# Clinical Insights into the Neurodevelopmental Impact of 16p CNVs in an Italian Clinical Cohort

**Authors:** Ilaria La Monica, Maria Rosaria Di Iorio, Antonia Sica, Lucio Pastore, Barbara Lombardo

PMC · DOI: 10.3390/genes17020247 · 2026-02-21

## TL;DR

This study explores how genetic changes in the 16p region of the genome affect neurodevelopment in an Italian patient group, highlighting the importance of genetic testing for diagnosis and treatment.

## Contribution

The study provides new clinical insights into the impact of 16p CNVs in an Italian cohort, emphasizing their diagnostic and management implications.

## Key findings

- CNVs in 16p were found in 8% of patients with neurodevelopmental disorders.
- Deletions and duplications in 16p were linked to distinct developmental and behavioral features.
- Phenotypic variability suggests modifying factors influence clinical outcomes.

## Abstract

Background: Neurodevelopmental disorders (NDDs) are a heterogeneous group of conditions characterized by cognitive, behavioral, and developmental impairments, frequently linked to structural genomic alterations. Copy number variants (CNVs) involving chromosome 16, particularly the short arm 16p, are recognized contributors to neurodevelopmental variability. Despite increasing international evidence, data from Italian clinical cohorts are still limited. Methods: We investigated 1200 patients referred for genetic evaluation due to suspected NDDs, including autism spectrum disorder (ASD), intellectual disability (ID), global developmental delay, and language impairment. All individuals underwent array comparative genomic hybridization (a-CGH) analysis, and identified variants were correlated with detailed clinical, cognitive, and behavioral assessments. The analysis focused on recurrent CNVs at 16p11.2, 16p13.3, and 16p13.11, regions containing dosage-sensitive genes relevant to neurodevelopment. Results: CNVs involving the 16p region were identified in 96 patients (8% of the cohort), encompassing both deletions and duplications. Deletions were mainly associated with developmental delay, language deficits, and ASD-related features, whereas duplications were more frequently linked to behavioral dysregulation, attentional deficits, and variable cognitive impairment. Marked phenotypic variability was observed among individuals carrying similar CNVs, suggesting the contribution of modifying genetic or environmental factors. In a subset of patients, additional CNVs were identified, potentially exacerbating clinical severity, consistent with the two-hit model. Conclusions: This study confirms a strong association between recurrent 16p CNVs and a wide spectrum of neurodevelopmental phenotypes in an Italian clinical cohort. The findings emphasize the diagnostic utility of systematic genomic screening and the importance of an integrated genotype–phenotype approach to improve clinical interpretation, management, and genetic counseling in NDDs.

## Linked entities

- **Diseases:** autism spectrum disorder (MONDO:0005258), intellectual disability (MONDO:0001071)

