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Journal of Pediatric Surgery (2008) 43, 391–393

Independent case reports

Two coding single nucleotide polymorphisms in the SALL1gene in Townes-Brocks syndrome: a case report and reviewof the literatureYing Liang, Dihua Shen, Wei Cai⁎

Department of Pediatric Surgery, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to School of Medicine,Shanghai Jiaotong University, Shanghai 200092, China

Received 16 July 2007; revised 20 September 2007; accepted 21 September 2007

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Index words:Townes-Brocks syndrome;SALL1 gene;Single nucleotidepolymorphism

Abstract Townes-Brocks syndrome (TBS) is an autosomal dominantly inherited malformation syndromecharacterized by imperforate anus and limb and earmalformationswith sensorineural hearing loss.Mutationsin SALL1, a gene mapping to chromosome 16q21.1, are responsible for TBS. Here, we described a16-month-old male patient with typical TBS clinical features including imperforate anus and preaxialpolydactyly. Two coding polymorphism sites were identified in this case. One is silent (rs1965024, 2574 C NT), whereas the other yields a new codon encoding a different amino acid (rs4614723, 3823 G NA). The hotspot mutations in exon 2 were not suggested. Therefore, lack of SALL1 gene mutations and the presence ofvariable phenotypes in the sporadic cases might suggest DNA alternations in the noncoding regions ofSALL1 gene and/or in other genes modulating SALL1 gene expression or functions.© 2008 Published by Elsevier Inc.

Townes and Brocks [1] described in 1972 an autosomaldominant malformation syndrome presenting with imperfo-rate anus, triphalangeal and supernumerary thumbs, fusion ofmetatarsals, absent bones, external ear anomalies (lop ears),and mild sensorineural deafness. Besides the anorectal, limb,and ear anomalies, further malformations are composed ofrenal, genitourinary, cardiac abnormalities and mentalretardation, including renal hypoplasia/dysplasia, ureterove-sical reflux, meatal stenosis, truncus arteriosus, pulmonaryvalve atresia, and tetralogy of Fallot [2-8]. Thus, the clinicalmanifestations of Townes-Brocks syndrome (TBS [MIM#23107480]) are highly variable. Mutations in SALL1 (MIM#

⁎ Corresponding author. Department of Pediatric Surgery,XinhuaHospitalffiliated to School of Medicine, Shanghai Jiaotong University, Shanghai00092, China. Tel.: +86 21 6501 1627; fax: +86 21 6501 1627.

E-mail address: caiw204@yahoo.com.cn (W. Cai).

022-3468/$ – see front matter © 2008 Published by Elsevier Inc.oi:10.1016/j.jpedsurg.2007.09.079

3602218), a human homologue of the Drosophila spalt gene,which encodes a transcription factor, have been identified tobe responsible for TBS [9]. Here, we analyzed one sporadicTBS case for SALL1 gene mutations.

1. Case report

The index boy is the second child of healthy nonconsan-guineous parents. He was delivered by cesarean birthbecause of breech presentation at 38 weeks of gestation. Atbirth, the patient was noted to have imperforate high anteriorpositioned anus with rectovesical fistula and preaxialpolydactyly of the left hand (Fig. 1). No external eardeformities were seen in this patient. Abdominal ultrasoundat day 5 and echocardiography at 16 months did not reveal

Fig. 1 Preaxial polydactyly of left hand.

392 Y. Liang et al.

any renal and cardiac abnormalities. Magnetic resonanceimaging scanning showed imperforate anus with no sacrumor coccygeal defect. Physical development at the age of16 months was normal. There were no affected familymembers, including his 9-year-old sister.

2. Genetic analysis

Genomic DNA was prepared from peripheral lympho-cytes by routine procedures. Mutation analysis of exons 1, 2,and 3 of SALL1 was performed by polymerase chain reactionand direct sequencing of polymerase chain reaction productsas described previously [10].

Two polymorphism sites in the SALL1 genewere identified.One is a synonymous single nucleotide polymorphism (SNP)rs1965024. The heterozygous nucleotide change at position2574 C N T was a silent polymorphism (Fig. 2A), which hasalso been reported in Marlin et al [11]. The other is anonsynonymous SNP rs4614723 at position 3823 G N A(V1275I,V =Val = valine =GTT, I = Ile = isoleucine =ATT) inexon 3 (Fig. 2B). The hot spot mutations in exon 2 were notsuggested by our data. No SALL1 gene mutations weredetected in his parents. The healthy sister is not available formutation analysis. Nucleotides of the transcriptwere numberedsequentially from the first nucleotide of the ATG initiationcodon according to the sequence of NM_002968.

ig. 2 Sequence analysis of the SALL1 gene showing a singleucleotide change at position 2574 C N T in exon 2 (asterisk in A)nd at position 3823 G N A in exon 3 (asterisk in B).

3. Discussion

Townes-Brocks syndrome is an autosomal dominantlyinherited malformation syndrome with multiple cases ofmale-to-male transmission. Serville et al [4] have mapped

chromosome 16q12.1 as one of the breakpoints in TBS,which is suggested to be the location of the gene for TBS.The gene SALL1, a human homologue of drosophila region-specific homeotic gene spalt (sal), located on 16q12.1,becomes the candidate gene for TBS [12]. Two differentheterozygous mutations in the SALL1 gene were firstidentified to cause TBS in 1998 [9].

The gene SALL1, a human putative zinc finger transcrip-tion factor gene, encodes a zinc finger protein thought to actas a transcriptional repressor. The SALL1 protein has 4highly conserved C2H2 double zinc finger units evenlydistributed. A single C2H2 motif is attached to the seconddomain and a C2HC motif at the amino terminus [9,12].

Fna

393Two coding SNPs in the SALL1 gene in Townes-Brocks Syndrome

To date, most of SALL1 gene mutations reported reside inexon 2, in particular, 5′ to or within the region encoding thefirst double zinc finger [8-11,13-15]. Among them, themutation 826 C N T in a CG dimmer identified by severalresearch groups revealed the existence of a mutation hotspot [8,10,11]. Therefore, it is predicted that mutations leadto a preterminal stop codon and produce a truncated SALL1protein lacking all 4 double zinc finger domains [9,10].In addition, Blanck et al [16] also reported that SALL1mutation could occur within the fourth double zinc finger–encoding region.

The SALL1 protein is expressed in human fetal and adultbrain and kidney, and is exclusively located in the nucleusand pericentromeric heterochromatin foci [12,17]. It interactswith an isoform of telomere repeat-binding factor andtherefore could function as a direct or indirect repressor inthe regulation of higher-order chromatin structures duringhuman development [17,18].

The index patient has the typical TBS manifestations,including imperforate anus and preaxial polydactyly. How-ever, no SALL1 gene mutations were detected, except that 2coding SNPs were suggested. Until now, most SNPs areidentified outside of coding sequences. Single nucleotidepolymorphisms found within the coding region are ofparticular interest because they are more likely to alter thebiologic function of the encoded protein. However, not allthe coding SNPs are functional, even including thoseyielding a new codon that encodes a different amino acid,in particular, not disrupting a well-characterized domain thataffects protein structure and function [19]. The presence of anormal SALL1 coding sequence in a patient with TBSindicates the possible involvement of the noncoding regionsof SALL1 gene and/or other genes regulating SALL1 geneexpression or functions during the pathogenesis of TBS.

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