Uncovering the Genetic Basis of Recurrent Split Hand/Foot Malformation: A Case Report and Review

Abstract

Split hand/foot malformation (SHFM) is a clinically and genetically heterogeneous condition, characterized by variable severity due to reduced penetrance and variable expressivity. We report a family in which the husband and several other family members exhibited non-syndromic SHFM. The couple experienced three pregnancies affected by severe SHFM, leading to pregnancy terminations. An autopsy performed on one of the fetuses revealed features consistent with isolated SHFM. Whole exome sequencing of the husband did not identify any pathogenic variants. However, chromosomal microarray analysis revealed a 481-kb likely pathogenic duplication of the 10q24.31q24.32 region on chromosome 10, associated with SHFM type 3. While SHFM can be detected on ultrasound, genetic evaluation is essential for families with a history of this condition and a high risk of recurrence. This evaluation is particularly beneficial if the couple opts for in vitro fertilization with preimplantation genetic testing to avoid multiple pregnancy terminations.

Keywords

split hand/foot malformation - chromosomal microarray - microduplication

Introduction

Split hand/foot malformation (SHFM), also known as ectrodactyly, is characterized by aplasia or hypoplasia of the phalanges, metacarpals, and metatarsals, leading to a deep median cleft of the hand and/or foot. SHFM can occur as an isolated condition, as part of a syndrome, or in association with other congenital anomalies.[1] Here, we report a likely pathogenic microduplication in the 10q24.32 region of chromosome 10 in a family with multiple affected members, including three fetuses.

Case Report

A non-consanguineous couple presented to the Genetics Department due to a history of three previous pregnancies affected by SHFMs. The husband and several members of his family, including his father, brother, and niece, also had similar deformities ([Fig. 1A]). None of the affected family members exhibited skin abnormalities, seizures, intellectual disability, or visual/hearing deficits.

Fig. 1 (A) Pedigree of the family. (B, C) Ultrasound and fetal autopsy findings of monodactyly in hands with lobster deformity in the foot in one of the fetuses. (D) Absent 1st and 2nd metacarpals, and hypoplastic 3rd metacarpal in both hands. Only the index finger is present in the right hand, and the index finger with a hypoplastic middle finger in the left hand, in the husband. (E) Absent middle three toes with hypoplasia and syndactyly of the middle three metatarsals in both feet in the husband. (F) Chromosomal microarray revealed a duplication of chromosome 10 encompassing the 10q24.31q24.32 region in the husband and one of the fetuses.

All three fetuses displayed monodactyly of the hands and lobster claw deformities of the feet. An autopsy was performed on the second fetus ([Fig. 1B, C]). The husband presented with bilateral absence of the first and second metacarpals and hypoplastic third metacarpals. He had only the index finger on his right hand, while his left hand exhibited an index finger and a hypoplastic middle finger ([Fig. 1D]). In the feet, the middle three toes were absent, with hypoplasia and syndactyly of the corresponding metatarsals ([Fig. 1E]). These findings suggested an autosomal dominant, non-syndromic genetic etiology.

Whole-exome sequencing (WES) and chromosomal microarray analysis were performed first on the husband, followed by chromosomal microarray analysis of the second fetus, whose DNA had been preserved.

Results

WES of the husband did not identify any pathogenic variants. However, chromosomal microarray analysis revealed a 481-kb likely pathogenic duplication on chromosome 10, encompassing the 10q24.31q24.32 region, which is associated with SHFM type 3 (SHFM3). Similarly, chromosomal microarray analysis of the second fetus identified a 479-kb duplication in the 10q24.32 region ([Fig. 1F]). This duplicated region includes several OMIM genes: LBX1, BTRC, POLL, DPCD, and FBXW4.

The couple was counseled that the phenotype is due to contiguous gene duplication in the 10q24 region. They were informed that the recurrence risk for SHFM in each pregnancy is 50%, consistent with autosomal dominant inheritance. Various reproductive options, including advanced reproductive techniques, were discussed to help them make informed decisions.

