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© 2023 The Authors. Société Internationale d'Urologie Journal, published by the Société Internationale d'Urologie, Canada.

Key Words Competing Interests Article Information

Case series, cystinuria, renal stones, 
mutations, South Africa, genetics

None declared. Received on July 24, 2022 
Accepted on October 18, 2022 
This article has been peer reviewed.

Soc Int Urol J. 2023;4(3):165–170

DOI: 10.48083/SRPF1472

165SIUJ.ORG SIUJ  •  Volume 4, Number 3  •  May 2023

ORIGINAL RESEARCH

A Case Series of Cystinuric Stone Formers in Western 
Cape, South Africa: SLC3A1 or SLC7A9 Mutations 
and Phenotype
Lisa-Ann Kaestner,1 John Lazarus,1 Azola Salukazana,1 Elmi Muller,2 Karl-Heinz Jehle3

1 Division of Urology, University of Cape Town, Cape Town, South Africa 2 Faculty of Health Sciences, University of Stellenbosch, Cape Town, South Africa  
3 Cape Urology, Vincent Palotti Hospital, Cape Town, South Africa

Abstract

Objective To describe the genetic mutations and phenotype in the first African series of patients with cystinuria.

Methods Patients with cystinuria were recruited from a specialist metabolic renal stone clinic in Cape Town, 
South Africa, for DNA sequencing to detect mutations in SLC3A1 and SLC7A9. Chart reviews and patient interviews 
were conducted to record demographics, previous medical history, family history, stone-specific history, age at first 
presentation, cystinuria complications, urine cystine:creatinine ratio, stone analysis, and serum creatinine. 

Results Nine patients were included: 3 male patients and 6 female patients. The mean age (± SD) of patients was 
33.43 ± 19.96 years. The median age (± IQR) at initial diagnosis of cystinuria was 16 ± 18 years, but the age ranged from 
2 to 66 years. Three of 9 patients included (33.3%) had chronic kidney disease (CKD); however, none were receiving 
dialysis. Most patients initially presented with a staghorn calculus (4/9; 44.4%). The mean serum creatinine (± SD) was 
84 ± 38 µmol/L. The mean urine cystine (± SD) was 2083 ± 1249 nmoL/mg creatinine. Eight patients had mutations 
in the SLC3A1 gene; 1 had mutations in both SLC3A1 and SLC7A9. Of the patients with only SLC3A1 mutations,  
1 patient was homozygous and the rest were compound heterozygotes (two different mutations identified in the same 
gene). Four patients had a pathogenic variant in addition to an “uncertain significance” variant in SLC3A1. There were 
9 mutations (5 pathogenic and 4 “unknown significance”) in SLC3A1 and 1 mutation in SLC7A9. Two of these were 
novel mutations.

Conclusion This “first in Africa” series of cystinuria patients showed marked heterogeneity in both phenotype and 
genotype, with a predominance of SLC3A1 mutations. This heterogeneity is similar to that reported in international 
cohorts. 

Introduction

Cystinuria is a rare genetic disorder that causes a defect in the transporter of dibasic amino acids across membranes in 
the proximal renal tubule[1,2]. Affected patients have a defect in the reabsorption of filtered dibasic amino acids and 
therefore excrete large amounts of cystine, arginine, lysine, and ornithine in their urine. Cystine is poorly soluble at 
physiological urine pH and crystallizes in the urinary tract, causing recurrent cystine renal calculi[1,3]. As the other 
amino acids (arginine, lysine, and ornithine) are more soluble in urine, there are no adverse clinical consequences of 
high urinary excretion. 

The dibasic amino acid transporter is a heterodimer composed of 2 subunits (encoded by SLC3A1 and SLC7A9) 
joined by a disulphide bridge[4,5]. There is a high prevalence of mutations in either subunit gene, or more rarely, 

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both genes. Biallelic mutations of SLC3A1 are classified 
as Type A cystinuria. SLC3A1, located on chromosome 
2, encodes the heavy subunit of the dibasic amino acid 
transporter, and inheritance is autosomal recessive with 
100% penetrance[6,7]. Heterozygotes do not have an 
elevated risk for nephrolithiasis, and urinary excretion 
of cystine is usually within the normal range. Some 
patients with duplications of exons 5–9 of SLC3A1 may 
however excrete increased levels of urinary cystine and 
form cystine stones[8]. Biallelic mutations of SLC7A9 
are classified as Type B cystinuria. SLC7A9 is located 
on chromosome 19 and encodes the light subunit of the 
amino acid transporter[6]. Heterozygotes may excrete 
increased levels of cystine and rarely form stones. Type 
B cystinuria therefore has either an autosomal recessive 
inheritance pattern or is autosomal dominant with 
incomplete penetrance[7,8]. Bigenetic mutations of both 
SLC3A1 and SLC7A9 rarely occur and are referred to as 
Type AB cystinuria. 

