Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland.
Department of Pediatrics and Internal Medicine Nursing, Department of Rare Disorders, Medical University of Gdansk, Gdansk, Poland.
Orphanet J Rare Dis. 2022 Aug 26;17(1):325. doi: 10.1186/s13023-022-02480-w.
Split-hand/ foot malformation with long bone deficiency 3 (SHFLD3) is an extremely rare condition associated with duplications located on 17p13.3, which invariably encompasses the BHLHA9 gene. The disease inherits with variable expressivity and significant incomplete penetrance as high as 50%.
We have detected 17p13.3 locus one-allele triplication in a male proband from family 1 (F1.1), and duplication in a male proband from family 2 (F2.1) applying array comparative genomic hybridization (array CGH). The rearrangements mapped to the following chromosomal regions-arr[GRCh38] 17p13.3(960254-1291856)×4 in F1.1 and arr[GRCh38] 17p13.3(1227482-1302716)×3 in F2.1. The targeted quantitative PCR revealed that the 17p13.3 locus was also duplicated in the second affected member from family 2 (F2.2; brother of F2.1). In the next step, we performed segregation studies using quantitative PCR and revealed that F1.1 inherited the triplication from his healthy father-F1.2, whereas the locus was unremarkable in the mother of F2.1 & F2.2 and the healthy son of F2.1. However, the duplication was present in a healthy daughter of F2.2, an asymptomatic carrier. The breakpoint analysis allowed to define the exact size and span of the duplicated region in Family 2, i.e., 78,948 bp chr17:1225063-1304010 (HG38). Interestingly, all symptomatic carriers from both families presented with variable SHFLD3 phenotype. The involvement of secondary modifying locus could not be excluded, however, the Sanger sequencing screening of BHLHA9 entire coding sequence was unremarkable for both families.
We have shed light on the one-allele CNV triplication occurrence that should be considered when a higher probe (over duplication range) signal is noted. Second, all SHFLD3 patients were accurately described regarding infrequent limb phenotypes, which were highly variable even when familial. Of note, all symptomatic individuals were males. SHFLD3 still remains a mysterious ultra-rare disease and our findings do not answer crucial questions regarding the disease low penetrance, variable expression and heterogeneity. However, we have presented some clinical and molecular aspects that may be helpful in daily diagnostic routine, both dysmorphological and molecular assessment, of patients affected with SHFLD3.
手部/足部裂畸形伴长骨发育不全 3 型（SHFLD3）是一种极为罕见的疾病，与位于 17p13.3 上的重复有关，该重复必然包括 BHLHA9 基因。该疾病具有可变的外显率和高达 50%的显著不完全外显率。
我们应用比较基因组杂交微阵列（array CGH）在来自家系 1（F1.1）的 1 名男性先证者中检测到 17p13.3 单等位基因三重复，在来自家系 2（F2.1）的 1 名男性先证者中检测到重复。这些重排在染色体区域映射为：F1.1 中 arr[GRCh38] 17p13.3(960254-1291856)×4，F2.1 中 arr[GRCh38] 17p13.3(1227482-1302716)×3。靶向定量 PCR 显示，17p13.3 位点在来自家系 2 的第二位受累成员（F2.2；F2.1 的兄弟）中也存在重复。在下一步中，我们使用定量 PCR 进行分离研究，结果显示 F1.1 从他健康的父亲 F1.2 中遗传了三重复，而 F2.1 和 F2.2 的母亲和 F2.1 的健康儿子的该位点无明显异常。然而，F2.2 的一名无症状携带者（其健康女儿）存在重复。断点分析允许定义家系 2 中重复区域的精确大小和范围，即 78,948 bp chr17:1225063-1304010（HG38）。有趣的是，来自两个家系的所有有症状的携带者均表现出可变的 SHFLD3 表型。不能排除次要修饰基因座的参与，但对两个家系的 BHLHA9 整个编码序列的 Sanger 测序筛查均无异常。
我们已经阐明了单等位基因 CNV 三重复的发生，当检测到更高的探针（超过重复范围）信号时应考虑该重复。其次，所有 SHFLD3 患者的罕见肢体表型均得到了准确描述，即使在家族中也具有高度的变异性。值得注意的是，所有有症状的个体均为男性。SHFLD3 仍然是一种神秘的超罕见疾病，我们的发现并没有回答关于疾病低外显率、可变表达和异质性的关键问题。然而，我们已经提出了一些临床和分子方面的问题，这些问题可能有助于 SHFLD3 患者的日常诊断常规，包括对他们的畸形和分子评估。
