E183D | 0.74 | 3.69 | pt | 0.068 | − |
| R | HMNP | KIF1B | c.2274G>T | p.E758D | 1.53 | 4.67 | nt | 0.998 | + |
| S | CMT2 | KIF1B | c.4073T>C | p.V1358A | 6.22 | −2.14 | nt | 0.034 | +/− |
| T | CMT1 | BICD2 | c.1079C>T | p.A360V | 2.95 | −0.249 | pt | 0.001 | − |
| U | HMN | BICD2 | c.1993G>T | p.V665L | 3.10 | 2.52 | pt | 0.056 | − |
The following GenBank accession numbers describe the genes and annotations in this table: NEFL; NM_006158.4, KIF1B; NM_183416.3 for sequence variant c.2274G>T and NM_015074.3 for sequence variant c.4073T>C, TRPV4; NM_021625.4, BICD2:NM_001003800.1 and SETX; NM_015046.5. SIFT scores: nt, not tolerated; pt, predict tolerated. Likely to Cause Disease: +, supportive evidence implicated to cause disease; −, mostly unsupportive unlikely to cause disease; +/−, both supportive and negative results. Polyphen-2 scores approaching 1 are more confidently predicted to be deleterious. For the vertebrate conservation by PhyloP scores, positive values are predicted to be conserved and negative values are predicted to be fast-evolving. GERP scores >2 are considered to be evolutionarily constrained.