Although cystinuria is a rare condition, patients 
develop stones at a young age and have an extremely 
high stone recurrence rate and a high risk for the devel-
opment of chronic kidney disease[8–10]. 

There are population-dependent variations in the 
proportion of type A and B genotypes, with an equal 
distribution in the American population and a higher 
preponderance of type A genotype in the United 
Kingdom, France, and Eastern Europe. There is a 
preponderance of type B genotype in cystinuria patients 
in Spain[11]. According to the Human Gene Mutation 
Database, there are 257 SLC3A1 and 170 SLC7A9 muta-
tions identified[12]. It is uncertain whether cystinuria 
patients in South Africa carry known mutations noted 
in other countries or whether novel mutations exist in 
our population. 

Although outcomes have been reported to be worse in 
male patients, clinical phenotype-genotype correlations 
have not been reported. Outcomes and management for 
both Type A or B cystinuria are similar[1]. 

There are no publications reporting on cystinuria 
patients in South Africa, therefore nothing is known 
about the local prevalence, pathology, or genetics of 
cystinuria. Knowledge of the local mutations in South 
Africa could contribute to the development of a Sanger 
sequencing technique for the most common local muta-
tions to provide a cost-effective locally accessible test. 
Considering South Africa’s colonial history, a “founder 
effect” mutation was considered possible, and there-
fore a predominant SLC3A1 or SLC7A9 mutation was 
expected.

This study aims to describe the genetic mutations and 
clinical phenotype (age at presentation, number of stone 

episodes, number of stone procedures) in the first South 
African cohort of patients with cystinuria.

Methods
Our unit is a general metabolic stone clinic at a tertiary 
referral center, Groote Schuur Hospital in Cape Town, 
South Africa. Patients are followed up every 3 months, 
every 6 months, or annually depending on their renal 
stone type and clinical status. Quantitative urinary 
amino acid measurement is done for all patients 
diagnosed with cystinuria on stone analysis or if 
clinical factors raise suspicion for cystinuria. Patients 
with cystinuria based on either stone analysis or 
elevated urine cystine excretion were identified from an 
existing stone registry (R003/2018) and were invited to 
participate. All patients with confirmed cystinuria who 
were willing to consent were included.

A single saliva sample or 2-cheek swabs were collected 
between September 2021 and December 2021 using 
a standard test kit provided by Invitae laboratories for 
DNA sequencing. Samples were packaged and shipped 
to Invitae laboratories. Genomic DNA was enriched 
using a hybridization protocol and sequenced using 
Illumina technology focusing on the coding exons and 
flanking intronic sequences. Copy number variations 
(deletions and duplications of exons) were assessed using 
Invitae laboratories in-house algorithm to determine 
copy number at each target by comparing read depth 
for each target in the proband sequence with mean read-
depth and read-depth distribution from a set of clinical 
samples. In cases where a copy number variation was 
identified, multiplex ligation-dependent probe amplifi-
cation (MLPA) was done to confirm the variant. 

Chart reviews and patient interviews were done 
to record patient demographics (age, gender), patient 
medical history (other illnesses, treatments for cystin-
uria), family history (relatives with calculi, relatives with 
“kidney problems,” relatives with known cystinuria, 
consanguinity), stone-specific history (type, location, 
age at first presentation, current stones), complications 
of cystinuria (renal failure, nephrectomy, chronic kidney 
disease, dialysis), previous investigations (24-hour urine 
collection, urine cystine:creatinine ratio, stone anal-
ysis), number of lifetime stone events, and number of 
stone procedures. Patient weight and height were also 
measured.

Continuous data was expressed with the appropri-
ate measures of central tendency. Categorical data was 
reported as percentages and proportions. IBM® SPSS 
version 27 was used for all analyses. This protocol was 
reviewed by UCT Human Research Ethics Committee 
(HREC REF: 215/2021). All patients completed informed 
consent before participation in the study. 