Discussion

SHFM is a rare condition with a prevalence of 1 to 5 per 100,000 live births, accounting for approximately 15% of all limb reduction defects. While most cases are sporadic, familial occurrences are relatively uncommon. SHFM is both clinically and genetically heterogeneous, presenting in various forms: as an isolated anomaly, in association with other malformations, or as part of a syndrome.[1] [Table 1] provides an overview of the different types of SHFM, along with associated findings and syndromes.[2]

Table 1 Different types of split hand foot malformation (SHFM)

Type	Chromosome/gene involved	Pattern of inheritance	Associated findings/syndromes
SHFM1	DLX5 gene Deletion/duplication/rearrangement of the 7q21.3 region	Autosomal dominant	Ectrodactyly, ectodermal dysplasia, and cleft lip palate (EEC) Sensorineural hearing loss Intellectual disability Triphalangeal thumb
SHFM1 with sensorineural hearing loss	DLX5 gene	Autosomal recessive	Sensorineural hearing loss
SHFM2	Xq26	X-linked	–
SHFM3	Duplication 10q24.31q24.32	Autosomal dominant	Triphalangeal/duplicated thumbs Facial dysmorphism Intellectual disability Other congenital anomalies
SHFM4	TP63 gene	Autosomal dominant	Triphalangeal/duplicated thumbs
SHFM5	Deletion 2q31	Autosomal dominant	Microcephaly Microphthalmia
SHFM6	WNT10B gene	Autosomal recessive	Sparse hair and interrupted eyebrows
SHFM7 with mesoaxial polydactyly	ZAK gene	Autosomal recessive	Hearing impairment
SHFM8	EPS15L1 gene	Autosomal recessive	–
SHFLD1	1q42.2q43	Autosomal dominant	Tibial aplasia/hypoplasia
SHFLD2	6q14.1	Autosomal dominant
SHFLD3	Duplication 17p13.3 Microduplications involving BHLHA9	Autosomal dominant

Abbreviation: SHFLD, split hand foot malformation with long bone deficiency.

The autosomal dominant mode of inheritance is the most common in SHFM, with the exception of SHFM types 6, 7, and 8, which follow an autosomal recessive pattern, and SHFM type 2, which is X-linked. A total of 36 cases of SHFM have been reported from India; however, only 7 cases each of SHFM1 and SHFM6, and 5 cases of SHFM3 have been molecularly confirmed.[3] [4] [5] SHFM exhibits high intrafamilial and inter-individual variability, as well as reduced penetrance. Additionally, variability can manifest as differing patterns of anomalies across the limbs of the same patient.[6] The clinical phenotype ranges from mild to severe, including hypoplasia of a single phalanx, aplasia of one or more central digits, or even monodactyly.[5] These variations may be influenced by epigenetic and/or environmental factors. Due to the marked clinical heterogeneity, establishing a specific diagnosis based solely on clinical presentation remains challenging.

SHFM is caused by abnormalities in the Wnt-BMP-FGF signaling pathway, which plays a crucial role in the development of the central portion of the apical ectodermal ridge (AER). To date, mutations in CDH3, DLX5, EVX2, FGFR1/2, HOXD, MAP3K20, TP63, and WNT10B genes have been identified as being associated with SHFM. Additionally, microdeletions in the 2q31 and 17q25 regions, as well as microduplications in the 10q24 and 17p13.3 regions, have been linked to the condition. In prenatal cases, deletions in the 2q21.33 region, a terminal deletion at 7q31, and a 22q11.2 deletion have been identified in fetuses with SHFM accompanied by congenital anomalies.[7] [8] Duplications at 17p13.3 encompassing the BHLHA9 gene are associated with SHFM with long bone deficiency. The BHLHA9 gene encodes a basic helix-loop-helix (bHLH) transcription factor that regulates target genes critical for the proliferative zone and maintenance of AER. These duplications are characterized by variable expressivity and a high degree of non-penetrance, particularly in females, suggesting possible sex-influenced modifiers or epigenetic regulation or environmental factors may modulate the phenotypic outcome.[9]

