A classification system for split-hand/ foot malformation (SHFM): A proposal based on 3 pedigrees with WNT10B mutations

SHFM6 (OMIM 225300) is caused by WNT10B pathogenic variants (12q13.12). It is one of the rarest forms of SHFM; with only seven pathogenic variants described in the world literature. Furthermore, it has not been determined if SHFM6 has specific phenotypic characteristics.In this paper, we present a case series of three unrelated families with SHFM6 caused by three novel WNT10B pathogenic variants. The index patient of the first family was homozygous for the nonsense variant c.676C > T (p.Arg226*) in the WNT10B gene. The index case of the second family had a homozygous splice variant c.338-1G > C in the WNT10B gene. Finally, the index case of the third family carried two different variants in the WNT10B gene: A nonsense variant (p.Arg226*), and a missense variant (p.Gln86Pro). The latter represents the first compound heterozygous pathogenic variant related to SHFM6. We also offer a classification system for the hand/foot defects to illustrate the specific phenotypic characteristics of SHFM6. Based on this classification and a review of all previously reported cases, we demonstrate that SHFM6 caused by WNT10B pathogenic variants have the following characteristics: more severe feet defects (compared to the hand defects), polydactyly, severe flexion digital contractures, and phalangeal dysplasia.     

A novel homozygous missense mutation in WNT10B in familial split-hand/foot malformation

Split-hand/foot malformation (SHFM) is a rare limb developmental malformation, characterized by variable degree of median clefts of hands and feet due to the absence of central rays of extremities. To date, six different forms of SHFM have been described. Four of these SHFM1, SHFM3, SHFM4 and SHFM5 show autosomal dominant, SHFM6 autosomal recessive and SHFM2 X-linked pattern of inheritance. In this study a large consanguineous Pakistani family, with autosomal recessive SHFM, appeared in the last two generations, was investigated. In total 15 individuals including 9 males and 6 females were affected with the syndrome. Affected members of the family exhibited SHFM phenotype with involvement of hands and feet. Most of the affected members showed syndactyly/polydactyly in hands and feet, dysplastic hand, aplasia of radial ray of hand and cleft foot. Investigating linkage to known autosomal SHFM loci mapped the family to SHFM6 locus on chromosome 12p11.1-q13.13. Mutation screening of the gene WNT10B revealed a novel sequence variant (c.986C>G, p.Thr329Arg) in all affected individuals who were studied. This is the third mutation reported in gene WNT10B causing autosomal recessive SHFM syndrome.     

Genetic regulatory pathways of split-hand/foot malformation

Split-hand/foot malformation (SHFM) is caused by mutations in TP63, DLX5, DLX6, FGF8, FGFR1, WNT10B, and BHLHA9. The clinical features of SHFM caused by mutations of these genes are not distinguishable. This implies that in normal situations these SHFM-associated genes share an underlying regulatory pathway that is involved in the development of the central parts of the hands and feet. The mutations in SHFM-related genes lead to dysregulation of Fgf8 in the central portion of the apical ectodermal ridge (AER) and subsequently lead to misexpression of a number of downstream target genes, failure of stratification of the AER, and thus SHFM. Syndactyly of the remaining digits is most likely the effects of dysregulation of Fgf-Bmp-Msx signaling on apoptotic cell death. Loss of digit identity in SHFM is hypothesized to be the effects of misexpression of HOX genes, abnormal SHH gradient, or the loss of balance between GLI3A and GLI3R. Disruption of canonical and non-canonical Wnt signaling is involved in the pathogenesis of SHFM. Whatever the causative genes of SHFM are, the mutations seem to lead to dysregulation of Fgf8 in AER cells of the central parts of the hands and feet and disruption of Wnt-Bmp-Fgf signaling pathways in AER.     

WNT10B mutations associated with isolated dental anomalies

Isolated hypodontia is the most common human malformation. It is caused by heterozygous variants in various genes, with heterozygous WNT10A variants being the most common cause. WNT10A and WNT10B are paralogs that likely evolved from a common ancestral gene after its duplication. Recently, an association of WNT10B variants with oligodontia (severe tooth agenesis) has been reported. We performed mutational analysis in our cohort of 256 unrelated Thai families with various kinds of isolated dental anomalies. In 7 families afflicted with dental anomalies we detected 4 heterozygous missense variants in WNT10B. We performed whole exome sequencing in the patients who had WNT10B mutations and found no mutations in other known hypodontia‐associated genes, including WNT10A, MSX1, PAX9, EDA, AXIN2, EDAR, EDARADD, LPR6, TFAP2B, LPR6, NEMO, KRT17, and GREM2. Our findings indicate that the variants c.475G>C [p.(Ala159Pro)], found in 4 families, and c.1052G>A [p.(Arg351His)], found in 1 family, are most probably causative. They also show that WNT10B variants are associated not only with oligodontia and isolated tooth agenesis, but also with microdontia, short tooth roots, dental pulp stones, and taurodontism.     

