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\title{Sodium taurocholate cotransporter polypeptide deficiency with
\selectlanguage{greek}α-\selectlanguage{english}Thalassemia and Coffin-Siris syndrome\selectlanguage{english}}



\author[1]{Jiwei Li}%
\author[1]{Meifen Wang}%
\author[1]{Mingying Wang}%
\author[1]{Juan Li}%
\author[1]{Qi Shao}%
\author[1]{Zhiying Lu}%
\author[1]{Suqi Xu}%
\author[1]{Junchao Peng}%
\author[1]{Rui Chen}%
\affil[1]{Kunming Medical University}%


\vspace{-1em}



  
  \date{May 07, 2026}


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\selectlanguage{english}
\begin{abstract}
NTCPD, \selectlanguage{greek}α-\selectlanguage{english}Thalassemia and CSS are three hereditary diseases associated
with autosome. Especially, NTCPD and CSS are rarely reported in
children. However, the co-occurrence of the three hereditary diseases
occurred in a child, and presented complex and diverse genotypes and
phenotypes, which has never been described.%
\end{abstract}%



\sloppy


\textbf{Introduction}

Sodium taurocholate cotransporting polypeptide deficiency (NTCPD) is an
inborn error of bile acid metabolism caused by the solute carrier family
10 member 1 (SLC10A1) gene variants, which diminishes the enterohepatic
circulation of bile acids by impairing the NTCP function as the primary
transporter of conjugated bile salts from the plasma into
hepatocytes\textsuperscript{{[}1{]}}. In 2015, Vaz et al. described the
first NTCPD patient\textsuperscript{{[}2{]}}. Since then, sporadic cases
with diverse genotypes have been reported in succession, but non of them
were NTCPD accompanied with other autosomal diseases. Here, we present a
rare pediatric case of NTCPD with \selectlanguage{greek}α -\selectlanguage{english}Tthalassemia and Coffin-Siris
syndrome (CSS).

\textbf{CASE}

A 2 months and 28 days old male, Han Nationality from the Jianshui
County of Yunnan Province, was born full term at 38.5 weeks gestation
with a birth weight of 3,200 g and a birth length 47 cm, who was not the
product of a consanguineous marriage. He presented skin yellowing, mild
anemia and feeding difficulty for 2 months. Physical examination
revealed a body weight of 6.5 kg, height 58 cm and head circumference
41.5 cm. Obvious jaundice was observed in the skin and sclera. No
stridor, crackles or crepitus was heard in the two lungs. There was no
abdominal distention, liver was palpable under the right costal margin
(2.0 cm), spleen was non-palpable. Echocardiography showed patent
foramen ovale (PFO). Laboratory test revealed that the serum levels of
total bilirubin (TBIL), direct bilirubin (DBIL), indirect bilirubin
(IBIL), total bile acids (TBA), aspartate transaminase (AST) and alanine
transaminase (ALT), thyroid stimulating hormone (TSH), and alkaline
phosphatase (ALP) were all elevated; 25-hydroxy vitamin D (VD) was
decreased (Table 1). Blood~routine~examination revealed that the mean
corpuscular volume (MCV), corpuscular hemoglobin (MCH) and hemoglobin
(HB) were decreased (Table 1). The baby was diagnosed to have
hypercholesterolemia, hyperbilirubinemia, mild anemia, abnormal liver
and thyroid function, and high suspicion of NTCPD. Sanger sequencing
revealed that the patient was a compound heterozygous for the
c.800C\textgreater{}T (p.Ser267Phe) and c.263T\textgreater{}C
(p.lle88Thr) SLC10A1 mutations, which was inherited from the mother and
father, respectively (Figures 1A-F); moreover, the patient and his
mother were both heterozygous missense mutation of
c.2698G\textgreater{}A (p.Ala900Thr) in AT-rich interaction domain 1A
(ARID1A) gene (Figure 1G and H), and heterozygous deletion type \selectlanguage{greek}α-
\selectlanguage{english}Thalassemia (--\textsuperscript{SEA}/\selectlanguage{greek}αα\selectlanguage{english}), while his father was normal
(Figure 1I). A diagnosis of NTCPD with heterozygous missense mutations
in c.800C\textgreater{}T and c.263T\textgreater{}C, ARID1A gene with a
heterozygous missense mutation in c.2698G\textgreater{}A, and
heterozygous deletion type \selectlanguage{greek}α- \selectlanguage{english}Thalassemia (--\textsuperscript{SEA}/\selectlanguage{greek}αα\selectlanguage{english})
was confirmed. Considering that the genotype of ARID1A is related to the
phenotype of CSS, we did a detailed physical examination for the child
again. However, except for feeding difficulties and PFO, we did not find
any typical characteristics of CSS, such as developmental delay (DD),
mental retardation, hypo/aplasia of the fifth digit phalanges/nails,
coarse facial features, or body hypertrichosis and so on, which may be
due to the baby was too young. The baby was started on symptomatic and
supportive treatment including phototherapy for neonatal indirect
hyperbilirubinemia, intravenous ademetionine1,4-butanedisulfonate, oral
ursodeoxycholic acid capsules, fat-solublevitamin~D and clostridium
butyricum powder. His transaminase, bilirubin, TSH, ALP, VD and foramen
ovale gradually returned to normal, but the levels of TBA remained high,
and mild anemia, which could only be continuously observed. After two
years of close clinic follow-up, the baby grew well and had no other
special clinical signs except mild hyperbilirubinemia and anemia
(Table1, Figure 1J). We will continue to follow up and observe the
patient. Written informed consent was obtained from the child's parents.

