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Genetic and environmental
risk factors for submucous
cleft palate
Rudolf Reiter
1
, Sibylle Brosch
1
,
Manuel Ldeke
2
, Elena Fischbein
2
,
Stephan Haase
3
, Anja Pickhard
4
,
Gnter Assum
2
, Anke Schwandt
2
,
Walther Vogel
2
, Josef Hçgel
2
*,
Christiane Maier
2
*
1
Section of Phoniatrics and Pedaudiology,
Department of Otolaryngology, Head and Neck
Surgery, University of Ulm, Ulm;
2
Institute of
Human Genetics, University of Ulm, Ulm;
3
Department of Cranio-Maxillo-Facial Surgery,
University of Ulm, Ulm;
4
Department of
Otolaryngology Head and Neck Surgery,
Technical University Munich, Munich, Germany
*Authors who contributed equally to this article.
Cleft lip with or without cleft palate (CL/P) and cleft
palate only (CP) are the most common congenital cra-
niofacial disorders, with a combined prevalence of 1:700
in newborns. The submucous cleft palate (SMCP) is a
subgroup of cleft palates with insufficient median fusion
of the muscles of the soft palate hidden under the mucosa
(Fig. 1) and has a prevalence of 1:1,250–1:5,000 (1).
About 70% of all orofacial celfts can occur as an isolated
anomaly and the rest are a part of a complex mal-
formation syndrome. A multifactorial aetiology with
genetic and environmental factors is assumed (2, 3).
Maternal exposure to potential teratogens during the
first trimester of pregnancy is a known risk factor for
complete clefts. Among the known teratogenic sub-
stances are alcohol (2, 4) and tobacco smoke (5, 6). In
fact, maternal smoking may be responsible for about 4%
of all clefts (7, 8). The use of anticonvulsants (9) and of
corticoids (10) during pregnancy is also associated with
an increased risk of clefts. Additionally, the risk for
OFCs increases with parental age (11, 12), and a positive
family history of OFCs in infants or parents is a known
risk factor for both CL/P and CP (13). A number of
genes have been reported to be associated with non-
syndromic CL/P; however, only a few reports on genes
associated with CP exist (3, 14). Cleft lip with or without
cleft palate and CP are assumed to have different aeti-
ologies (14), and SMCP occurs frequently in syndromes
but also as a non-syndromal form (15). However, no
association studies have yet been performed for the
SMCP phenotype.
We therefore performed such an association study
with 12 candidate genes. These were selected for one or
more of the following reasons: their expression is asso-
ciated with palate growth during embryogenesis, knock
out of the gene leads to OFCs (mainly CP or SMCP) in
mice, or they are known to be associated in humans with
syndromal or non-syndromal OFCs. In these 12 genes we
genotyped 24 single nucleotide polymorphisms (SNPs) in
a sample of 103 patients, of German origin, with non-
syndromic SMCPs and compared the allele frequencies
with 279 healthy (population) controls. Furthermore, the
possible role of environmental risk factors, such as
alcohol and nicotine exposure, of the mothers during
pregnancy was evaluated.
Material and methods
Population
Collection of clinical data for the patients with SMCP was
performed according to the International Consortium for
Oral Clefts Genetics (16). We studied 103 patients with
SMCP (58 male subjects and 45 female subjects, median age
15.0 yr, range 3.2–68.0 yr) of German origin for this case–
control study. German background was assumed if their
grandparents had been born in Germany. Clinical assess-
Reiter R, Brosch S, Lu
¨deke M, Fischbein E, Haase S, Pickhard A, Assum G, Schwandt
A, Vogel W, Ho
¨gel J, Maier C. Genetic and environmental risk factors for submucous
cleft palate.
