# Submicroscopic 16q24.2–q24.3 deletion in a family with nonsyndromic short stature

**Authors:** Chisato Narita, Hidekazu Utsunomiya, Junpei Hamada, Ikuko Kageyama, Maki Fukami, Akie Nakamura

PMC · DOI: 10.1038/s41439-026-00336-4 · 2026-01-26

## TL;DR

A family with unexplained short stature was found to have a rare genetic deletion on chromosome 16, suggesting a possible link to growth-related genes.

## Contribution

The study reports a novel ~1.5-Mb deletion at 16q24.2–q24.3 associated with nonsyndromic short stature.

## Key findings

- Array-based comparative genomic hybridization identified a heterozygous deletion in the 16q24.2–q24.3 region.
- Whole-exome sequencing found no pathogenic variants, pointing to the deletion as a likely cause.
- The deletion region may contain genes or regulatory elements important for skeletal growth.

## Abstract

Array-based comparative genomic hybridization for a boy, his mother and his half-sister with etiology-unknown nonsyndromic short stature identified a hitherto unreported heterozygous ~1.5-Mb deletion at 16q24.2–q24.3. Whole-exome sequencing detected no pathogenic variants. Our results, in conjunction with previous reports of cases with similar deletions, indicate that the 16q24.2–q24.3 region provides a platform for submicroscopic deletions and possibly contains a gene(s) or regulatory elements involved in skeletal growth.

## Full-text entities

- **Genes:** GH1 (growth hormone 1) [NCBI Gene 2688] {aka GH, GH-N, GHB5, GHN, IGHD1A, IGHD1B}, ACAN (aggrecan) [NCBI Gene 176] {aka AGC1, AGCAN, CSPG1, CSPGCP, MSK16, SEDK}, NPR2 (natriuretic peptide receptor 2) [NCBI Gene 4882] {aka AMDM, ANPRB, ANPb, ECDM, GC-B, GCB}, IGF1 (insulin like growth factor 1) [NCBI Gene 3479] {aka IGF, IGF-I, IGFI, MGF}, TRAPPC2L (trafficking protein particle complex subunit 2L) [NCBI Gene 51693] {aka HSPC176, PERRB}, ZNF778 (zinc finger protein 778) [NCBI Gene 197320], SHOX (SHOX homeobox) [NCBI Gene 6473] {aka GCFX, PHOG, SHOX1, SHOXY, SS}, ZNF469 (zinc finger protein 469) [NCBI Gene 84627] {aka BCS, BCS1, Zfp469}, CDT1 (chromatin licensing and DNA replication factor 1) [NCBI Gene 81620] {aka DUP, RIS2}, ZFPM1 (zinc finger protein, FOG family member 1) [NCBI Gene 161882] {aka FOG, FOG1, PRDM18, ZC2HC11A, ZNF89A}, ANKRD11 (ankyrin repeat domain 11) [NCBI Gene 29123] {aka ANCO-1, ANCO1, LZ16, T13}, BANP (BTG3 associated nuclear protein) [NCBI Gene 54971] {aka BEND1, SMAR1, SMARBP1}, ZC3H18 (zinc finger CCCH-type containing 18) [NCBI Gene 124245] {aka NHN1}, GALNS (galactosamine (N-acetyl)-6-sulfatase) [NCBI Gene 2588] {aka GALNAC6S, GAS, GalN6S, MPS4A}, PIEZO1 (piezo type mechanosensitive ion channel component 1 (Er blood group)) [NCBI Gene 9780] {aka DHS, ER, FAM38A, LMPH3, LMPHM6, Mib}
- **Diseases:** dysmorphic facial appearance (MESH:C535655), heart anomalies (MESH:D006330), Nonsyndromic short stature (MESH:C580334), recurrent otitis (MESH:D010031), congenital anomalies (MESH:D000013), intellectual disability (MESH:D008607), congenital malformations (OMIM:163000), KBG syndrome (MESH:C537015), VSD (MESH:D006345), autosomal dominant short stature (MESH:D006130), spina bifida (MESH:D016135), skeletal anomalies (MESH:C535534), skeletal dysplasia (MESH:C535858), otitis media (MESH:D010033), genetic (MESH:D030342), epilepsy (MESH:D004827)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** Chr16: 87,800,485-89,304,370, Chr16: 87,800,426-89,304,429

## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12855966/full.md

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Source: https://tomesphere.com/paper/PMC12855966