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Table 2 Genetic results for patients with short stature

From: Clinical relevance of targeted exome sequencing in patients with rare syndromic short stature

Family Previous clinical assessment Previous conventional analysis Final diagnosis Gene Nucleotide/AA change Inheritance mode In silico analysis Initial classification Re-classification Novel References
SIFT Polyphen-2 Mutation taster
1 NS PTPN11
SOS1, KRAS, and NRAS
Cleidocranial dysplasia RUNX2 c.578G>A/p.Arg193Gln De novo     LPV PV No [45]
2 TS 46,XX Hajdu–Cheney syndrome NOTCH2 c.2816C>T/p.Pro939Leu De novo Deleterious (0.013) Benign (0.008) Disease causing (0.99) VUS VUS Yes  
3 USGD 46,XY CMA Cerebral creatine deficiency syndrome SLC6A8 c.942_944del/p.Phe315del Het, mat     LPV PV No [46]
4 NS PTPN11
SOS1, KRAS, and NRAS
Coffin–Lowry syndrome RPS6KA3 c.1606G>T/p.Val536Phe Het, mat Deleterious (0.00) Probably damaging (1.00) Disease causing (0.99) LPV PV Yes  
5 USGD 46,XY Acid-labile subunit deficiency IGFALS c.1346T>G/p.Leu449Arg Com het, pat, mat Tolerated (0.06) Probably damaging (0.997) Disease causing (0.99) VUS LPV Yes  
      c.1783C>T/p.Arg595Trp)   Deleterious (0.00) Probably damaging (1.000) Disease causing (0.99) VUS LPV Yes  
6A GHS 46,XY, CMA Sheldon–Hall syndrome TNNT3 c.47_49del/p.Glu18del Het, pat     VUS VUS Yes  
7 USGD 46,XY, CMA Meckel syndrome (Type 7) NPHP3 c.73G>T/p.Gly25Cys Het, pat
Het, mat
Deleterious (0.00) Benign (0.001) (1.00) Disease causing (0.99) VUS LPV Yes  
      c.489T>G/p.His163Gln   Tolerated (0.19) Probably damaging (0.723) Disease causing (0.99) VUS LPV Yes  
8 CdLS NIPBL Coffin–Siris syndrome ARID1B c.5547delC/p.Leu1850* De novo     PV PV Yes  
9 Achondroplasia FGFR3 AMDM NPR2 c.2326C>T/p.Arg776Trp Het, pat     PV PV No [29, 47]
10 NS PTPN11
SOS1, KRAS, and NRAS
MR, AD type51 KMT5B c.2422_2425del/p.Leu808Trpfs*50 De novo     PV PV Yes  
11 USGD 46,XX, CMA MR, AR type3 CC2D1A c.1610C>T/p.Ser537Leu Homo Deleterious (0.03) Probably damaging (0.997) Disease causing (0.99) VUS LPV Yes  
12 CdLS NIPBL CdLS type3 SMC3 c.1453_1455delGCT/p.Ala485del De novo     LPV PV Yes  
13 CATCH22 CMA MEIS2-related syndrome MEIS2 c.998_1000del/p.Arg333del De novo     PV PV No [48]
14 Skeletal dysplasia ND MOPD2 PCNT c.3716G>A/p.Arg1239His Compound hetero Tolerated (0.28) Probably damaging (0.856) Tolerated (0.00) VUS LPV No [49]
      c.7459C>G/p.Leu2487Val   Deleterious (0.00) Probably damaging (0.997) Tolerated (0.00) VUS LPV No [50]
15 USGD 46,XY
MLPA
Hajdu–Cheney syndrome NOTCH2 c.5471G>A/p.Arg1824His De novo Deleterious (0.001) Benign (0.008) Disease causing (0.99) VUS VUS Yes  
16 CATCH22 CMA MED13L syndrome MED13L c.5444C>T/p.Thr1815Met Het, mat Tolerated (0.17) Probably damaging (1.000) Disease causing (0.99) VUS LPV Yes  
  1. AA amino acid, AD autosomal dominant, AMDM acromesomelic dysplasia Maroteaux-type, AR Autosomal recessive, CdLS Cornelia de Lange syndrome, CMA chromosomal microarray, GHS Goldenhar syndrome, hemi hemizygote, het heterozygote, LPV likely pathogenic variant, mat maternal origin, MOPD2 microcephalic osteodysplastic primordial dwarfism type II, MR mental retardation, N/A not available, ND not done, NS Noonan syndrome, pat paternal origin, Pts patients, PV pathogenic variant, Ref references, TS Turner syndrome, USGD unrecognizable syndromic growth disorder, VUS variant of uncertain significance