166 SIUJ  •  Volume 4, Number 3  •  May 2023 SIUJ.ORG

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Results
Of the 12 patients identified for possible inclusion in 
the study, 9 patients were included; 1 patient died of 
renal failure at the age of 83 years a month prior to the 
initiation of this study, 1 patient could not be traced, and 
1 patient declined to participate. The mean age (± SD) 
of patients was 33.43 ± 19.96 years. Three male patients 
and 6 female patients were included. The median age (± 
IQR) at initial diagnosis of cystinuria was 16 ± 18 years, 
but the age ranged from 2 to 66 years. Three of 9 patients 
included (33.3%) had chronic kidney disease (CKD); 
however, none were receiving dialysis. The number of 
previous stone procedures per patient was difficult to 
assess, as 2 patients reported “too many to remember.” 
As both received treatment at multiple sites, the exact 
number of previous procedures could not be identified 
for either of these patients. For the other 7 patients, the 
number of stone episodes varied from 1 to 7 and the 
number of procedures from 3 to 7. Most patients initially 
presented with a staghorn calculus (4/9; 44.4%). None 
of the patients reported consanguinity. One patient 
reported a cousin with renal calculi since infancy, but 
the diagnosis of cystinuria could not be confirmed 
in this relative. One patient reported a brother known 
with cystinuria and recurrent renal calculi since teenage 
years; however, he declined to participate in the study 
(Table 1).

TABLE 1. 

Clinical features of cystinuria patients 

Case
BMI

(kg/m2)
Age

(years)
Gender

Affected 
relatives

Age at 
diagnosis

(years)
CKD

Initial 
presentation

Number of 
stones

Number 
of stone 

procedures

1 28.6 71 Female No 66 Yes Staghorn 2 7

2 19.5 33 Female No 14 Yes Staghorn Innumerable Innumerable

3 20.4 16 Female
Yes  

Cousin
16 No Staghorn 1 3

4 33.7 47 Female No 19 No Staghorn Innumerable Innumerable

5 25.1 39 Male No 24 Yes
Lower pole 

stone
6 3 

6 20.8 42 Female No 6 No
Passing small 

stones
5 3

7 19.1 14 Male No 2 No Bladder stone 7 7

8 29.3 34 Female
Yes

Brother 
20 No Bladder stone 4 5

9 9.1* 5 Male No 2 No Bladder stone 2 2

*This case is a child. BMI: Body mass index; CKD: chronic kidney disease. 

The mean serum creatinine (± SD) was 84 ± 38 
µmol/L. The mean urine cystine (± SD) was 2083 ± 1249 
nmoL/mg creatinine; however, results were only avail-
able for 6 patients. One result was reported as “very 
high.” It is unclear why it was not reported as a numer-
ical value. As the result was in keeping with the clinical 
picture and a stone analysis confirmed cystine nephroli-
thiasis, urine cystine measurement was not repeated for 
this patient. 

Eight patients had mutations in the SLC3A1 gene; 1 
patient had mutations in both SLC3A1 and SLC7A9. Of 
the patients with only SLC3A1 mutations, 1 patient was 
homozygous and the rest were compound heterozygotes 
(two different mutations identified in the same gene). 
Four patients had two pathogenic mutations in SLC3A1, 
and 3 patients had a pathogenic variant in addition to 
an “uncertain significance” variant in SLC3A1 (Table 2).

There were 5 pathogenic variants identified in SLC3A 
and 4 variants of “uncertain significance” reported. The 
most common mutations in SLC3A1 was c.638C>G 
(p.Pro213Arg) in 5/9 (55.5%) patients. The second most 
common was duplication of exons 5–9 (copy number = 
3) seen in 4/9 (44.4%) patients (Figure 1) The SLC3A1 
variant c.638C>G (p.Pro213Arg) was reclassified from 
“uncertain significance” to “pathogenic” by Invitae labo-
ratories during the course of this study.

167SIUJ.ORG SIUJ  •  Volume 4, Number 3  •  May 2023

A Case Series of Cystinuric Stone Formers in Western Cape, South Africa: SLC3A1 or SLC7A9 Mutations and Phenotype

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TABLE 2. 

Biochemical and molecular features of cystinuria patients

Cases
Biochemical Molecular

Cystine nmoL /mg 
creatinine

Creatinine
µmol/L

SLC3A1

1 2816 121

Gain (exons 5–9),  
copy number = 3
c.638C>G (p.Pro213Arg)
heterozygous

Both pathogenic

2 986 106
c.1400T>C(p.Met467Thr);
c.1366C>A(p.Arg456Ser)

Pathogenic
Uncertain  

significance

3 4278 68

c.1012-3A>G (intronic), 
heterozygous
c.638C>G (p.Pro213Arg), 
heterozygous

Uncertain  
significance
Pathogenic

4 1291 83
c.1400T>C (p.Met467Thr), 
homozygous

Pathogenic

5 Not available 155

Gains (exons 5–9),  
copy = 3
Deletion (exons 2–3), 
heterozygous

Both pathogenic

6 Not available 64

Gain (exons 5–9),  
copy number = 3
c.808C>T(p.Arg270*),
heterozygous

Both pathogenic

7* 1359 52

c.638C>G(p.Pro213Arg), 
heterozygous
c.762C>G(p.Asn254Lys), 
heterozygous

Pathogenic
Uncertain  

significance

8 1773 85

Gain (exons 5–9), 
number = 3
c.638C>G (p.Pro213Arg)
heterozygous

Both pathogenic

9 “Very high” 25

c.638C>G (p.Pro213Arg), 
heterozygous
c.1237C>G (p.Leu413Val)
heterozygous

Pathogenic
Uncertain

significance

* This patient had additional mutation in SLC7A9: c.1402C>T (p.Pro468Ser), heterozygous. Uncertain significance.

