Table 5.

Summary of the HPO analysis.

HPO terms	DEGs associated with phenotypic abnormalities⁎
Abnormal appendicular skeleton morphology (HP:0011844) and abnormality of limb bone morphology (HP:0002813)	CYP19A1, SHOX, LFNG, ANKH, RIPK4, PTCH1, CBS, HOXA11, CRLF1, DSP, EGR2, PYCR1, WNT5A, CHN1, BMPER, GDF6, CCBE1, TBX3, COL5A1, TFAP2A, EDNRB, RBPJ, SNORD116-1, SEMA3A, KIT, COMP, MASP1, HOXD10, CNTN1
Abnormality of the digits (HP:0011297)	SHOX, LFNG, RIPK4, PTCH1, CBS, HOXA11, CRLF1, DSP, EGR2, WNT5A, CHN1, BMPER, GDF6, CCBE1, TBX3, TFAP2A, EDNRB, RBPJ, SNORD116-1, COMP, MASP1, CNTN1
Abnormality of the periorbital region (HP:0000606)	BDNF, ANKH, LDLR, RIPK4, PTCH1, CDON, DSP, PYCR1, WNT5A, CHN1, BMPER, CCBE1, AFF2, TBX3, COL5A1, TFAP2A, EDNRB, RBPJ, SNORD116-1, KIT, MASP1
Abdominal wall defect (HP:0010866)	BDNF, BMPER, LFNG, CCBE1, TBX3, COL5A1, CBS, ZEB1, PTCH1, MASP1, PYCR1, WNT5A
Aplasia/hypoplasia involving hands and bones of the upper limbs (HP:0005927, HP:0006496)	CHN1, SHOX, CCBE1, TBX3, TFAP2A, RIPK4, PTCH1, RBPJ, CRLF1, COMP, MASP1, WNT5A
Thoracoabdominal wall defects (HP:0100656)	BDNF, BMPER, LFNG, CCBE1, TBX3, COL5A1, CBS, ZEB1, PTCH1, MASP1, PYCR1, WNT5A
Abnormality of spinal cord (HP:0002143)	CHN1, ENPP1, BMPER, GDF6, LFNG, CCBE1, PTCH1, COMP, MASP1
Vertebral segmentation defect (HP: 0003422)	PTCH1, CHN1, BMPER, GDF6, LFNG, WNT5A

^⁎Genes down-regulated in affected sisters are reported in bold.