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. 2015 Jul 1;78(2):323–328. doi: 10.1002/ana.24457

Table 1.

De Novo CNVs in 349 Trios

Trio CNV Size Candidate or Known Epilepsy Genes or Known Disease Association De Novo SNV Calls from Exome2 Validation Platform Gene(s) Enriched in CNVs Found in Patients with Neurodevelopmental Phenotypesa Age at Onset Seizure Typesb
Likely pathogenic CNVs
fx 2q24 dup 7.5Mb SCN2A, SCN1A SMG9 (mis), EPHB1 (synon) CGH SCN1A, SCN2A 7 mo IS
iq 2q24 del 296kb SCN1A None CGH, SNP SCN1A <1 yr GTC, aA
hj 5p15 del 3.8Mb SEMA5A, CTNND2 SDCBP2 (mis) CGH TAS2R1, FAM173B, CCT5, MTRR 6 mo FS, focal, GTC, aA, SE
cy 7q11 del 11.4Mb MAGI2, YWHAG, HIP1 ZNF12 (UTR), FPGT‐TNNI3K (mis), FAM50A CGH, SNP HIP1 3 mo IS, aA
aia 9p ter del 8.7Mb 9p deletion syndrome None SNP DMRT2, DMRT3 5 mo IS
iz 14q23 del 585kb GPHN HRG (mis), PCDHB13 (mis) CGH c 2.5 yr FS+SE, T, drop
eh 15q11 dup 5.0Mb 15q11q13 dup syndrome; GABRB3 PAQR8 (synon) CGH GABRB3 2 wk IS, multiple other
ag 15q11 dupd 12.0Mb 15q11q13 dup syndrome; GABRB3 MLL4 (mis) CGH, karyo GABRB3 8 mo IS
gq∧ 15q11 dup 8.4Mb 15q11q13 dup syndrome; GABRB3 None CGH, SNP GABRB3 8 mo GTC, T, atonic
fu t(15;16)d 1.8Mb del, 16.3Mb dup Large unbalanced translocation None CGH, karyo SNRPA1, FANCA 8 mo IS
CNVs of uncertain clinical significance
ig 1p22 dup 140kb 1 gene: ZNF644 IQSEC1 (mis) CGH, SNP c 2 yr A, GTC, M, T, drop
ad 1q21 dup 249kb TAR region dup NFE2L1 (mis) SNP LIX1L 8 mo IS
aib 2q37 del 154kb 4 genes: PPP1R7, HDLBP, ANO7, SEPT2 CXXC11 (synon) SNP PPP1R7 5 mo IS, T
gc 7q22 del 622kb 15 genes in region NR1H2 (mis) CGH MUC17, MYL10, TRIM56 8 mo IS
ahp 7q31 dup 94kb 2 genes: CPED1, ING3 ADAMSL4 (mis), PPP6R2 (mis) SNP c 7 mo IS
le 8p23 del 140kb 2 genes: MCPH1, AGTP2 DACH2 (mis) CGH, SNP ANGPT2 3 y 10 mo GTC, drop, T, M, A, aA
bda 17q12 del 1.5Mb 15 genes in region None h.c. 8 mo IS, M, SE, GTC

Additional information is available in Supplementary Table 7.

a

Genes listed represent those with mean probability value < 0.05 for known disease gene(s) in region or peak probability value < 0.05 for novel regions as described by Cooper and colleagues.21 See Supplementary Table 5 for details.

b

Seizure types include all reported; first type listed was the initial seizure type.

c

No gene within region with p < 0.05.

d

Upon review of records, diagnosis made prior to enrollment.

A = absence; aA = atypical absence; CGH = comparative genome hybridization; CNV = copy number variant; FS = febrile seizures; GTC = generalized tonic clonic; h.c. = high‐confidence CNV call by CoNIFER; IS = infantile spasms; M = myoclonic; SE = status epilepticus; SNP = single nucleotide polymorphism; SNV = single nucleotide variant; T = tonic; UTR = untranslated region.