Novel mutation in the SALL1 gene in a four-generation Chinese family with uraemia: A case report.

BACKGROUND: Approximately 10% of adults and nearly all children who receive renal replacement therapy have inherited risk factors or are related to genetic factors. In the past, due to the limitations of detection technology and the nonspecific manifestations of uraemia, the etiological diagnosis is unclear. In addition to common monogenic diseases and complex disorders, advanced testing techniques have led to the recognition of more hereditary renal diseases. Here, we report a four-generation Chinese family in which four individuals had a novel SALL1 mutation and presented with uraemia or abnormal urine tests. CASE
SUMMARY: A 32-year-old man presented with end-stage renal disease with a 4-year history of dialysis. His father and paternal aunt both had a history of unexplained renal failure with haemodialysis, and his 10-year-old daughter presented with proteinuria. The patient had multiple congenital abnormalities, including bilateral overlapping toes, unilateral dysplastic external ears, and sensorineural hearing loss. His family members also presented with similar defects. Genetic testing revealed that the proband carried a novel heterozygous shift mutation in SALL1_exon 2 (c.3437delG), and Sanger sequencing confirmed the same mutation in all affected family members.
CONCLUSION: We report a novel SALL1 exon 2 (c.3437delG) mutation and clinical syndrome with kidney disease, bilateral overlapping toes, unilateral dysplastic external ears, and sensorineural hearing loss in a four-generation Chinese family. ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.

Core Tip: We report a novel SALL1 exon 2 (c.3437delG) mutation and clinical syndrome with kidney disease, bilateral overlapping toes, unilateral dysplastic external ears, and sensorineural hearing loss in a four-generation Chinese family. As patients with kidney diseases do not have specific clinical presentations, symptoms other than kidney disease were relatively hidden or easily ignored, thus resulting in missed diagnosis. Gene sequencing is recommended in patients with a family history and with extrarenal phenotypes to avoid blind use of immunosuppressive drugs, which may cause adverse effects.

INTRODUCTION

Hereditary kidney disease is one of the important causes of end-stage renal disease (ESRD) in patients requiring renal replacement therapy. Rapid advances in detection techniques have allowed more unexplained kidney diseases to be accurately diagnosed, including polycystic kidney disease, Alport syndrome, Fabry disease, Bartter syndromes, Gitelman syndromes, and other multifactorial disorders[1]. New genetic mutations causing kidney disease are constantly identified, along with other extrarenal phenotypes.

Townes-Brocks syndrome (TBS), first described by Townes and Brocks[2] in 1972, is a rare autosomal dominant disease resulting from mutations in the developmental gene SALL1[2]. Its main features are the triad of anorectal, hand, and external ear malformations. Another key characteristic of TBS is kidney involvement, which results in progression to ESRD early in life. A report of 154 patients with TBS identified renal anomalies in 43% of affected individuals[3]. Previous reports have shown that syndrome-related kidney and genitourinary defects include renal hypoplasia, unilateral renal agenesis, dysplastic kidneys, vesicoureteric reflux, meatal stenosis, and glandular hypoplasia[3]. Here, we report a four-generation family including four affected individuals suffering from kidney disease who carry a novel SALL1 mutation. Among them, three patients progressed to ESRD.

CASE PRESENTATION

Chief complaints

A 32-year-old man was admitted to our hospital because of ESRD characterized by severe hypertension and elevated serum creatinine (SCr) for 9 years and he had received renal dialysis for 4 years.

History of present illness

Nine years ago, the patient was admitted to a hospital because of syncope and was diagnosed with uraemia. After diagnosis, he was treated with traditional Chinese medicine. He started renal dialysis 4 years ago because of gradually deteriorating kidney function with a SCr level of 900 μmol/L. A kidney biopsy was not performed during the course of the kidney disease.

History of past illness

The patient was born with multiple congenital abnormalities, including limb malformation (bilateral overlapping toes) and unilateral dysplastic external ears (Figure 1). A unilateral moderate degree of sensorineural hearing loss was noted when he was 10 years old.

Figure 1

Clinical features of the proband. A: Unilateral dysplastic external ears. The left ear of the proband had a neoplasm on the earlobe; B: Bilateral overlapping toes, especially the second toes.

Personal and family history

The family pedigree for the patient (proband, III.3) is shown in Figure 2A. The patient’s grandmother (I.2) died at an early age without a clear diagnosis due to the poor level of medical care. However, she presented with a sixth finger malformation, unilateral dysplastic external ears, and hearing loss. The patient’s father (II.5) had unilateral dysplastic external ears, hearing loss, and bilateral overlapping toes. At the age of 53 years, he began dialysis therapy. The patient’s aunt (II.4) was born with unilateral dysplastic external ears, hearing loss, and limb malformation (unilateral preaxial polydactyly of one hand). At the age of 53 years, she also began haemodialysis due to unexplained ESRD. The patient’s daughter (IV.1) was born with bilateral dysplastic external ears, without limb malformation, and was found to have unilateral hearing dysfunction misdiagnosed as otitis media.