Eur J Oral Sci 2012; 120: 97–103. 2012 Eur J Oral Sci
A multifactorial aetiology with genetic and environmental factors is assumed for
orofacial clefts. Submucous cleft palate (SMCP), a subgroup of cleft palates with
insufficient median fusion of the muscles of the soft palate hidden under the mucosa,
has a prevalence of 1:1,250–1:5,000. We described the prevalence of risk factors among
103 German patients with the subtype SMCP and genotyped 24 single nucleotide
polymorphisms (SNPs) from 12 candidate genes for orofacial clefts. Analysis of risk
factors yielded a positive history for maternal cigarette smoking during pregnancy in
25.2% of the patients, and this was significantly more frequent than in the normal
population. The group of patients differed in allele frequencies at SNP rs3917192 of
the gene TGFB3 (nominal P= 0.053) and at SNP rs5752638 of the gene MN1
(nominal P= 0.075) compared with 279 control individuals. Our results indicate a
potential role of maternal smoking during pregnancy for the formation of SMCP. The
analysis of genetic variants hints at the contribution of TGFB3 and MN1 in the
aetiology of SMCPs.
Rudolf Reiter, Section of Phoniatrics and
Pedaudiology, Department of Otolaryngology,
Head and Neck Surgery, University of Ulm,
Frauensteige 12, 89070 Ulm, Germany
Telefax: +49–731–50039702
E-mail: rudolf.reiter@uniklinik-ulm.de
Key words: genetics; MN1; smoking;
submucous cleft palate; TGFB3
Accepted for publication January 2012
Eur J Oral Sci 2012; 120: 97–103
DOI: 10.1111/j.1600-0722.2012.00948.x
Printed in Singapore. All rights reserved
2012 Eur J Oral Sci
European Journal of
Oral Sciences
ment of the patients was carried out by an ear, nose, and
throat (ENT) surgeon, a specialist for phoniatrics, a surgeon
for oral and maxillofacial surgery and, if necessary, by a
medical geneticist to exclude a possible syndrome. A de-
tailed questionnaire was filled out to identify possible
additional malformations and any possible risk factors for
clefts, including a positive family history for OFCs, mater-
nal smoking, and ingestion of known teratogenic medica-
tions or toxins such as alcohol.
For the association study, we used a sample of 279
unrelated healthy young persons (mostly between 20 and
30 yr of age) as population controls. They had a gender
distribution about equal to that of the study group and were
of German origin, as determined by first and last name, and
by maiden name in married women. DNA was originally
prepared for paternity testing between 1995 and 2000, as
described below, and these data were later (after the legal
period) made anonymous to allow this sample to be used as
population controls for association studies. A screening for
cleft status was not made in these controls, but an appre-
ciable reduction in power was not expected because the
prevalence of OFCs is very low in the general population
(17, 18). Information on maternal exposure to risk factors
during pregnancy was not available for these controls. In
order to ascertain the influence of environmental factors on
the occurrence of SMCP, we had to rely on the literature
and chose a population-based study of 3,103 pregnant wo-
men of German origin (19) that did not include the popu-
lation controls used for the genetic association study.
However, these pregnant women were not screened for
having a child with any malformation.
The study was approved by the local Ethics Committee.
Written,informedconsentwasobtainedfromallpatientsortheir
parents. Peripheral venous blood samples were taken. DNA was
extracted from leucocytes as described by Miller et al. (20).
Selection of genes for association
The following 12 genes were selected for our study because
they have been reported to be associated with palate growth
in gene-expression analyses, with OFCs in knockout mice,
or in humans with (non-)syndromal clefts.
Expression of the T-box transcription factor gene 22
(TBX22) is associated with palate growth during embryo-
genesis. In healthy C57BL/6N mice, expression of TBX22
mRNA was observed during embryogenesis in distinct
regions of the posterior palatal shelves before fusion, indi-
cating its function in palatogenesis (21). This functional rel-
evance was confirmed in TBX22
)/)
knockout mice, which
exhibit an SMCP phenotype caused by reduced palatal bone
formation during embryogenesis (22), and in patients with
X-linked cleft palate and ankyloglossia (CPX) who had
mutations in TBX22 (23). TBX22 mutations are also often
found in non-syndromic cleft palate in the Thai population
(24). Sequencing of the TBX22 promoter region in 137 pa-
tients with CP revealed seven SNPs, two of which (rs41307258
and rs7055763) are associated with CP (25).