SHFM3 is one of the most common causes of SHFM and follows an autosomal dominant inheritance pattern.[1] It is characterized by complete penetrance and variable expressivity. In SHFM3, preaxial involvement of the upper extremities, such as triphalangeal thumb or preaxial polydactyly, is frequently observed.[6] [10] Complex polydactyly has been reported in one case and cutaneous syndactyly has also been reported in a few cases.[5] [11] [12]

Duplications of the 10q24 region are the most common cause of SHFM, accounting for approximately 20% of cases, followed by 17p13.3 duplications in 13% of cases.[1] The phenotype of SHFM3 is attributed to the involvement of several OMIM genes within or near the duplicated region, including TLX1, LBX1, BTRC, POLL, FBXW4, DPCD, FBXW4, and FGF8. The size of duplication varies from 325 to 650 Kb. In most cases, the chromosomal duplication encompasses an intergenic segment extending from a region centromeric to LBX1 to a region telomeric to FBXW4.[12] [13]

According to Dimitrov et al, duplication in the 10q24.31q24.32 region can result in a syndromic form of SHFM that includes intellectual disability, seizures, hearing loss, and congenital anomalies.[2] [13] In addition, gonadal mosaicism was reported in one family. However, in our family, no other abnormalities or intellectual disability were observed.

The exact reason why 10q24 duplications cause isolated SHFM3 in some patients while being associated with additional anomalies and intellectual disability in others remains unknown. Variability in intellectual disability may be attributed to triplication and duplication of the 10q24.31q24.32 region, with triplication associated with an increased risk[13]; however, the underlying cause of extra-skeletal abnormalities remains unexplained. Notably, there is no correlation between the size of the 10q24 duplication and the presence of additional anomalies.[14] The precise mechanisms underlying the phenotypic variability remain to be elucidated.

Among the genes, BTRC, FBXW4, SUFU, and FGF8 are expressed in the developing limbs. FGF8, a fibroblast growth factor expressed in the AER, is required for limb patterning. Tandem duplications at chromosome 10q24 consistently include at least the FBXW4 gene.[15] FBXW4 is involved in ubiquitin-mediated protein degradation and is considered the most likely candidate gene.[13] Duplications typically encompass the BTRC and POLL genes but were initially thought to be insufficient to cause SHFM3. Recently, it has been proposed that overexpression of BTRC (duplication of the first exon of the BTRC gene), which is involved in key signaling pathways such as the Wnt/β-catenin and Sonic Hedgehog pathways, contributes to the phenotype.[12] In our case, the duplicated region included the genes LBX1, BTRC, POLL, DPCD, and FBXW4 ([Fig. 1F]).

As per Cova et al structural variants including inversions at the Lbx1/Fgf8 locus disrupt chromatin architecture and result in misexpression of the FGF8 gene and activation of the LBX1 and BTRC genes, highlighting the complex regulatory mechanisms underlying SHFM3.[16] A microduplication of 120 Kb involving only the BTRC gene has been identified in a Chinese family.[17]

To date, no intragenic sequence variants have been reported in these genes.

The differential diagnosis of SHFM includes oligodactyly and digit amputation due to amniotic band syndrome. While the diagnosis of SHFM can be made through ultrasound, it cannot distinguish between non-syndromic and syndromic SHFM, nor can it determine the specific type of SHFM or provide an accurate prognosis for the fetus.

Conclusion

Although ultrasound can detect SHFM, identifying the genetic etiology is crucial for classifying the type of SHFM, especially in cases of sporadic occurrence. Some cases are syndromic and may have additional features that are not detectable by ultrasound, or may evolve later in gestation, or to identify mildly affected fetuses where the anomaly is not clear on scan. In families with a history of non-syndromic SHFM and an increased risk of recurrence, genetic testing becomes particularly useful for couples considering reproductive options such as in vitro fertilization with preimplantation genetic testing.

