Table 2.

Copy number variants of uncertain significance (including likely pathogenic).

Patient	Ocular Phenotype	Non-ocular phenotype	Region	Copy state	Position	Size (Mb)a	Genes in region	Phenotype for gene/region	Significance for ocular disease
Patient 5	B severe microphthalmia	None	3q29	Gain	195383130–197550799	2.2 (1018)	SDHAP2, MUC20, MUC4, MIR570, TNK2, SDHAP1, TFRC, LOC401109, ZDHHC19, SLC51A, PCYT1A, TCTEX1D2, TM4SF19-TCTEX1D2, TM4SF19, UBXN7, RNF168, C3orf43, WDR53, FBXO45, LRRC33, CEP19, PIGX, PAK2, SENP5, NCBP2, LOC152217, PIGZ, MFI2-AS1, MFI2, DLG1, MIR4797, DLG1-AS1, BDH1, LOC220729, KIAA0226, MIR922, FYTTD1, LRCH3	3q29 duplication syndrome: developmental delay, obesity, heart defects, microcephaly, variable other features	Ocular anomalies (A/M, anterior segment dysgenesis) occasionally reported
Patient 6b	B microphthalmia, congenital cataract, glaucoma, retinal detachment, optic nerve hypoplasia	Mild microcephaly, hypotonia, history of gross motor delay, pituitary hypoplasia, ADHD	11p13	Gain	31609664–32486962	0.88 (707)	ELP4, PAX6, DKFZp686K1684, RCN1, WT1, WT1-AS	Variable ocular defects (typically mild), facial dysmorphism, other features	Mice with Pax6 overexpression show embryonic eye defects
Patient 7b	R microphthalmia, iris coloboma, corneal leukoma	Neurofibromatosis type 1; B clinodactyly, redundant periumbilical skin	17q11.2	Loss	28997779–30420528	1.4 (621)	SUZ12P1, CRLF3, CORPS, ATAD5, TEFM, ADAP2, RNF135, DPRXP4, MIR4733, NF1, OMG, EVI2B, EVI2A, RAB11FIP4, MIR4724, MIR193A, MIR4725, MIR365B, UTP6, SUZ12, LRRC37B, SH3GL1P1	Neurofibromatosis type 1	Ocular anomalies in some patients; Nf1 mutant mice have embryonic eye defects
Patient 8b	B microphthalmia, microcornea, congenital cataract	Microcephaly, developmental delays, short stature	2q14.2	Gain	120078243–120623545	0.55 (298)	C2orf76, DBI, TMEM37, SCTR, PCDP1, TMEM177, PTPN4	None	Nanophthalmos 3 locus; TMEM37, ptpn4a, dbi are expressed in lens
Patient 9	B anophthalmia	Choanal atresia, broad nasal bridge, indented nasal tip	2q21.1	Gain	130783696–131157859	0.37 (111)	POTEF CCDC74B-AS1, CCDC74B, SMPD4, MZT2B, TUBA3E CCDC115, IMP4, PTPN18	None	SMPD4 enriched in the lens in mouse embryos
Patient 10	R severe microphthalmia	None	15q26.3	Gain	102025982–102311246	0.29 (183)	PCSK6, TM2D3, TARSL2	Levy-Shanske (tetrasomy): facial dysmorphism, craniosynostosis and other defects	PCSK6 is enriched in the lens in mouse embryos

^anumber of probes indicative of CNV is specified in parentheses;

^bfamilial cases (details are provided in the text); regions/genes associated with likely pathogenic variants are shown in bold