Patient ID | Age* (years) | Gender | Phenotype | Aberration | Chromosome band | Genome coordinates | Size (kb) | Confidence value (%) | Marker count | Affected gene(s) | Validation | Pathogenicity |
---|---|---|---|---|---|---|---|---|---|---|---|---|
52253 | 5 | M | Developmental delay, marked hypotonia, agenesis of corpus callosum and facial dysmorphic features | Deletion (heterozygous) | 17q21.31 | hg18, chr17: 41049320-41522088 | 473 | N/A | 329 | 9 genes including MAPT | MLPA/-(parents N/A, likely de novo) | Pathogenic (recurrent microdeletion syndrome)58 |
69234 | 2 | F | Developmental delay, hypotonia, microcephaly and minor morphological abnormalities | Deletion (heterozygous) | Xp11.4 | hg19, chrX: 41339667-41811516 | 472 | 91 | 1040 | CASK, GPR34 and GPR82 | MLPA/de novo | Pathogenic (phenotypic spectrum associated with CASK loss of function has been described)59 |
71264 | 2 | M | Developmental delay, hypotonia, mild facial dysmorphic features and stridor | Deletion (heterozygous) | 17q21.31 | hg19, chr17: 43703800-44163085 | 459 | 90 | 857 | 9 genes including MAPT | MLPA/de novo | Pathogenic (recurrent microdeletion syndrome)58 |
59248 | 4 | F | Developmental delay, severe hypotonia since birth, refractory epilepsy, facial dysmorphic features and oedematous hands and feet with tapering fingers | Deletion (heterozygous) | 1q24.3 | hg18, chr1: 170135864-170505998 | 372 | N/A | 244 | DNM3 | FISH/de novo | VOUS (WES of the patient and both parents did not reveal any obvious candidate gene mutation. DNM3 encodes dynamin 3, involved in vesicular transport) |
71156 | 1 | F | Developmental delay, microcephaly and facial dysmorphic features | Deletion (heterozygous) | 16p13.3 | hg19, chr16: 3788867- 3935836 | 147 | 91 | 353 | CREBBP | MLPA/de novo | Pathogenic (OMIM gene for Rubinstein–Taybi syndrome)48 |
62848 | 5 | F | Developmental delay, hyperactivity and microcephaly | Duplication (heterozygous) | 12q24.23 | hg18, chr12: 117061815- 117183853 | 122 | N/A | 71 | TAOK3 and PEBP1 | MLPA/de novo | Likely benign (pathogenic heterozygous mutation in SHANK2: c.2669_2670insC (p.P891Sfs*32) was found in this patient by WES) |
62563 | 11 | F | Learning difficulties, short attention, deficits in social-emotional behaviour and mild facial dysmorphic features | Deletion (heterozygous) | 5p15.2 | hg18, chr5: 11431816- 11545236 | 113 | N/A | 99 | CTNND2 | MLPA/de novo | Pathogenic (implicated in the ID phenotype of cri-du-chat syndrome.17 Further patients are discussed in this paper) |
72125 | 7 | F | Developmental delay, and mild facial dysmorphic features | Duplication (heterozygous) | 10p14 | hg19, chr10: 7932363-8033508 | 101 | 90 | 108 | TAF3 | MLPA/de novo | VOUS (TAF3 encodes TAF3 RNA polymerase II, TATA box binding protein-associated factor) |
70229 | 3 | M | Global developmental delay with prominent speech delay, truncal ataxia, agenesis of corpus callosum and repaired cleft palate | Deletion (heterozygous) | 12q24.33 | hg19, chr12: 132552537-132623611 | 71 | 90 | 48 | EP400, EP400NL, and DDX51 | MLPA/de novo | VOUS (there is patient 262376 in Decipher database with a duplication encompassing the same genes) |
43552 | 19 | M | Intellectual disability (ID), speech problems, spastic movement disorder and tall stature | Deletion (heterozygous) | 16p13.3 | hg18, chr16: 4986264- 5046682 | 60 | 89 | 53 | NAGPA, C16orf89, and SEC14L5 | MLPA/de novo | VOUS (a smaller deletion including only SEC14L5 and NAGPA is present in 1/1038 of a world-wide control cohort by Affymetrix) |
70886 | 4 | M | Developmental delay, a doubled row of upper incisors and cleft palate | Duplication (heterozygous) | 2q33.1 | hg19, chr2: 200278502- 200310272 | 32 | 89 | 68 | SATB2 | MLPA/de novo | Pathogenic (deletions of SATB2 have been implicated as causative for cleft palate and ID)26 |
45333 | 9 | M | Severe ID, hypotonia, macrocephaly, haemangioma of the upper lip, bilateral postaxial foot polydactyly and obesity | Deletion (heterozygous) | 20q13.32 | hg19, chr20: 57556968- 57575495 | 19 | 94 | 28 | TH1L and CTSZ | MLPA/de novo | Likely benign (pathogenic mosaic heterozygous mutation in PIK3CA: c.2740G>A (p.G914R) was found in this patient by WES)34 |
56366 | 4.5 | F | Developmental delay, hypotonia, gross and fine motor coordination problems, facial dysmorphic features, and complex congenital heart defect (details reported elsewhere)13 | Deletion (heterozygous) | 12q24.21 | hg18, chr12: 115158648- 115175505 | 17 | 87 | 18 | MED13L | MLPA/de novo | Pathogenic (described elsewhere)13 |
617 | 24 | F | ID, epilepsy, loss of motor function, lissencephaly type I | Deletion (heterozygous) | 17p13.3 | hg18, chr17: 2519114- 2523280 | 4 | 96 | 6 | PAFAH1B1 (LIS1) | MLPA/-(parents N/A, likely de novo) | Pathogenic (OMIM gene for lissencephaly)60 |
*Age at the time of array.
CNV, copy number variant; N/A, not available; VOUS, variant of uncertain significance; WES, whole-exome sequencing.