\textbf{Discussion}

Since NTCP was cloned in 1994, its function has been studied
extensively, while a number of SLC10A1 genetic variants have been
identified in humans\textsuperscript{{[}3{]}}, such as
c.800C\textgreater{}T (p. Ser267Phe), c.263T\textgreater{}C (p.
Ile88Thr), c.595A\textgreater{}C (p. Ser199Arg), c.755G\textgreater{}A
(p.Arg252His), c.615\_618del (p.Ser206Profs*12),
c.776G\textgreater{}A/p.G259E, c.374dupG (p. Cys125TrpfsTer23) and
c.682\_683delCT (p. Leu228AspfsTer49), which were commonly homozygous
mutations. Among these mutations, c.800C\textgreater{}T (p. Ser267Phe)
as a predominant variant accounting for 94.50\% of all mutated
alleles\textsuperscript{{[}4{]}}, and c.263T\textgreater{}C (p.
Ile88Thr) as a secondary one. In addition, SLC10A1 genetic variants
could also be composed of compound heterozygotes, such as
c.800C\textgreater{}T (p.S267 Phe) and c.263T\textgreater{}C (p.I88T),
which were rarely reported. According to the literature and the case we
provided, no matter the homozygous or heterozygous mutation of
c.800C\textgreater{}T (p.S267 Phe) and/or c.263T\textgreater{}C (p.I88T)
in SLC10A1 gene, it will lead to NTCPD and induce the phenotype of
persistent hypercholesterolemia. However, knowledge about the laboratory
and clinical presentations of patients with NTCPD remains rather
limited, and the co-occurrence of several autosome hereditary diseases
in one case is unusual. To date, there has been no report of NTCPD
complicated with other autosomal diseases, such as Thalassemia or/and
CSS.

Thalassemia is a group of inherited autosomal recessive hemolytic anemia
disease with varied phenotype, which is caused by human globin gene
synthesis disorders\textsuperscript{{[}5{]}}, including \selectlanguage{greek}α-\selectlanguage{english}Thalassemia
and \selectlanguage{greek}β-\selectlanguage{english}Thalassemia. In Chinese populations, \selectlanguage{greek}α-\selectlanguage{english}Thalassemia is mainly
caused by three types of genotypes: Southeast Asian deletion
(--\textsuperscript{SEA} deletion), the right deletion
(-\selectlanguage{greek}α\selectlanguage{english}\textsuperscript{3.7}), and the left deletion
(-\selectlanguage{greek}α\selectlanguage{english}\textsuperscript{4.2}). Southeast Asian deletion is the main
\selectlanguage{greek}α-\selectlanguage{english}Thalassemia genotype, and the heterozygous deletion
(--\textsuperscript{SEA}/\selectlanguage{greek}αα\selectlanguage{english}) genotype accounts for approximately 66.0 of
all the \selectlanguage{greek}α-\selectlanguage{english}Thalassemia mutation carriers\textsuperscript{{[}6{]}}.

