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Table 2 Homozygous mutations and clinical phenotypes in five Pakistani CMT patients

From: Novel homozygous mutations in Pakistani families with Charcot–Marie–Tooth disease

Family ID Gene Mutationa Type Onset age (year) Other symptom Allele frequency GERP In silico predictionb Note
1000G gnomAD PP2 MU PRO Fath
PaC2 SH3TC2 c.2599C > T;p.Q867* CMT4C 3 Scoliosis UR UR 2.17 P
PaC3 SH3TC2 c.3650G > A;p.G1217D CMT4C 3 Scoliosis, short stature UR 1.6E−5 6.17 1.00* 0.10 − 5.79* − 2.66* P
PaC4 HK1 c.19C > T;p.R7* CMT4G 1   UR 2.0E−5 1.13 P
PaC6 REEP1 c.247delG;p.G83Afs*44 SMARD/dHMN5B  < 1   UR UR 5.33 LP
PaC14 MFN2 c.334G > A;p.V112M CMT2A2B 5 Vocal cord hoarseness UR 1.6E−5 4.70 1.00* 0.32 − 2.76* − 3.86* P
  1. 1000G: 1000 Genomes Project, CMT: Charcot–Marie–Tooth disease, GERP: genomic evolutionary rate profiling score, gnomAD: Genome Aggregation Database, LP: likely pathogenic, P: pathogenic, LP: likely pathogenic, UR: unreported
  2. aReference DNA and protein sequences: SH3TC2: NM_024577.4 and NP_078853.2, HK1: NM_033498.3 and NP_277033.1, REEP1: NM_022912.3 and NP_075063.1, MFN2: NM_014874.3 and NP_055689.1
  3. bScores of PolyPhen-2 (PP2) ~ 1, MUpro (MU) < 0, PROVEAN (PRO) <  − 2.5, and Fathmm (Fath) <  − 1.5 indicate pathogenic prediction (*denotes a pathogenic prediction)