Figure 2

Pedigree and gene mutation of the family. A: Pedigree of the four-generation family; B: Analysis of SALL1 mutations revealed the heterozygous mutation c.3473delG in the proband (III.3).

Physical examination

Vital signs were in the normal ranges: Body temperature, 36.7 °C; respiratory rate, 18 breaths/min; pulse rate, 80 bpm; and blood pressure (under antihypertensive treatment), 134/85 mmHg. Limb malformation (bilateral overlapping toes) and unilateral dysplastic external ears existed. His ophthalmic examination results were normal, and no anorectal abnormalities were found.

Laboratory examinations

Laboratory analysis revealed an increased SCr level (941.9 μmol/L), high potassium level (6.87 mmol/L), high phosphate level (2.73 mmol/L), normal haemoglobin level (145 g/L), and high parathyroid hormone level (663.6 pg/mL). The patient was anuria.

Imaging examinations

Ultrasound examination revealed bilaterally small kidneys (left kidney, 52 mm × 34 mm; right kidney, 50 mm × 25 mm) with multiple 5-7 mm medullary cysts. The urinary tract was normal, and no additional abnormalities of the liver, spleen, or pancreas were detected in the imaging studies.

FINAL DIAGNOSIS

After obtaining informed consent, we conducted high-throughput detection and analysis of approximately 20000 genes of the proband, focusing on the genes related to uraemia and nephropathy. One pathogenic mutation, a heterozygous shift mutation in SALL1_ exon 2 (c.3437delG), was found to be related to the patient’s symptoms (Figure 2B). It was verified that the three relatives mentioned above carried the same mutation (Figure 2B). The genetic pattern of SALL1 associated with TBS is autosomal dominant. It is speculated that this pathogenic mutation is the main cause of familial hereditary disease. Finally, based on clinical features and the presence of the SALL1 pathogenic variant, the suspected diagnosis of TBS without imperforate anus was confirmed.

TREATMENT

The patient received maintenance haemodialysis three times a week, sevelamer carbonate tablets of 1.6 g three times per day, calcitriol soft capsules of 0.5 μg per day, and nifedipine controlled-release tablets of 60 mg per day.

OUTCOME AND FOLLOW-UP

The patient and two relatives were on dialysis and received regular follow-up. His daughter currently presents with minimal proteinuria and normal SCr. She was treated with losartan potassium tablets of 25 mg per day and was followed every 3 mo.

DISCUSSION

In this four-generation family diagnosed with TBS with renal manifestations, uraemia was the first symptom to prompt the affected members to go to the hospital. The diagnosis of TBS was confirmed by a genetic test in four family members, three of whom had already progressed to ESRF. This indicates that symptoms other than kidney disease were relatively hidden or easily ignored and resulted in missed diagnosis.

The transcoding mutation resulted in a change in the amino acid at position 1158 from glycine to glutamate, which changed the subsequent reading frame and caused advanced termination at the downstream codon 45. This mutation site has not been previously included in the ClinVar database. The frequency of mutation at this locus in the normal East Asian population has not been reported.

Since Townes and Brocks[2] first described TBS in 1972, hundreds of similar cases have been reported. It is characterized by ear anomalies, thumb anomalies (preaxial polydactyly, triphalangeal thumbs, and hypoplastic thumbs), and anal anomalies. The prevalence of TBS is estimated to be 1/250000[4]. The gene mutated in TBS is SALL1, which is located on chromosome 16q12.1 and encodes a zinc finger protein believed to act as a transcriptional repressor[5]. SALL1 is expressed in the metanephric mesenchyme surrounding the ureteric bud. Homozygous deletion of SALL1 produces incomplete ureteric bud outgrowth. Therefore, SALL1 is important for metanephros development[6]. Most mutations occur within a hotspot prior to the first C2H2 zinc finger domain encoded within exon 2 and result in the truncation of the protein upstream of the DNA binding domain[7].