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Although most of the mutations identified were either 
present in population databases or had been previously 
observed in other individuals with cystinuria who 
submitted samples to Invitae laboratories for geno-
typing, there were two novel mutations identified. The 
novel mutation c.762C>A (p.Asn254Lys) in SLC3A1 and 
c.1402C>T(p.Pro468Ser) in SLC7A9 were both identified 
in the same patient who also had another known patho-
genic mutation in SLC3A1 (Table 2).

Discussion
This is the first single-population study of genetic 
mutations in cystinuria patients in Africa. There was 
marked heterogeneity in both genotype and phenotype, 
as has been described in other populations[5,6,8,10,13]. 

We have reported two novel mutations, one each 
in SLC3A1 and SLC7A9 in a single patient (case 7). 
Although both novel mutations are of unknown signif-
icance, the patient also has a heterozygous pathogenic 
mutation of SLC3A1 and a clear clinical history of recur-
rent cystine calculi since infancy. It is therefore likely 
that one or both mutations are pathogenic and that the 
patient is a double compound heterozygote. 

Three patients (cases 2,3,9) with SLC3A1 mutations 
were compound heterozygotes with one pathogenic 
mutation and one “unknown significance” mutation. 
Considering the clear cystinuria phenotype (based on 
recurrent cystine renal stones and elevated urine cystine 
excretion) in all 3 cases, the mutations classed as “uncer-
tain significance” are extremely likely to be pathogenic. 

A pathogenic mutation of SLC3A1 [c.638C>G 
(p.Pro213Arg)], not present in population databases, 
was the most common mutation reported in this series. 

1 2 3 54 6

Ex5–9 GAIN

c.638C>G (p.Pro213Arg)

c.762C>A(p.Asn254Lys)

c.808C>T (p.Arg270*)

c1012-3A>G (inotronic)

c 13 66C> A(p .Arg456Ser)

c.1400T > C(p.Met467Thr)

Ex2–3 DEL

c.1237C>G (p. Leu413Val)

0

Frequency

There were 9 mutations (5 pathogenic and 4 “unknown 
significance”) in SLC3A1 and 1 in SLC7A9. Two of these 
were novel mutations.

The predominance of SLC3A1 mutations in this 
population is similar to that of populations from the 
United Kingdom, France, and Eastern Europe[11,13]. 
The exon 5–9 duplication in SLC3A1, which was one 
of the most common mutations in this cohort (4/9; 
44.4%), was the most common mutation encountered 
in a large UK series (24/88; 27%)[13]. Considering that 
South Africa was a former English and Dutch colony, 
we postulated that a single founder gene could be iden-
tified in this series. No predominant founder gene could 
be identified. Although there was an overwhelming 
predominance of SLC3A1 mutations, there were many 
different types of SLC3A1 mutations and most of the 
participants were compound heterozygotes. 

This study was limited by the small number of 
patients included and the incomplete urine cystine 
results for the group. These limitations restricted the 
potential for genotype-phenotype correlations in the 
series. No other patients could be identified for recruit-
ment at three other state-funded healthcare services, 
both within the region and beyond. Limited access to 
renal stone analysis and metabolic renal stone services in 
the region could lead to underdiagnosis of cystinuria in 
South Africa and on the rest of the continent. The lack of 
inclusion of family members for genotyping and pheno-
typing in cases of variants of unknown significance 
limited the assessment of variant significance to clinico-
pathological correlation alone. 

In the future, recruitment of patients from privately 
funded healthcare services and founding a national or 
African registry for rare stone diseases could enable 
broader recruitment for a large-scale South African or 
African study. This would facilitate collaboration and 
data sharing with international groups to allow for pool-
ing of cohorts to glean further insights into this rare 
condition. 

Conclusion
This “first in Africa” series of cystinuria patients showed 
marked heterogeneity in both phenotype and genotype 
with a predominance of SLC3A1 mutations. The 
heterogeneity in genetics and clinical features seems 
similar to findings reported in populations in Europe 
with cystinuria.

Acknowledgements
Funding: The study was funded by the South African 
Urology Association and Division of Urology, University 
of Cape Town Research fund. 

FIGURE 1. 

SLC3A1 mutations

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