Knockout of the following genes led to OFCs (mainly CP
or SMCP) in mice. The meningeoma 1 gene (MN1) has been
reported to be associated with OFCs in MN1
)/)
or MN1
+/)
knockout mice, which showed a CP phenotype as a result of
reduced palatal bone formation during embryogenesis (26).
Mice lacking the transforming growth factor b3 gene
(TGFB3
)/)
) exhibit a failure of the palate shelves to fuse,
causing CP with incomplete penetrance (27).
In a mouse model for induction of CP with 2,3,7,8,-ter-
achlorodibenzo-p-dioxin (TCDD) the fibroblast growth
factor receptor 1 gene (FGFR1) was not expressed in the
medial edge epithelium after the fusion phase of the palate
shelves (28), and 80% of mice with a homozygous knockout
of FGFR1 have craniofacial defects, such as CP with open
palatine shelves. It is assumed that palatal shelf elevation is
blocked (29). In humans, association studies/genotyping of
SNPs in FGFR1 found borderline significant associations
between non-syndromal CL/P and the SNP rs13317 in
FGFR1 in 294 multiplex Filipino families. Furthermore a
nonsense mutation (R609X) was found in FGFR1 in
patients with CL/P (30).
Association of genes with syndromal or non-syndromal
OFCs in humans were also used as a source for selection of
our genes. In syndromes with CP or SMCP, some genes were
found to be mutated, such as interferon regulatory factor 6
(IRF6), which was present as a nonsense mutation (Y67Z) in
a German family with Van der Woude syndrome (31).
Variants of IRF6 were associated with non-syndromal CL/P
in a case–control association study of 460 patients and 952
controls from central Europe (17). Genotyping of 1,536
SNPs from 357 candidate genes in samples from Norway
(562 case–parent and 592 control–parent triads) and Den-
mark (235 case–parent triads) showed significant associa-
tions of IRF6 and alcohol dehydrogenase 1C (ADH1C) with
CL/P and of aristaless-like homeobox 3 (ALX3), ETS var-
iant gene 5 (ETV5), and platelet-derived growth factor C
(PDGFC) with CP. (3). Associations with non-syndromic
CL/P were also found for methylenetetrahydrofolate reduc-
tase (MTHFR) and muscle segment homeobox 1 (MSX1)ina
study of 176 haplotype-tagging SNPs in 18 candidate genes in
a case–control study in an Estonian sample (32). In addition,
transforming growth factor a(TGFA) influences the risk for
CL/P with an apparent parent-of-origin effect, as shown in a
case–parent trio design (33).
Selection of SNPs
For genes known to be associated with OFCs we did not use
the SNPs already studied, but selected tagging SNPs con-
sidering linkage disequilibrium (LD) patterns within the
candidate gene loci by using the HapMap genome browser
(release #24, phase 1 and 2 data sets). For every gene
obviously covered by a single block of LD (D¢> 0.9) we
selected a first SNP, preferably with two equally common
Fig. 1. Submucous cleft palate with the three main morpho-
logical symptoms: (A) bifid uvula and (B) a transluscent zone
lacking (C) a posterior nasal spine, leading to a bony notch in
the posterior end of the hard palate.
98 Reiter et al.
alleles. If, in the single block gene, a second SNP was
present that was likely to split the allele of one of the first
SNPs into two equally frequent haplotypes, this additional
SNP was also genotyped. For genes with interrupted LD
patterns, at least one SNP was chosen per block, and one
further SNP from the same block was selected if considered
useful for defining equally common haplotypes. One
exception to this selection scheme was the MN1 gene, which
did not exhibit a defined block structure but rather diffuse
LD patterning. From this gene locus two SNPs with com-
mon alleles were arbitrarily selected for genotyping. Can-
didate genes and genotyped SNPs are shown in Table 1.