In a murine experiment, all of the SALL1 knockout mice (SALL1-/-) died within 24 h after birth owing to renal agenesis or severe dysgenesis[6]. Mutant mice that produced a truncated SALL1 protein exhibited more severe defects than SALL1-null mice, including renal agenesis, exencephaly, and limb and anal deformities[8]. This finding may be explained by the fact that truncated proteins arising from certain SALL1 mutations can disrupt cilia formation and function. Therefore, TBS might be considered a ciliopathy-like disease, just as the proband presented with multiple renal cysts. A recent study showed that the Dishevelled Binding Antagonist Of Beta Catenin 1 (DACT1) c.1256G>A nonsense variant was causative of a specific genetic syndrome with features overlapping those of TBS[3]. Therefore, genetic testing to identify the mutated gene is critical for the diagnosis.

Newman first drew attention to symptomatic renal failure in TBS[9]. A previous study of TBS showed that 43% of affected individuals exhibited renal abnormalities. To determine genotype-phenotype correlations in the renal manifestations of TBS, we reviewed 76 affected individuals from 51 families, including 44 men (57.9%), 29 women (38.1%), and three (3.9%) for whom sex was not reported, giving a female-to-male ratio of 0.5:1. The details of the SALL1 gene variations and renal manifestations in these 76 patients with TBS are summarized in Table 1. Overall, 43 different variants were identified, including 29 frameshift mutations, 12 nonsense mutations, one intronic mutation, and one exonic deletion. The most common renal manifestations were renal hypodysplasia and unilateral renal agenesis (n = 25), followed by vesicoureteral reflux (n = 17). Almost half of the individuals had varying degrees of renal impairment, and 22% of the individuals progressed to renal failure. Some of the patients successfully underwent kidney transplantation, and two of them experienced graft rejection[3,7,9,10].

Table 1

Details of SALL1 gene variations in 76 patients diagnosed with Townes-Brocks syndrome with renal manifestations

Genetic finding	F/N	Gender	Phenotype						Ref.
			BRA	URA	PK	VR	RF	RFI
c.313delA	FA/N1	F	0/1	0/1	0/1	0/1	0/1	1/1	[7]
c.419delC	FA/N1	M	0/1	1/1	0/1	0/1	0/1	1	[15]
c.764delT	FA/N1	M	0/1	0/1	1/1	0/1	1/1	0/1	[3]
c.792delGC	FA/N2	M/F	0/2	1/2	0/2	2/2	0/2	0/2	[16]
c.817delG	FA/N1	M	0/1	1/1	0/1	0/1	1/1	0/1	[17]
c.981insTGGC	FA/N1	M	0/1	1/1	0/1	0/1	0/1	1/1	[18]
c.995delC	FA/N1	M	1/1	0/1	0/1	0/1	0/1	0/1	[7]
c.1047dupC	FA/N1	M	0/1	0/1	0/1	1/1	0/1	0/1	[7]
c.1119del79	FA/N1	F	1/1	0/1	0/1	0/1	1/1	0/1	[7]
c.1134delT	FA/N1	F	0/1	1/1	0/1	0/1	0/1	0/1	[7]
c.1145insTA	FA/N1	M	0/1	0/1	1/1	0/1	0/1	1/1	[3]
	FB/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[7]
c.1146delT	FA/N3	2F/M	0/3	2/3	0/3	0/3	0/3	3/3	[15]
c.1174delCT	FA/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[7]
c.1200del7	FA/N1	M	1/1	0/1	0/1	0/1	1/1	0/1	[15]
c.1263delC	FA/N1	F	1/1	0/1	0/1	0/1	1/1	0/1	[3]
c.1273delC	FA/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[7]
c.1277del2bp	FA/N1	F	0/1	0/1	0/1	0/1	0/1	1/1	[15]
c.1291del10	FA/N2	2M	2/2	0/2	0/2	0/2	0/2	2/2	[15]
c.1321dupA	FA/N1	F	0/1	1/1	0/1	0/1	0/1	1/1	[3]
c.1327delG	FA/N2	M/?	1/2	1/2	0/2	0/2	0/2	0/2	[3]
c.1347delCA	FA/N1	M	1/1	0/1	0/1	0/1	0/1	0/1	[19]
c.1404dupG	FA/N9	4F/5M	3/9	3/9	0/9	2/9	2/9	1/9	[3]
c.1451del7insT	FA/N1	M	0/1	1/1	0/1	0/1	1/1	0/1	[18]
c.1470delG	FA/N1	M	0/1	0/1	0/1	1/1	0/1	1/1	[20]
c.1487del562	FA/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[19]
c.1516dupAT	FA/N2	2M	2/2	0/2	0/2	2/2	0/2	0/2	[7]
c.1819delG	FA/N3	2F/M	2/3	0/3	0/3	1/3	1/3	1/3	[21]
c.3249del7	FA/N1	M	1/1	0/1	0/1	1/1	0/1	0/1	[7]
c.3414delAT	FA/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[7]
	FB/N1	M	0/1	0/1	0/1	1/1	0/1	0/1	[22]
Total (%)	F31N47	15F/31M/1?	16/47 (34)	18/47 (38)	2/47 (4)	11/47 (23)	9/47 (19)	14/47 (30)
p.Gln272X	FA/N1	M	0/1	1/1	0/1	0/1	0/1	0/1	[7]
p.Leu275X	FA/N1	M	0/1	0/1	0/1	1/1	0/1	0/1	[12]
p.Arg276X	FA/N2	/	1/2	0/2	0/2	0/2	1/2	0/2	[19]
	F B/N1	F	1/1	0/1	0/1	0/1	0/1	0/1	[23]
	F C/N3	3M	0/3	0/3	0/3	0/3	1/3	2/3	[24]
	FD/N2	2M	0/2	1/2	1/2	0/2	0/2	1/2	[15]
	FE/N1	F	0/1	1/1	0/1	0/1	0/1	1/1	[25]
	FF/N1	F	0/1	1/1	0/1	0/1	0/1	0/1	[26]
P.Gln243X	FA/N2	F	2/2	0/2	0/2	0/2	2/2	0/2	[10]
p.Gln323X	FA/N2	2M	1/2	0/2	0/2	1/2	2/2	0/2	[3]
p.Ser371X	FA/N1	M	1/1	0/1	0/1	1/1	0/1	1/1	[3]
p.Ser372X	FA/N2	M/F	0/2	1/2	0/2	1/2	0/2	0/2	[17]
p.Lys419X	FA/N2	2F	2/2	0/2	0/2	0/2	1/2	0/2	[3]
	FB/N2	2F	0/2	2/2	0/2	0/2	0/2	0/2	[27]
p.Tyr503X	FA/N1	F	1/1	0/1	0/1	0/1	0/1	0/1	[21]
p.Gln507X	FA/N1	F	1/1	0/1	0/1	0/1	1/1	0/1	[3]
p.Gln927X	FA/N1	M	0/1	0/1	0/1	1/1	0/1	0/1	[3]
p.Arg1054X	FA/N1	F	0/1	0/1	1/1	0/1	0/1	1/1	[28]
Total (%)	F17/N27	13F/12M/2?	10/27 (37)	7/27 (26)	2/27 (7)	5/27 (18)	8/27 (30)	6/27 (22)
del 3384 dp	FA/N1	F	0/1	0/1	0/1	1/1	1/1	0/1	[3]
IVS2/19T	FA/N1	M	1/1	0/1	0/1	0/1	1/1	0/1	[21]
Total (%)	F51/N76	29F/44M/3?	25/76 (33)	25/76 (33)	4/76 (5)	17/76 (22)	17/76 (22)	20/76 (26)

