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Microduplication of chromosome 1q21.1 is observed in ~0.03% of adults. It has a highly variable, incompletely penetrant phenotype that can include intellectual disability, global developmental delay, specific learning disabilities, autism, schizophrenia, heart anomalies and dysmorphic features. We evaluated a 10-year-old-male with a 1q21.1 duplication by CGH microarray. He presented with major attention deficits, phonological dysphasia, poor fine motor skills, dysmorphia and mild autistic features, but not the typical macrocephaly. Neuropsychiatric evaluation demonstrated a novel phenotype: an unusually large discrepancy between non-verbal capacities (borderline-impaired WISC-IV index scores of 70 for Working Memory and 68 for Processing Speed) vs. strong verbal skills – scores of 126 for Verbal Comprehension (superior) and 111 for Perceptual Reasoning (normal).  HYDIN2  has been hypothesized to underlie macrocephaly and perhaps cognitive deficits in this syndrome, but assessment of  HYDIN2  copy number by microarray is difficult because of extensive segmental duplications. We performed whole-genome sequencing which supported  HYDIN2  duplication (chr1:146,370,001-148,590,000, 2.22 Mb, hg38). To evaluate copy number more rigorously we developed droplet digital PCR assays of  HYDIN2  (targeting unique 1 kb and 6 kb insertions) and its paralog  HYDIN  (targeting a unique 154 bp segment outside the  HYDIN2  overlap). In an independent cohort, ddPCR was concordant with previous microarray data. Duplication of  HYDIN2  was confirmed in the patient by ddPCR. This case demonstrates that a large discrepancy of verbal and non-verbal abilities can occur in 1q21.1 duplication syndrome, but it remains unclear whether this has a specific genomic basis. These ddPCR assays may be useful for future research on  HYDIN2  copy number.

1q21.1 microduplication: large verbal–nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number