Genotyping was performed using predesigned allelic dis-
crimination probes on a TaqMan 7900HT instrument
(Applied Biosystems, Darmstadt, Germany) in a 384-well
plate format. Reactions were carried out, according to the
manufacturerÕs instructions, in a sample reaction volume of
5ll using approximately 10 ng of genomic DNA as
template.
All markers were checked for deviations from Hardy–
Weinberg equilibrium. For association tests, allele or hap-
lotype frequencies were compared between cases and con-
trols using the chi-square test of association, and genotype
frequencies were compared using the Cochran–Armitage
test for trend. Allelic ORs are given together with their 95%
CI. Deviations of proportions (e.g. the proportion of
smokers) from population values were tested using the (two-
sided) chi-square goodness-of-fit test. All analyses were
considered to be explorative without adjustments for mul-
tiple testing. Calculations were carried out using plink
(version 1.03, http://pngu.mgh.harvard.edu/purcell/plink )
and the reported significance (P-value) is nominal. None of
the associations reached nominal significance and the
threshold for Bonferroni corrections would be much lower
(P< 0.002). plink was also used to estimate haplotype
frequencies and to test for differences between cases and
controls.
Results
Description of risk factors
Description of maternal and paternal risk factors for
OFCs yielded a positive family history (up to second-
degree relatives) in 14 out of 103 patients with SMCP.
The distribution of cleft types among relatives was as
follows: nine out of 14 had SMCP, four out of 14 had
CP, and one out of 14 had CL/P. Twenty-nine mothers
of patients (28.2%) with SMCP smoked cigarettes during
pregnancy and 18 mothers (17.5%) took alcohol.
Smoking during pregnancy appeared to be significantly
more frequent in this cohort of mothers of patients with
SMCP (prevalence = 28.2%) compared with the prev-
alence in a previously reported and independent study of
mothers in Bavaria (9.8%, P< 0.0001) (19), whereas
alcohol consumption was less frequent (two-sided
P= 0.068, Table 2). Two of these mothers took folic
acid, five took iodine, three took analgesics, and 18 took
medicinal drugs without any known risk for OFC. The
median age of the mothers at the birth of their children
with SMCP was 30.2 (range 20–43) yr.
Table 1
Candidate genes and genotyped single nucleotide polymorphisms (SNPs), together with the international SNP identification (rs) number
Gene rs number
Alcohol dehydrogenase 1C (ADH1C) rs1614972, rs3133158
Aristales-like homeobox 3 (ALX3) rs2360635, rs3754443
Ets variant gene 5 (ETV5) rs1356292, rs7433760
Fibroblast growth factor receptor 1 (FGFR1) rs2304000, rs6987534, rs6996321
Interferon regulatory factor 6 (IRF6) rs6685182, rs861019
Meningioma 1 (MN1) rs2189132, rs5752638
Muscle segment homeobox 1 (MSX1) rs12532
Methylenetetrahydrofolate reductase (MTHFR) rs1801132
Platelet-derived growth factor C (PDGFC) rs342311, rs6822796, rs6819797
Transforming growth factor, alpha (TGFA) rs6546610, rs7561997, rs7606793
Transforming growth factor, beta-3 (TGFB3) rs3917192
T-box 22 (TBX22) rs1429591, rs195294
Table 2
Frequency of the risk factors smoking and alcohol consumption during pregnancy of mothers of children with a submucous cleft palate
(SMCP) compared with population-based data of a control group of pregnant women of German origin (19)
Risk factor
Mothers of patients with
SMCP (n= 103), %
Controls (n= 3103)
P-value
Exposure to risk factor at
any time during pregnancy (%)
Exposure to risk factor
during first trimester only (%)
Smoking 28.2 9.8 9.2 <0.0001
Alcohol consumption 17.5 25.2 15.3 0.068
The controls are not the same set of controls that were used for the analysis of genetic markers. Deviations of proportions (e.g. the
proportion of smokers) from population values were tested using the (two-sided) chi-square goodness-of-fit test.