The clinical features of patient with heterozygous deletion
\selectlanguage{greek}α-\selectlanguage{english}Thalassemia are asymptomatic carrier or mild anemia. In our case, the
patient and his mother were heterozygous carriers for the Southeast
Asian \selectlanguage{greek}α-\selectlanguage{english}Thalassemia mutation, and both presented mild anemia.

ARID1A harbors an Nterminal DNA-binding ARID domain and a C-terminal
folded region, and as one of the six genes (ARID1A, ARID1B, SMARCA4,
SMARCB1, SMARCE1), encodes for the BRG1/BRM-associated factor chromatin
remodeling complex\textsuperscript{{[}7{]}}. As a subunit of the
evolutionarily, ARID1A plays an important role in the maintenance of
cell identity and the determination of cell fate, and is associated with
a wide array of developmental disorders and cancers, such as CSS and
hepatoblastoma. Approximately 5--7\% of molecularly-confirmed CSS was
caused by the heterozygous missense variants of
ARID1A\textsuperscript{{[}8{]}}, such as c.5954C\textgreater{}G
(p.Ser1985Cys), c.6314C\textgreater{}T (p.Thr2105Ile),
c.6334C\textgreater{}T (p.Leu2112Phe), and c.6843G\textgreater{}T
(p.Leu2281Phe). The case we reported, accompanied by a de novo
heterozygous missense variant ARID1A, which has not been described in
large population cohorts.

It is worth noting that the clinical features of CSS, especially
facial~features, there is a wider degree of variation in patients with
mutations in ARID1A and ARID1B. Some scholars even divided CSS into two
groups: ``classic'' group with coarse facies, and ``variant'' group with
less coarse, more refined features, including thinner eyebrows and thin
vermillion border of the lips\textsuperscript{{[}9{]}}. In our case, the
patient and his mother were heterozygous missense mutation in ARID1A,
but only the baby had feeding difficulties and PFO at birth, and neither
the child nor his mother had any other clinical features of CSS during
the 2-year follow-up. Therefore, we summarize some problems. First,
changing phenotypes according to age, especially craniofacial features
and physical or intellectual development. There was a report that
patient had only feeding difficulties at birth and other symptoms
gradually presented, but our patient still lacked typical symptoms
during his growth. Should we consider it as ``variant'' CSS? Perhaps as
a result of a selection bias for the diagnosis, all reports displayed
DD, coarse facial appearance and hypo/aplasia of the fifth digit
phalanges/nails. Because of this, these features were considered
prerequisite for clinical diagnosis of CSS. Second, NTCPD, Thalassemia
and CSS are three hereditary diseases associated with autosome. Due to
the early onset age, their clinical symptoms are mild or may be similar
to some newborn physiological manifestations, such as jaundice. Even
some symptoms of the three diseases overlap with each other, such as
development disorders. Therefore, it is difficult to diagnose any of the
autosomal inherited diseases based on the atypical symptoms, and
requires a high level of suspicion for a comprehensive evaluation. In
recent years, genetic testing plays an important role in the diagnosis
of hereditary diseases. However, it is difficult to find other
coexisting hereditary diseases by detecting only one gene mutation site,
and hard to carry out whole-gene screening for most patients. Third, due
to reports of CSS probands with or without a mildly affected parent,
both autosomal recessive and autosomal dominant inheritance have been
suggested. But the recessive carrier of ARID1A genetic mutation, like
our patient's mother, has not been reported. The main reasons are
attributed to the small number of cases with ARID1A mutations and the
incomplete clinical assessment and examinations.

