Etiology and the Genetic Basis of Intellectual Disability in the Pediatric Population

Abstract

Intellectual disability/mental retardation (ID/MR) is defined as incomplete mental and cognitive development present before the age of 18. There are number of pre-natal and post-natal risk factors that can cause ID/MR but 25 %-50 % of all have genetic causes. In the general population, the prevalence of ID/MR is about 2 %-3 %. Use of standard cytogenetic methods analysis of chromosomes (GTG banding) and FISH (Fluorescent in Situ Hybridization) reveals only a small number of causes, but when using new molecular genetics techniques (like chromosomal microarray and next generation sequencing), the rate of causes of ID/MR is increased and new candidate genes for ID/MR have been discovered. Establishing a diagnosis of ID/MR is important for the patient and it provides genetic counseling for parents.

Full text

SEEMEDJ 2017, VOL 1, NO. 1 Etiology and the Genetic Basis of Intellectual Disability in the Pediatric Population
144 Southeastern European Medical Journal, Vol 1, 2017.
Etiology and the Genetic Basis of Intellectual Disability in the
Pediatric Population
1
Višnja Tomac1,2, Silvija Pušeljić1,2, Ivana Škrlec3, Mirna Anđelić3, Martina Kos1, Jasenka Wagner3
1 Pediatric Clinic, Clinical Hospital Centre Osijek, Osijek, Croatia
2 Department of Pediatrics, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Osijek,
Croatia
3 Department of Medical Biology and Genetics, Faculty of Medicine, Josip Juraj Strossmayer University of Osijek,
Osijek, Croatia
Corresponding author: Višnja Tomac, MD - visnja.tomac@yahoo.com
Definition and prevalence of ID/MR
Intellectual disability/ mental retardation
(ID/MR) is defined as a disability characterized
by significant limitations in intellectual
functioning and in adaptive behavior; condition
covers everyday social and practical skills and
begins before the age of 18. Intellectual
functioning, also called intelligence, refers to
Received: March 15, 2017; revised version accepted: May 25, 2017; published: June 2. 2017
KEYWORDS: mental retardation, intellectual disability, etiology, submicroscopic chromosome aberrations, genes
general mental capacity, such as learning,
reasoning, problem solving and so on. Adaptive
behavior is the collection of conceptual
(language and literacy), social (interpersonal
skills, social responsibility) and practical skills
(activities of daily living and personal care,
occupational skills, healthcare) that are learned
and performed by people in their everyday living
(1).
Abstract
Intellectual disability/mental retardation (ID/MR) is defined as incomplete mental and cognitive
development present before the age of 18. There are number of pre-natal and post-natal risk factors
that can cause ID/MR but 25 %-50 % of all have genetic causes. In the general population, the
prevalence of ID/MR is about 2 %-3 %. Use of standard cytogenetic methods analysis of
chromosomes (GTG banding) and FISH (Fluorescent in Situ Hybridization) reveals only a small
number of causes, but when using new molecular genetics techniques (like chromosomal microarray
and next generation sequencing), the rate of causes of ID/MR is increased and new candidate genes
for ID/MR have been discovered. Establishing a diagnosis of ID/MR is important for the patient and
it provides genetic counseling for parents.
(Tomac V, Pušeljić S, Škrlec I, Anđelić M, Kos M, Wagner J. Etiology and the Genetic Basis of
Intellectual Disability in the Pediatric Population. SEEMEDJ 2017;1(1);144-153)

SEEMEDJ 2017, VOL 1, NO. 1 Etiology and the Genetic Basis of Intellectual Disability in the Pediatric Population
145 Southeastern European Medical Journal, Vol 1, 2017.
The intelligence quotient test (IQ test) is a major
tool in measuring intellectual functioning, which
is the mental capacity for learning, reasoning,
problem solving and so on. A test score below or
around 70 or as high as 75 indicates a limitation
in intellectual functioning. IQ testing became the
way to define groups and classify people within
them (1). According to IQ testing, ID/MR is
categorized as: mild (IQ 50 - 55 to 70), moderate
(IQ 35 - 49 to 50 - 55), severe retardation (IQ 25 -
20 to 35-40), or profound retardation (IQ below
20).
The prevalence of ID/MR varies considerably
due to the different criteria and methods used in
the diagnosis. This problem is present in 2 % to 3
% of the children's population, especially
because 5 % to 10 % of children have motor
impairment, isolated speech and language
delay, severe primary sensorial deficits and
pervasive disabilities. ID/MR is more frequent in
countries of lower socioeconomic status due to
increased incidence of anoxia, birth trauma and
newborn brain infections (2). The prevalence of
mental retardation in developed countries is
thought to be 2% to 3%. The prevalence of mild
ID/MR more often depends on external
environmental factors (level of maternal
education, access to education, opportunity and
access to healthcare), while the prevalence of
severe ID/MR is relatively stable (3).
Diagnosis is highly dependent on a
comprehensive personal and family medical
history, a complete physical examination and a
careful developmental assessment of the child.
When diagnosing ID/MR, it is very important to
know how it is defined and classified.
Etiology and epidemiology of ID/MR
The etiology of ID/MR has heterogeneous
environmental and genetic causes, summarized
in Table 1 (4, 5). Prenatal factors are
environmental (mother infection in pregnancy
such as rubella infections, syphilis,
toxoplasmosis, cytomegalovirus and HIV
infections), teratogenic (the use of drugs such as
thalidomide, phenytoin and warfarin sodium in
early pregnancy, radiation), chromosomal
abnormalities (e.g. trisomy 21), cryptic
chromosomal abnormalities (deletions or
duplications) and genetic mutations. Perinatal
factors are prematurity and asphyxia, while
postnatal factors are sepsis, meningitis,
encephalitis (commonly caused by HSV 1/2) and
various multifactorial causes (poverty and
cultural factors).
Genetic factors are thought to cause ID/MR in
about 25% to 50% of cases (6). Specifically,
genetic factors are estimated to be the cause of
moderate and severe ID/MR (IQ<50) in 0.3 % to
0.5 % of cases, of mild ID/MR (IQ ranging from 50
to 70) in 1 % to 3 % of cases and of severe ID/MR
in 25 % to 50 % of cases (7).
Table 1. Environmental and genetic causes of intellectual disability
Prenatal factors
Perinatal factors
Postnatal factors
Genetic:
chromosomal abnormalities
cryptic chromosome abnormalities
deletions/duplications
contiguous gene syndromes
monogenic diseases
prematurity
low birth weight
asphyxia
sepsis/meningitis,
encephalitis (HSV 1/2)
various multifactorial causes
(poverty and cultural factors)
Environmental:
infections (toxoplasmosis, syphilis, rubella,
cytomegalovirus and HIV infections)
mother disease (diabetes)
teratogenic factors (drugs and radiation)
Metabolic:
neonatal hypothyroidism