Submucous cleft palate 99
Case–control association results on allele level for the
investigated SNPs
The distribution of genotypes at selected markers was in
accordance with Hardy–Weinberg equilibrium (HWE),
except for the SNP rs6996321 in FGFR1 (P= 0.0083 vs.
controls). Therefore, this marker was excluded from the
analysis. A borderline nominally significant deviation
(P= 0.053) in allele frequency was observed for the SNP
rs3917192 of TGFB3 between cases (allele C= 0.888,
and allele T= 0.112) and controls (allele C= 0.831, and
allele T= 0.169). The OR of being a case given the allele
C was 1.61 (95% CI: 0.99–2.63). A tendency towards a
significant deviation (P= 0.075) was also present for the
SNP rs5752638 of MN1, for which allele frequencies were
T= 0.820 and C= 0.180 in cases vs. T= 0.760 and
C= 0.240 in controls (Table 3). The OR of MN1 being a
case, given the presence of allele T, was 1.44 (95% CI:
0.96–2.17). The Cochrane–Armitage trend test confirmed
the test results based on allele frequency (TGFB3,
P= 0.046; and MN1,P= 0.077). These P-values are all
nominal and apply only to single tests. After adjustment
for multiple testing, the P-values were not significant and
a trend towards significance was not seen (all P-values
>0.05).
Association results at the haplotype level
Candidate genes with multiple SNPs were additionally
analysed at the haplotype level using two (ADH1C,
ALX3, ETV5, IRF-6, MN1, and TBX22) or three
(FGFR1, PDGFC, and TGFA) SNPs. No significant
differences in haplotype frequencies were observed
between cases and controls. TGFB3 was one gene in
which an SNP approached significance; however, this
was the only SNP investigated in this gene and we do not
have haplotype information. In MN1, the other gene
with a suggestive association of an SNP, two SNPs were
analyzed and all four possible haplotypes were observed.
In this gene, the SNP rs5752638 had revealed a tendency
towards (nominally) a significant association. The C
(ÔprotectiveÕ) allele of this SNP (rs5752638) is split by the
alleles of the second SNP (rs2189132, alleles A/G) into
unequal parts, and the haplotype (C-A) with the lowest
frequency (controls = 0.056 and cases = 0.026) was
associated with a P-value (P= 0.072) similar to
rs5752638 alone (P= 0.076). Thus, the haplotype data
are consistent with the observation for the single SNPs.