Split hand-foot malformation and a novel WNT10B mutation

We report an Indian girl with split-hand/foot malformation (SHFM), sparse hair, and interrupted eyebrows, who carries a novel homozygous deletion c.695_697delACA in WNT10B. The variant is deduced to cause an in-frame deletion of Asn residue 232 (p.Asn232del). According to the protein model, this single amino acid deletion at the critical position in the protein structure is likely to severely affect the protein structure and function. This deletion is likely to lead decreased lifetime and make it unable to bind to its receptors and other ligands. The patient and all family members had normal bone density and they were not obese like some of the patients with WNT10B variants. Here we report a patient with SHFM6 who carried a novel WNT10B mutation. Sparse hair and interrupted eyebrows may be associated findings of SHFM6.     

一个非综合征手足裂畸形家系的临床调查及遗传学分析

目的分析一先天性手足裂伴并指／趾畸形家系的临床表现，并从分子水平查找致病原因，为罹患家庭提供遗传咨询。方法通过X线检查资料及手足裂外观照片，对家系3代现存3例患者（共4例患者）进行临床分析，对3例患者用常规方法制备外周血淋巴细胞染色体标本，进行G显带核型分析。从7名家系成员（包含3例患者）外周血样品中提取基因组DNA。针对p63基因全部15个外显子及删rJ0b基因5个外显子进行引物设计合成、PCR扩增、回收纯化并测序。结果家系中现存3名患者均表现为双手中央分裂，其中1例患者双足呈楔形裂开，2例患者右足均为第3、4趾并指，皮肤黏连；G显带核型分析未发现染色体畸变；p63基因未检测到突变，删rJ0b基因的外显子5a中发现一个碱基突变c．1058C〉T。结论通过家系内息者临床表型分析，可将该疾病类型确定为非综合征手足裂畸形，且临床症状逐代加重。测序结果提示p63基因和删rJ0b基因关键区域内的点突变都不是引起该家系手足裂畸形的原因。     

Frequency of genomic rearrangements involving the SHFM3 locus at chromosome 10q24 in syndromic and non-syndromic split-hand/foot malformation

Split-hand/foot malformation (SHFM), or ectrodactyly, is characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM occurs as both an isolated finding and a component of many syndromes. SHFM is a heterogeneous condition caused by multiple loci, including SHFM1 (chromosome region 7q21-q22), SHFM2 (Xq26), SHFM3 (10q24), SHFM4 (3q27), and SHFM5 (2q31). Mutations in TP63 at the SHFM4 locus are known to underlie both syndromic and non-syndromic forms SHFM, but the causes of most non-syndromic SHFM cases remain unknown. The recent identification of submicroscopic tandem chromosome duplications affecting the SHFM3 locus in seven families with non-syndromic SHFM has helped to further unravel the molecular basis of this malformation. In our ongoing studies of the SHFM3 locus in 44 additional cases of syndromic and non-syndromic SHFM, we have identified similar chromosome rearrangements in eight additional cases (18%), using pulsed-field gel electrophoresis (PFGE). We have also utilized real-time quantitative PCR (qPCR) to test for the duplications. Seven of the cases with rearrangements were non-syndromic. The current findings bring the total of SHFM3-associated cases with chromosome rearrangements to 15, which constitute 29% (15 of 51) of the cases screened to date. This includes 9 of 9 cases (100%) with known linkage to the SHFM3 locus, all of whom have non-syndromic SHFM, and 6 of 42 additional cases (14%), four of whom have non-syndromic SHFM. Thus, SHFM3 abnormalities underlie a substantial proportion of SHFM cases and appear to be a more frequent cause of non-syndromic SHFM than mutations in TP63.     

