A clinical case report and literature review of the 3q29 microdeletion syndrome

Abstract

We report on a 15-year-old male with the 3q29 microdeletion syndrome and summarize the medical literature. He had intellectual disability, autism spectrum disorder, anxiety, obsessive compulsive tendencies, speech delay, delayed walking, a hypernasal voice, gait abnormalities, chronic constipation, gastroesophageal reflux disorder, urinary voiding dysfunction, abnormal skin pigmentation, and dysmorphic features. We present a review of the literature for the 3q29 microdeletion syndrome by comparing both the phenotype and the genetic defects in reported cases. Of the 38 previously reported cases with deletion size information, the most common chromosome deletion was 1.6 Mb in size including ∼ 30 genes. This emerging microdeletion syndrome is characterized by intellectual disability, speech delay, behavioral problems, craniofacial dysmorphism, and musculoskeletal abnormalities.

Fig. 1

A 1.24 Mb deletion (arrow) was found within the chromosome 3q29 band at genomic coordinates 195 788 299–197 033 296 with microarray analysis (NCBI build 37, February 2009, hg 19). Genes included within this deletion are TFRC, LINC00885, ZDHHC19, SLC51A, PCYT1A, TCTEX1D2, TM4SF19-TCTEX1D2, TM4SF19, UBXN7, RNF168, C3orf43, WDR53, FBXO45, NRROS, CEP19, PIGX, PAK2, SENP5, NCBP2, NCBP2-AS2, PIGZ, MFI2-AS1, MFI2, DLG1, MIR4797, and DLG1-AS1.

Fig. 2

Location of interstitial chromosome 3q29 deletions, genomic coordinates, and size for our patient and others reported in the literature. Deletions of previously reported patients are as follows: A, patient 1 del(3)(q29q29)(197 262 362–198 794 848, hg 18) 1.5 Mb deletion (Digilio et al., 2009); B, patient 2 del(3)(q29q29) (197 262 362–198 794 848, hg 18) 1.5 Mb deletion (Digilio et al., 2009); C, patient 1 del(3)(q29q29)(197 194 509–198 823 098, hg 18) 1.6 Mb deletion (Quintero-Rivera et al., 2010); D, patient 2 del(3) (q29q29)(196 941 615–199 043 290, hg 18) 2.1 Mb deletion (Quintero-Rivera et al., 2010); E, only patient del(3)(q29q29) (197 256 140–198 570 020, hg 18) 1.3 Mb deletion (Cobb et al., 2010); F, patient 1 del(3)(q29q29)(197 174 369–198 842 531, hg 18) 1.66 Mb deletion (Dasouki et al., 2011); G, patient 2 del(3)(q29q29) (197 174 769–198 842 531, hg 18) 1.66 Mb deletion (Dasouki et al., 2011); H, patient 3 del(3)(q29q29)(197 085 422–198 217 248, hg 18) 1.13 Mb deletion (Dasouki et al., 2011); I, only patient del(3)(q29q29) (197 224 799–198 804 500, hg 18) 1.58 Mb deletion (Sagar et al., 2013); J, patient 1 del(3)(q29q29) (197 224 754–198 794 789, hg 18) 1.57 Mb deletion (Citta et al., 2013); K, patient 2 del(3)(q29q29) (197 216 353–198 823 667, hg 18) 1.607 Mb deletion (Citta et al., 2013); L, patient 4 del(3)(q29q29) (197 232 253–198 823 667, hg 18) 1.59 Mb deletion (Citta et al., 2013); Our patient, del(3)(q29q29) (197 272 696–198 517 693, converted to hg 18) 1.24 Mb deletion.