Conflict of Interest

None declared.

• References

• 1 Holder-Espinasse M, Jamsheer A, Escande F. et al. Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet 2019; 27 (04) 525-534
• 2 Umair M, Hayat A. Nonsyndromic split-hand/foot malformation: recent classification. Mol Syndromol 2020; 10 (05) 243-254
• 3 Sivasankaran A, Srikanth A, Kulshreshtha PS, Anuradha D, Kadandale JS, Samuel CR. Split hand/foot malformation associated with 7q21.3 microdeletion: a case report. Mol Syndromol 2016; 6 (06) 287-296
• 4 Kantaputra PN, Kapoor S, Verma P, Intachai W, Ketudat Cairns JR. Split hand-foot malformation and a novel WNT10B mutation. Eur J Med Genet 2018; 61 (07) 372-375
• 5 Langeh N, Ansari MT, Kabra M, Gupta N. Split-hand/foot malformation 3 resulting from microduplications in 10q24 region in five patients from India. Am J Med Genet A 2024; 194 (05) e63520
• 6 Elliott AM, Reed MH, Roscioli T, Evans JA. Discrepancies in upper and lower limb patterning in split hand foot malformation. Clin Genet 2005; 68 (05) 408-423
• 7 Elliott AM, Evans JA. The association of split hand foot malformation (SHFM) and congenital heart defects. Birth Defects Res A Clin Mol Teratol 2008; 82 (06) 425-434
• 8 Lu J, Vaidya N, Meng H. et al. Prenatally diagnosed fetal split-hand/foot malformations often accompany a spectrum of anomalies. J Ultrasound Med 2014; 33 (01) 167-176
• 9 Klopocki E, Lohan S, Doelken SC. et al. Duplications of BHLHA9 are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion. J Med Genet 2012; 49 (02) 119-125
• 10 Sowińska-Seidler A, Socha M, Jamsheer A. Split-hand/foot malformation - molecular cause and implications in genetic counseling. J Appl Genet 2014; 55 (01) 105-115
• 11 Ockeloen CW, Cobben JM, Marcelis CLM, Koolen DA. A rare complex malformation of the hand in split hand foot malformation type 3 (SHFM3). Clin Dysmorphol 2013; 22 (03) 106-108
• 12 Li CF, Angione K, Milunsky JM. Identification of critical region responsible for split hand/foot malformation type 3 (SHFM3) phenotype through systematic review of literature and mapping of breakpoints using microarray data. Microarrays (Basel) 2015; 5 (01) 2
• 13 Dimitrov BI, de Ravel T, Van Driessche J. et al. Distal limb deficiencies, micrognathia syndrome, and syndromic forms of split hand foot malformation (SHFM) are caused by chromosome 10q genomic rearrangements. J Med Genet 2010; 47 (02) 103-111
• 14 Cao L, Yang W, Wang S, Chen C, Zhang X, Luo Y. Molecular genetic characterization of a chinese family with severe split hand/foot malformation. Genet Test Mol Biomarkers 2017; 21 (06) 357-362
• 15 Lyle R, Radhakrishna U, Blouin JL. et al. Split-hand/split-foot malformation 3 (SHFM3) at 10q24, development of rapid diagnostic methods and gene expression from the region. Am J Med Genet A 2006; 140 (13) 1384-1395
• 16 Cova G, Glaser J, Schöpflin R. et al. Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3. Nat Commun 2023; 14 (01) 1475
• 17 Qiu L, Li C, Zheng G, Yang T, Yang F. Microduplication of BTRC detected in a Chinese family with split hand/foot malformation type 3. Clin Genet 2022; 102 (05) 451-456

Publication History

Article published online:
12 December 2025