First direct evidence of involvement of a homozygous loss‐of‐function variant in the EPS15L1 gene underlying split‐hand/split‐foot malformation

Split‐hand/split‐foot malformation (SHFM) is a severe form of congenital limb deformity characterized by the absence of 1 or more digits and/or variable degree of median clefts of hands and feet. The present study describes an investigation of a consanguineous family of Pakistani origin segregating SHFM in an autosomal recessive manner. Human genome scan using SNP markers followed by whole exome sequencing revealed a frameshift deletion (c.409delA, p.Ser137Alafs*19) in the EPS15L1 gene located on chromosome 19p13.11. This is the first biallelic variant identified in the EPS15L1 gene underlying SHFM. Our findings report the first direct involvement of EPS15L1 gene in the development of human limbs.     

一个中国手足裂畸形家系的遗传学分析

目的研究中国人手足裂畸形家系产生的分子遗传基础。方法通过X光片对一家系4代手足裂畸形患者进行了临床分析,采集了家系成员中18人的外周静脉血并提取基因组DNA。利用微卫星标记对该家系进行基因组扫描、连锁分析以及单倍型分析,并对于候选区域内的指趾发育相关基因Dactylin(DAC)基因的编码区、外显子/内含子交界区域以及部分的启动子区域进行测序分析。结果该家系大部分患者食指缺失或者发育不全,中指以缺指或以3、4并指出现,脚趾畸形程度略高于手指,表型特征符合已报道的手足裂畸形症的基本特征。两点间连锁分析在D10S192处获得最大的LOD值Z=3.50(θ=0.00),将该家系临床类型确定为SHFM3型手足裂畸形,单倍型分析将该家系的致病基因定位于D10S185和D10S1693之间约21cM的范围内,在对DAC基因测序中,未检测到任何的序列突变。结论通过对家系内表型分析,可将疾病类型确定为典型的手足裂畸形症,并将致病基因定位于10q23-q26约21cM范围内,测序结果显示DAC基因的点突变不是引发该家系手足裂畸形的原因。     

Wolf-Hirschhorn syndrome and a split-hand malformation

Ectrodactyly has not previously been reported in children with Wolf-Hirschhorn syndrome (WHS). Based on this premise and the identification of an unbalanced translocation between chromosomes 4p15 and 10q25 in a fetus with ectrodactyly and hemimelia, a second locus for dominantly inherited split hand/foot malformation (SHFM3) was mapped to chromosome 10q24–q25. We present the clinical findings of an infant with WHS and SHFM and suggest that the presence of additional loci on 4p which modify/cause SHFM cannot be excluded. Am. J. Med. Genet. 75:351-354, 1998. © 1998 Wiley-Liss, Inc.     

Split hand/foot malformation associated with 20p12.1 deletion: A case report

Split hand/foot malformation (SHFM) or ectrodactyly is a rare congenital disorder affecting limb development characterized by clinical and genetic heterogeneity. SHFM is usually inherited as an autosomal dominant trait with incomplete penetrance. Isolated and syndromic forms are described. The extent of associated malformations is highly variable and multiple syndromes with clinical and genetic overlap have been described. We report here a 28 year-old man presenting with SHFM, sparse hair and widespread freckles. Array-CGH identified a 450 kb de novo 20p12.1 microdeletion encompassing three exons (exon 6 to 8) of MACROD2. Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Additionally, the deletion encompassed a histone modification H3K27ac mark, known as a provider of quantitative readout of promoter and enhancer activity during human limb development. Altogether, these findings suggest that the 20p12.1 CNV is causative of SHFM in the present case through disturbance of regulatory elements functioning.     

Deletion 7q21.2-q22.1 in a case with split hand-split foot malformation,sensorineural hearing loss and intellectual disability: Phenotype subtypes and the correlation with genotypes

The split hand/split foot malformation (SHFM) or ectrodactyly is a rare congenital heterogeneous limb developmental disorder with at least 6 associated loci. It is characterized by absence of central rays of hands and feet and fusion of remaining digits. It can present as an isolated malformation or in combination with additional anomalies (non-syndromic or syndromic ectrodactyly). This is a report of a 4 year old male child with SHFM with facial dysmorphism, profound sensorineural hearing loss, microcephaly and developmental delay associated with a large deletion of 7.242 MB on chromosome 7q21.2-q22.1. This is the region of SHFM1 (OMIM No. 183600) and deletions of varying sizes have been reported. We have reviewed the phenotypes and genotypes of this locus. The deletions with this severe phenotype are large and some of them detected on traditional karyotyping. The cases with submicroscopic deletions are few but show some correlation of genotype with phenotype which will help in counseling the families with prenatally or neonatally detected deletion at this locus.     