At present, as three genetic diseases, there are no good cure, mainly
rely on symptomatic and supportive treatment. Thus, can we learn from
the prevention and control strategy of Thalassemia to intervene with
NTCPD and CSS? Primary prevention is to reduce the occurrence of
congenital disorders and fetus's disabilities, through health education
and genetic screening before pregnancy and in the early stage of
pregnancy. Secondary prevention is the treatment of birth defects
diagnosed as intermedia or major at an early
stage\textsuperscript{{[}10{]}}.

In summary, the co-occurrence of three autosome hereditary diseases in a
child is unusual. We presented an exceptionally rare male baby with
complex and diverse genotypes and phenotypes. Further research is needed
to provide more clues and comprehensive insights into this disease.

\textbf{Data Availability Statement}

All data, models, and code generated or used during the study appear in
the submitted article.

\textbf{References}

1. Song YZ, \& Deng M. (2017). Sodium taurocholate cotransporting
polypeptide deficiency manifesting as cholestatic jaundice in early
infancy: a complicated case study.{[}J{]}. Zhongguo Dang Dai Er Ke Za
Zhi, 19(3):350--354.

2. Vaz FM. et al. (2015). Sodium taurocholate cotransporting polypeptide
(SLC10A1) deficiency: conjugated hypercholanemia without a clear
clinical phenotype.{[}J{]}. Hepatology, 61(1):260--267.

3. Yan H. et al. (2014). Viral entry of hepatitis B and D viruses and
bile salts transportation share common molecular determinants on sodium
taurocholate cotransporting polypeptide.{[}J{]}. Journal of Virology,
88(6):3273--84.

4. Deng LJ. et al. (2021). Clinical characterization of NTCP deficiency
in paediatric patients : A case-control study based on SLC10A1
genotyping analysis.{[}J{]}. Liver Int, 41(11): 2720-2728.

5. Hemminki K. et al. (2015). Thalassemia and sickle cell anemia in
Swedish immigrants: genetic diseases have become global.{[}J{]}. SAGE
open medicine. 3:2050312115613097.

6. Chong SS. et al. (2000). Single-tube multiplex-PCR screen for common
deletional determinants of alpha-thalassemia.{[}J{]}. Blood,
95(1):360--2.

7. Lee CG, \&~Ki CS. (2021). A Novel De Novo Heterozygous ARID1A
Missense Variant Cluster in cis
c.{[}5954C\textgreater{}G;6314C\textgreater{}T;6334C\textgreater{}T;6843G\textgreater{}C{]}
causes a Coffin--Siris Syndrome.{[}J{]}. Ann Lab Med, 41(3):350-353.

8. Sekiguchi F. et al. (2019). Genetic abnormalities in a large cohort
of Coffin-Siris syndrome patients.{[}J{]}. J Hum Genet, 64(2):1173-86.

9. Vergano SS, \& Deardorff MA. (2014). Clinical features, diagnostic
criteria, and management of Coffin-Siris syndrome.{[}J{]} .Am J Med
Genet C Semin Med Genet, 166(3): 252-6.

10. Lei C. (2015). Study on the intervention of Mediterranean anemia in
Guangxi Zhuang Region.{[}J{]}. China Contin Med Educ, 17:27-28.

Table 1. The 2-year follow-up records of physical, blood routine and
serology examination of the child.

Figure 1. A-C Sanger sequencing of exon 4 in SLC10A1 gene with the
heterozygous c.800C\textgreater{}T (p.Ser267Phe) mutation in the
heterozygous state in the proband and his mother (Red arrow). D-F Sanger
sequencing of exon 1 in SLC10A1 gene with the heterozygous
c.263T\textgreater{}C (p.lle88Thr) mutation in the heterozygous state in
the proband and his father (Red arrow). G-I Sanger sequencing of exon 8
in ARID1A gene with the heterozygous c.2698G\textgreater{}A
(p.Ala900Thr) mutation in the heterozygous state in the proband and his
mother (Red arrow). J The 2-year follow-up records of growth and
development, facial and the fifth digit phalanges/nails features of the
child and his mother.\selectlanguage{english}
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