Table 2 Detection of pathogenic variants and estimated carrier frequencies of 73 genes for bone dysplasias.

From: Estimation of the carrier frequencies and proportions of potential patients by detecting causative gene variants associated with autosomal recessive bone dysplasia using a whole-genome reference panel of Japanese individuals

Gene Pathogenic variants in 3.5KJPNv2 (3552 individual)
  Set 1a Set 2a Set 3a Set 4a
  No. Var Allele Cnt Carrier Frq. No. Var Allele Cnt Carrier Frq. No. Var Allele Cnt Carrier Frq. No. Var Allele Cnt Carrier Frq.
Osteogenesis imperfecta
 BMP1 0 0 0.00000 9 9 0.00282 9 9 0.00282 9 9 0.00282
 LEPRE1 0 0 0.00000 2 2 0.00056 2 2 0.00056 2 2 0.00056
 CRTAP 0 0 0.00000 1 2 0.00056 1 2 0.00056 1 2 0.00056
 PPIB 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 PLOD2 0 0 0.00000 2 2 0.00056 2 2 0.00056 2 2 0.00056
 SERPINH1 0 0 0.00000 8 22 0.00618 8 22 0.00618 8 22 0.00618
 FKBP10 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
 SERPINF1 0 0 0.00000 1 1 0.00141 1 1 0.00141 2 91 0.02721
 SEC24D 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
 WNT1 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 CREB3L1 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 SP7 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Hypophosphatemic rickets
 DMP1 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 ENPP1 0 0 0.00000 0 0 0.00000 0 0 0.00000 2 5 0.00141
 SLC34A3 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Metaphyseal dysplasia
 POP1 0 0 0.00000 2 3 0.00085 2 3 0.00085 2 3 0.00085
 SBDS 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Mucopolysaccharidosis
 ARSB 1 1 0.00028 1 1 0.00028 1 1 0.00028 1 1 0.00028
 GALNS 1 2 0.00056 4 4 0.00113 4 4 0.00113 5 5 0.00141
 GLB1 3 3 0.00085 5 5 0.00141 5 5 0.00141 6 6 0.00169
 GNS 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 GUSB 0 0 0.00000 1 1 0.00028 1 1 0.00028 2 2 0.00056
 HSGNAT 0 0 0.00000 1 1 0.00028 1 1 0.00028 2 2 0.00056
 IDUA 1 1 0.00028 3 3 0.00085 4 4 0.00113 5 5 0.00141
 NAGLU 1 1 0.00028 2 2 0.00056 2 2 0.00056 3 3 0.00085
 SGSH 0 0 0.00000 1 1 0.00028 1 1 0.00028 2 2 0.00056
Osteopetrosis
 CA2 1 1 0.00028 1 1 0.00028 1 1 0.00028 1 1 0.00028
 CLCN7 0 0 0.00000 9 13 0.00366 9 13 0.00366 9 13 0.00366
 FERMT3 0 0 0.00000 3 4 0.00113 3 4 0.00113 3 4 0.00113
 OSTM1 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
 PLEKHM1 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 RASGRP2 0 0 0.00000 2 2 0.00056 2 2 0.00056 2 2 0.00056
 SNX10 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 TCIRG1 0 0 0.00000 0 0 0.00000 1 1 0.00028 2 2 0.00056
 TNFRSF11A 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 TNFSF11 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Pyknodysostosis
 CTSK 1 2 0.00056 2 3 0.00085 2 3 0.00085 2 3 0.00085
Spondylometaphyseal dysplasias (SMD)
 PCYT1A 2 2 0.00056 2 2 0.00056 2 2 0.00056 2 2 0.00056
Stickler syndrome, recessive type
 COL9A1 1 1 0.00028 3 3 0.00113 3 3 0.00113 3 3 0.00113
Spondylocostal dysostosis
 DLL3 1 1 0.00028 2 2 0.00056 2 2 0.00056 2 2 0.00056
 HES7 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 LFNG 0 0 0.00000 0 0 0.00000 0 0 0.00000 1 1 0.00028
 MESP2 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Hypophosphatasia             
 ALPL 2 18 0.00506 5 22 0.00618 6 34 0.00953 13 156 0.04404
Mucolipidosis
 GNPTAB 5 8 0.00225 6 9 0.00253 6 9 0.00253 6 9 0.00253
 GNPTG 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
Ehlers–Danlos sydrome
 B4GALT7 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
Chondroectodermal dysplasia (Ellis–van Creveld)
 EVC 0 0 0.00000 1 1 0.00028 1 1 0.00028 3 10 0.00281
 EVC2 2 3 0.00085 7 8 0.00226 7 8 0.00226 8 9 0.00254
Acromesomelic dysplasia type Maroteaux (AMDM)
 NPR2 0 0 0.00000 1 1 0.00028 2 5 0.00141 2 5 0.00141
Desbuquois dysplasia
 CANT1 0 0 0.00000 2 3 0.00085 3 6 0.00169 3 6 0.00169
 XYLT1 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Spondylo-epi-metaphyseal-dysplasias (SEMD)
 DDR2 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 MATN3 0 0 0.00000 0 0 0.00000 0 0 0.00000 2 17 0.00478
RAPADILINO syndrome Poland
 RECQL4 2 2 0.00056 6 9 0.00253 7 10 0.00281 7 10 0.00281
Metaphyseal anadysplasia
 MMP13 0 0 0.00000 1 3 0.00084 1 3 0.00084 1 3 0.00084
 MMP9 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Antley–Bixler syndrome
 POR 3 15 0.00422 5 17 0.00478 5 17 0.00478 8 41 0.01148
Oto-spondylo-mega-epiphyseal dysplasia (OSMED)
 COL11A2 0 0 0.00000 4 4 0.00113 4 4 0.00113 5 6 0.00169
Diastrophic dysplasia (DTD)/ Atelosteogenesis type2 (AO2)
 SLC26A2 0 0 0.00000 0 0 0.00000 1 2 0.00056 2 14 0.00393
Duggve–Melchior–Clausen dysplasia (DMC)
 DYM 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
 RAB33B 0 0 0.00000 0 0 0.00000 0 0 0.00000 0 0 0.00000
Dyssegmental dysplasia (Silverman–Handmaker type/Rolland–Desbuquios type)
 HSPG2 0 0 0.00000 6 7 0.00197 6 7 0.00197 9 16 0.00450
Progressive peudorheumatoid dysplasia (PPRD; SED with progressive arthropathy)
 WISP3 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
Asphyxiating thoracic dysplasia (ATD; Jeune)
 DYNC2H1 2 4 0.00113 6 8 0.00225 6 8 0.00225 7 12 0.00337
 WDR34 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
 IFT80 0 0 0.00000 3 14 0.00393 3 14 0.00393 3 14 0.00393
 IFT172 1 1 0.00028 5 5 0.00141 5 5 0.00141 5 5 0.00141
 IFT140 0 0 0.00000 3 3 0.00085 3 3 0.00085 5 5 0.00141
 WDR19 1 2 0.00056 4 6 0.00169 4 6 0.00169 4 6 0.00169
 TTC21B 0 0 0.00000 4 5 0.00141 4 5 0.00141 6 7 0.00197
Craniometaphyseal dysplasia
 GJA1 0 0 0.00000 1 1 0.00028 1 1 0.00028 1 1 0.00028
Robinow syndrome
 ROR2 0 0 0.00000 1 1 0.00028 1 1 0.00028 2 2 0.00056
  1. aSee “Materials and Methods” and Fig. 1.
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