Mutations in WNT9B are associated with Mayer–Rokitansky–Küster–Hauser syndrome

Mayer–Rokitansky–Küster–Hauser syndrome (MRKHS) is a well‐known malformation pattern of the Müllerian ducts (MDs) characterized by congenital absence of the uterus and vagina. To date, most cases remain unexplained at molecular level. As female Wnt9b‐/‐ mice show a MRKHS‐like phenotype, WNT9B has emerged as a promising candidate gene for this disease. We performed retrospective sequence analyses of WNT9B in 226 female patients with disorders of the MDs, including 109 patients with MRKHS, as well as in 135 controls. One nonsense mutation and five likely pathogenic missense mutations were detected in WNT9B. Five of these mutations were found in cases with MRKHS accounting for 4.6% of the patients with this phenotype. No pathogenic mutations were detected in the control group (p = 0.017). Interestingly, all of the MRKHS patients with a WNT9B mutation were classified as MRKHS type 1, representing 8.5% of the cases from this subgroup. In previous studies, two of the patients with a WNT9B mutation were found to carry either an additional deletion of LHX1 or a missense mutation in TBX6. We conclude that mutations in WNT9B were frequently associated with MRKHS in our cohort and some cases may be explained by a digenic disease model.     

Split hand/foot malformation with long‐bone deficiency and BHLHA9 duplication: report of 13 new families

Split hand/foot malformation (SHFM) with long‐bone deficiency (SHFLD, MIM#119100) is a rare condition characterized by SHFM associated with long‐bone malformation usually involving the tibia. Previous published data reported several unrelated patients with 17p13.3 duplication and SHFLD. Recently, the minimal critical region had been reduced, suggesting that BHLHA9 copy number gains are associated with this limb defect. Here, we report on 13 new families presenting with ectrodactyly and harboring a BHLHA9 duplication.     

Congenital posterior cervical spine malformation due to biallelic c.240‐4T>G RIPPLY2 variant: A discrete entity

The clinical and radiological spectrum of spondylocostal dysostosis syndromes encompasses distinctive costo‐vertebral anomalies. RIPPLY2 biallelic pathogenic variants were described in two distinct cervical spine malformation syndromes: Klippel–Feil syndrome and posterior cervical spine malformation. RIPPLY2 is involved in the determination of rostro‐caudal polarity and somite patterning during development. To date, only four cases have been reported. The current report aims at further delineating the posterior malformation in three new patients. Three patients from two unrelated families underwent clinical and radiological examination through X‐ray, 3D computed tomography and brain magnetic resonance imaging. After informed consent was obtained, family‐based whole exome sequencing (WES) was performed. Complex vertebral segmentation defects in the cervico‐thoracic spine were observed in all patients. WES led to the identification of the homozygous splicing variant c.240‐4T>G in all subjects. This variant is predicted to result in aberrant splicing of Exon 4. The current report highlights a subtype of cervical spine malformation with major atlo‐axoidal malformation compromising spinal cord integrity. This distinctive mutation‐specific pattern of malformation differs from Klippel–Feil syndrome and broadens the current classification, defining a sub‐type of RIPPLY2‐related skeletal disorder. Of note, the phenotype of one patient overlaps with oculo‐auriculo‐vertebral spectrum disorder.     

Novel association of Dandy–Walker malformation with CAPN15 variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome

Oculogastrointestinal neurodevelopmental syndrome has been described in seven previously published individuals who harbor biallelic pathogenic variants in the CAPN15 gene. Biallelic missense variants have been reported to demonstrate a phenotype of eye abnormalities and developmental delay, while biallelic loss of function variants exhibit phenotypes including microcephaly and craniofacial abnormalities, cardiac and genitourinary malformations, and abnormal neurologic activity. We report six individuals from three unrelated families harboring biallelic deleterious variants in CAPN15 with phenotypes overlapping those previously described for this disorder. Of the individuals affected, four demonstrate radiographic evidence of the classical triad of Dandy–Walker malformation including hypoplastic vermis, fourth ventricle enlargement, and torcular elevation. Cerebellar anomalies have not been previously reported in association with CAPN15-related disease. Here, we present three unrelated families with findings consistent with oculogastrointestinal neurodevelopmental syndrome and cerebellar pathology including Dandy–Walker malformation. To corroborate these novel clinical findings, we present supporting data from the mouse model suggesting an important role for this protein in normal cerebellar development. Our findings add six molecularly confirmed cases to the literature and additionally establish a new association of Dandy–Walker malformation with biallelic CAPN15 variants, thereby expanding the neurologic spectrum among patients affected by CAPN15-related disease.