Discussion
Like all OFCs, SMCPs occur as an isolated anomaly or
in the context of malformation syndromes. The velo-
cardio-facial syndrome (VCFS; 22q11 deletion syn-
drome) represents one of the most common examples of
a syndrome in which SMCP is frequently seen, occurring
in about 1/2,000 births. In a recent study of over 300
patients with VCFS, 77% had a cleft palate and, of these,
68% were either SMCP or occult SMCP (15). In addi-
Table 3
Genes, single nucleotide polymorphisms (SNPs), alleles, and allele frequencies in patients with submucous cleft palate (SMCP) and
controls
Gene SNP
Alleles
(major/minor)
Controls
(n= 279)
SMCP
(n= 103)
P-value
MAF MAF
TGFA rs7606793 T/C 0.274 0.262 0.739
rs7561997 G/A 0.453 0.437 0.683
rs6546610 G/A 0.444 0.452 0.863
TGFB3 rs3917192 C/T 0.169 0.112 0.053
MSX1 rs12532 A/G 0.292 0.248 0.225
IRF6 rs861019 A/G 0.439 0.418 0.593
rs6685182 C/A 0.351 0.387 0.359
FGFR1 rs2304000 C/G 0.208 0.223 0.556
rs6987534 G/C 0.437 0.442 0.644
MTHFR rs1801133 G/A 0.328 0.364 0.912
ADH1C rs1614972 C/T 0.312 0.345 0.349
rs3133158 C/G 0.286 0.277 0.388
TBX22 rs1429591 G/T 0.126 0.118 0.801
rs195294 T/C 0.353 0.313 0.378
MN1 rs5752638 T/C 0.240 0.180 0.075
rs2189132 G/A 0.328 0.309 0.617
ALX3 rs2360635 G/A 0.350 0.325 0.531
rs3754443 G/T 0.394 0.427 0.410
PDGFC rs6819797 T/C 0.367 0.417 0.215
rs342311 A/G 0.181 0.209 0.384
rs6822796 C/T 0.335 0.369 0.382
ETV5 rs1356292 T/C 0.195 0.194 0.971
rs7433760 A/G 0.283 0.325 0.257
Nominal significance of the different P-values between the patients with SMCP and controls was determined using the chi-square test.
All but two P-values were >0.2. P-values smaller than 0.1 are shown in bold.
MAF, minor allele frequency.
100 Reiter et al.
tion, in ankyloblepharon-ectodermal defects-cleft lip/
palate (AEC) syndrome, 17% of the patients were noted
to have SMCPs (34).
In patients with SMCP as an isolated anomaly the
aetiological relationship of the SMCP with other clefts is
much less clear. In our 14 familial cases, nine had a
relative with SMCP. This observation may indicate a
specific genetic factor for SMCP, which may be inter-
esting to study specifically. We chose 12 candidate genes
and analyzed 24 SNPs, but none of these reached the
usual level of nominal significance (P< 0.05). Never-
theless, two SNPs – one in TGFB3 and one in MN1 –
yielded P-values between 0.1 and 0.05, an observation
that may indicate a true association. However, this
remains to be shown in a larger sample size.
The above-mentioned borderline significant associa-
tions with SMCPs seem to be in accordance with
observations for TGFB3 in humans with complete OFCs.
Variants in TGFB3 have previously been studied for an
association with complete OFCs. Whereas some of these
studies revealed unequivocal evidence for an association
between OFCs and TGFB3 in ethnically different popu-
lations (35–37), others did not (38, 39). One European
study of trios (40) did not observe an association with
TGFB3, but found a clearly increased risk for CL/P with
paternal transmission. This observation may explain the
borderline association seen in other studies, including the
present one. In contrast to observations in humans, the
role of TGFB3 in OFCs in a murine model is obvious.
Mice lacking TGFB3 (TGFB3
)/)
knockout mice) exhibit
a cleft palate phenotype (27). Transforming growth fac-
tor signalling may also play a role in the subphenotype of
SMCP, as heterozygous germline mutations in TGFBR1
and TGFBR2 have recently been found to cause Loeys–
Dietz syndrome, which includes familial aortic aneu-
rysms and shows SMCP in this phenotype (41). To our
knowledge, the present study is the first that associates
TGFB3 with non-syndromal SMCP.
MN1, which encodes a cofactor for activating the
nuclear receptor of vitamin D and retinoic acid, and by
this means influences cell proliferation and cell differen-
tiation (26), is the second gene with borderline signifi-
cance in our study. Variants in this gene associated with
palate growth and clefts have been described in animal
models, but not yet in humans (2, 42). Mice deficient for
the transcription factor MN1 (MN1
)/)
mutant mice)
exhibit a complete cleft of the secondary palate (cleft
palate), whereas no significant growth deficiency was
found in the anterior plate at any stage of palate devel-
opment. The palatal shelves failed to elevate, in partic-
ular in the middle and posterior regions of MN1
)/)
mutant mice. It was also shown that the MN1 tran-
scription factor regulates expression of the transcription
factor, TBX22, during posterior palate growth in mice
(42). TBX22 knockout mice have SMCP phenotypes.