BRA: Bilateral renal agenesis; URA: Unilateral renal agenesis; PK: Polycystic kidney; VR: Vesicoureteral reflux; RF: Renal failure; RFI: Renal function impaired; F/N: Family/number of the patients.

Because TBS is a polymorphic syndrome, it needs to be distinguished from the following syndromes: Vertebral, anal, cardiac, tracheal-esophageal, renal (VACTER) and limb anomalies association[11], Goldenhar syndrome (oculo-auriculo-vertebral; impaired development of structures such as the eyes, ears, lip, tongue, palate, mandible, and maxilla and deformations of the tooth structures)[12], Okihiro syndrome (forearm malformations with Duane syndrome of eye retraction)[13], branchio-oto-renal syndrome (hearing loss, auricular malformations, branchial arch remnants, and renal anomalies)[3], and syndactyly, telecanthus, anogenital, and renal malformations syndrome[14].

As patients with kidney diseases do not have specific clinical presentations, it is possible to find rare diseases in any dialysis patients. Doctors are advised to concern about the following issues: Ask patients for family history of kidney diseases, see whether the patient has ocular or hear pathologies, see whether there is poliglobulia or abdominal masses or a family history of cerebral aneurysms, and verify that if there is neuropathy or cardiopathy when they do not obey to uremia or hypertension alone. Gene sequencing is recommended in the following categories of patients with kidney disease: Individuals with a family history of kidney disease; individuals with an unexplained renal phenotype associated with extrarenal phenotypes, especially in the eyes and ears; and individuals with polycystic kidney disease. Patients and their families can avoid the blind use of immunosuppressive drugs, which may cause adverse effects.

CONCLUSION

We report a novel SALL1 exon 2 (c.3437delG) mutation and clinical syndrome with kidney disease, bilateral overlapping toes, unilateral dysplastic external ears, and sensorineural hearing loss in a four-generation Chinese family.

ACKNOWLEDGEMENTS

The authors are grateful to the family for their participation.