## Full-text entities

- **Genes:** ATP2A1 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1) [NCBI Gene 487] {aka ATP2A, SERCA1}, NDE1 (nudE neurodevelopment protein 1) [NCBI Gene 54820] {aka HOM-TES-87, LIS4, MHAC, NDE, NUDE, NUDE1}, NPIPA1 (nuclear pore complex interacting protein family member A1) [NCBI Gene 9284] {aka NPIP, NPIPA, morpheus}, KCTD13 (potassium channel tetramerization domain containing 13) [NCBI Gene 253980] {aka BACURD1, FKSG86, PDIP1, POLDIP1, hBACURD1}, BP5 [NCBI Gene 474301], TAOK2 (TAO kinase 2) [NCBI Gene 9344] {aka MAP3K17, PSK, PSK1, PSK1-BETA, TAO1, TAO2}, MYH11 (myosin heavy chain 11) [NCBI Gene 4629] {aka AAT4, FAA4, SMHC, SMMHC, SMMS-1, VSCM2}, PRRT2 (proline rich transmembrane protein 2) [NCBI Gene 112476] {aka BFIC2, BFIS2, DSPB3, DYT10, EKD1, FICCA}, HIRIP3 (HIRA interacting protein 3) [NCBI Gene 8479], ABCC6 (ATP binding cassette subfamily C member 6) [NCBI Gene 368] {aka ABC34, ARA, EST349056, GACI2, MLP1, MOAT-E}, TUFM (Tu translation elongation factor, mitochondrial) [NCBI Gene 7284] {aka COXPD4, EF-TuMT, EFTU, P43}, SPNS1 (SPNS lysolipid transporter 1, lysophospholipid) [NCBI Gene 83985] {aka HSpin1, LAT, PP2030, SLC62A1, SLC63A1, SPIN1}, NTAN1 (N-terminal asparagine amidase) [NCBI Gene 123803] {aka PNAA, PNAD}, BP2 [NCBI Gene 474257], NOMO1 (NODAL modulator 1) [NCBI Gene 23420] {aka Nomo, PM5}, LGR5 (leucine rich repeat containing G protein-coupled receptor 5) [NCBI Gene 8549] {aka FEX, GPR49, GPR67, GRP49, HG38}, MAPK3 (mitogen-activated protein kinase 3) [NCBI Gene 5595] {aka ERK-1, ERK1, ERT2, HS44KDAP, HUMKER1A, P44ERK1}, QPRT (quinolinate phosphoribosyltransferase) [NCBI Gene 23475] {aka HEL-S-90n, QPRTase}, SEZ6L2 (seizure related 6 homolog like 2) [NCBI Gene 26470] {aka BSRPA, PSK-1}, SH2B1 (SH2B adaptor protein 1) [NCBI Gene 25970] {aka PSM, SH2B}, MVP (major vault protein) [NCBI Gene 9961] {aka LRP, VAULT1}, DOC2A (double C2 domain alpha) [NCBI Gene 8448] {aka Doc2}, MARF1 (meiosis regulator and mRNA stability factor 1) [NCBI Gene 9665] {aka KIAA0430, LKAP, LMKB, PPP1R34}, ATXN2L (ataxin 2 like) [NCBI Gene 11273] {aka A2D, A2LG, A2LP, A2RP}, PDXDC1 (pyridoxal dependent decarboxylase domain containing 1) [NCBI Gene 23042] {aka LP8165}, MIR484 (microRNA 484) [NCBI Gene 619553] {aka MIRN484, hsa-mir-484, mir-484}, BP3 [NCBI Gene 474259], CEP20 (centrosomal protein 20) [NCBI Gene 123811] {aka C16orf63, FOPNL, FOR20, PHSECRG2}, ABCC1 (ATP binding cassette subfamily C member 1 (ABCC1 blood group)) [NCBI Gene 4363] {aka ABC29, ABCC, DFNA77, GS-X, MRP, MRP1}, CORO1A (coronin 1A) [NCBI Gene 11151] {aka CLABP, CLIPINA, HCORO1, IMD8, TACO, p57}, LAT (linker for activation of T cells) [NCBI Gene 27040] {aka IMD52, LAT1, pp36}, BP4 [NCBI Gene 474258], RBFOX1 (RNA binding fox-1 homolog 1) [NCBI Gene 54715] {aka 2BP1, A2BP1, FOX-1, FOX1, HRNBP1}, ALDOA (aldolase, fructose-bisphosphate A) [NCBI Gene 226] {aka ALDA, GSD12, HEL-S-87p}
- **Diseases:** ID (MESH:D008607), tremors (MESH:D014202), CNV (MESH:D000092342), PDD (MESH:D011596), Man (MESH:D016750), hypotonia (MESH:D009123), epilepsy (MESH:D004827), language delay (MESH:D007805), motor delay (MESH:D006968), neuropsychiatric phenotypes (MESH:C000631768), ADHD (MESH:D001289), deletion syndrome (MESH:D002872), psychosis (MESH:D011618), executive dysfunction (MESH:D006331), 16p-associated disorders (MESH:C563050), neurodevelopmental impairment (MESH:D009422), cognitive impairment (MESH:D003072), behavioral and sleep problems (MESH:D020187), deficits in adaptive functioning (MESH:D018489), cardiovascular anomalies (MESH:D018376), restricted interests and repetitive behaviors (MESH:D002313), NDDs (MESH:D002658), ASD (MESH:D000067877), injury to (MESH:D014947), neurological conditions (MESH:D019636), dysmorphic features (MESH:D000013), autism (MESH:D001321), anxiety (MESH:D001007), Mental Disorders (MESH:D001523), neuromotor impairment (MESH:D060825), executive function disorders (MESH:D003291), impaired fine motor skills (MESH:D019957), learning difficulties (MESH:D007859), microdeletion syndrome (OMIM:613675), verbal apraxia (MESH:D001072), absence of expressive language (MESH:D007806), difficulty in concentration (MESH:C567712), neurological disorders (MESH:D009461), behavioral dysregulation (MESH:D021081), seizures (MESH:D012640)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** G2600D

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12940275/full.md

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Source: https://tomesphere.com/paper/PMC12940275