These mice exhibit reduced bone formation of the pos-
terior hard palate with a typical notch associated with
SMCP (22). Investigations in humans show that TBX22
mutations represent the most common single cause of
cleft palate known to date (24, 25). Therefore, the
TBX22/MN1 axis is an excellent candidate pathway for
SMCP susceptibility, and the trend towards an associa-
tion of MN1 variants would be worth following up with
larger study sizes.
Furthermore, not only genetic factors, but also envi-
ronmental factors, might influence the risk for SMCP. A
multifactorial mode of inheritance is often discussed (2,
43, 44). Known risk factors for OFCs are maternal
smoking and alcohol consumption during the first tri-
mester of pregnancy. We observed these risk factors in
25.2% (smoking) and 17.5% (alcohol consumption) of
our mothers. Smoking at any time during pregnancy was
significantly associated with SMCP (P< 0.0001).
Unfortunately, we did not have any timing information
for exposure to nicotine or alcohol consumption of
pregnant mothers in our patients (throughout pregnancy
vs. first trimester only). It is known that fetuses in the
first trimester (when fusion of the palate takes place) are
most susceptible to these teratogens (45).
Shi et al. (46) demonstrated, in a large collection of
1,244 cleft patients, that maternal nicotine consumption in
the 3-month period prior to, and during, pregnancy is a
significant risk factor for CL/P and CP, and risk occurs in
a dose-dependent manner. A meta-analysis confirmed this
observation (7). In particular, the combination of mater-
nal smoking during pregnancy and carrying a specific gene
variant of TGFB3 was a risk factor for CP (46, 47).
However, we did not see such an association in our pa-
tients with SMCP. The intake of drugs, such as anticon-
vulsants (9), and the maternal use of corticoids (10) are
also known risk factors for oral clefts. A positive history
for maternal drug intake was present in 17.5% of our
patients; however, drugs with a known specific risk were
not included. In our cohort, age was also considered to be
a risk factor (11, 12), but age was quite similar to that of
pregnant mothers in the general population (19).
A limitation of our investigation was that information
on possible risk factors for clefts was not available for
the control group in the genetic study. Therefore, a
comparison of samples (e.g. children of smoking and
non-smoking mothers) was not possible and the envi-
ronmental factors of our patients were compared with
population-based data of pregnant women of German
origin (19).
The genetic background may also influence our results
because allele frequencies are known to vary in different
populations and different ethnic backgrounds. Although
geographical origin was verified in our case–control
study, we cannot rule out hidden population stratifica-
tion as a cause for false-positive association.
It is known that the risk for a subsequent sibling to be
affected increases with the severity of cleft (13). Submu-
cous cleft palate is a mild form of cleft palates with a
hidden defect below the mucosa, compared with con-
tinuous/open clefts. This mild form might correlate with
a specific genetic susceptibility. On the other hand, pa-
tients with the VCFS had either an SMCP or a CP
phenotype (15). This indicates that there may be other
factors that influence the cleft type.
However, the milder (SMCP) form would probably
require an even larger group of patients in order to detect
differences of risk factors between cases and controls.
Submucous cleft palate 101
Thus, sample size is the most critical limitation of our
study, as a lack of power may cause no or insignificant
associations, even for actually causal genes.
Our results show that maternal smoking during preg-
nancy may contribute to the formation of SMCPs. The
analysis of genetic variants hints at the contribution of
TGFB3 and MN1 to SMCPs. These results need further
confirmation by larger case–control groups or functional
studies.
Acknowledgements – We thank all patients and their families for
participation in the study. Margot Brugger and Indira Wiest are
acknowledged for excellent technical assistance.
Conflicts of interest – The authors report no conflicts of interest.
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