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Based on the symptoms’ presentation, ID/MR is
divided into two groups: syndromic and non-
syndromic ID/MR. In non-syndromic ID/MR, the
only pathological manifestation is cognitive
deficit, and there are no changes in phenotype
and no associated anomalies of organ systems.
It can be inherited in three ways: autosomal
recessive, autosomal dominant or X-linked
mode. Syndromic ID/MR is related to
phenotypic dysmorphy (craniofacial, skeletal),
growth changes, neuromuscular changes and
metabolic diseases (8).
Chromosomal abnormalities
Aberrations in the autosomal chromosome
number in live-born babies are restricted to
aneuploidies. These abnormalities represent
about 10 % of the ID/MR that can be detected
with conventional cytogenetic methods (9). The
majority of cases involve trisomy 21 with a
prevalence of 1 to 700, which is clinically
expressed as Down syndrome (10). Other rare
chromosomopathies include trisomy 13 (Patau
syndrome) with a prevalence between 1 in 5,000
and 1 in 29,000 live births (11), trisomy 18
(Edwards syndrome) with a prevalence of 1 to
3600 and 1 to 8500 (12), and they are usually
lethal in the first week of life. Monosomy of any
autosomal chromosome is lethal in the earliest
stage of embryonic life. There are autosomal
structural abnormalities such as Wolf-
Hirschhorn syndrome (microdeletion 4p) with a
prevalence of 1 to 50,000 (13), Cri du Chat
syndrome (microdeletion 5p) with a prevalence
of 1 to 50 000 (14) and sex chromosomal
aneuploidies such as Klinefelter syndrome
(47,XXY) with a prevalence of 1 in 500 to 1,000
newborn males (15).
Contiguous gene syndromes
Contiguous gene syndromes are disorders
caused by chromosomal abnormalities, such as
deletions and duplications, which result in an
alteration of normal gene dosage. For most
autosomal loci, deletion causes a reduction of
gene dosage to structural and functional
monosomy. Haploinsufficiency for specific
genes in the critical interval is implicated for
del(7)(q11.23q11.23) in Williams syndrome, for
del(8)(q24.1q24.1) in Langer-Giedion syndrome,
del(17)(p13.3) in Miller-Dieker syndrome, and for
del(22)(q11.2q11.2) in DiGeorge syndrome and
velocardiofacial syndrome (16).
Genomic imprinting
Genomic imprinting is a situation in which there
is gene expression from only one of the two
alleles inherited from each parent, and it is
based on epigenetic modifications of specific
allele, such as histone acetylation/methylation
and DNA methylation (17).
The deletion of a chromosome segment
containing the active allele of an imprinted gene
results in structural monosomy but functional
nullisomy (e.g., paternal del(15)(q11.2q13) in
Prader-Willi syndrome and maternal
del(15)(q11.2q13) in Angelman syndrome).
Uniparental disomy for the homologue
containing the inactive allele results in structural
disomy but functional nullisomy (e.g., maternal
disomy 15 in Prader-Willi syndrome and paternal
disomy 15 in Angelman syndrome).
Idiopathic ID/MR
Current research has been directed to clarify the
genetic base of what was accepted as
“'idiopathic ID/MR”. The most prevalent
structural variations in the human genome are
copy number variations (CNVs), which appear
predominantly in the subtelomeric regions.
Genomic variations are a frequent cause of
miscarriage, congenital anomalies (CA) and
intellectual disability (ID) (18).
Pathogenic CNVs have been detected in 10 % to
15 % of patients with idiopathic ID/MR, especially
with use of microarray technology. Most of CNVs
are de novo mutations, but there are also rare
inherited mutations with unknown significance
(19).
Over the last few years, cryptic chromosomal
anomalies, particularly subtelomeric and
interstitial rearrangements (including
microdeletions as well as balanced
translocations and other chromosomal

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aberrations) less than 3–5 Mb, have emerged as
a significant cause of “idiopathic ID/MR” (20-22).
About half of all segmental aneusomies are
found on subtelomeric and terminal regions of
chromosomes that are gene-rich, and they are
responsible for 5% to 7% of all cases of ID/MR
(23, 24).
Monogenic causes
X-linked mental retardation (XLMR) is a common
cause of monogenic intellectual disability,
because most of genes causing ID/MR are
found on the X chromosome. X-linked forms of
mental retardation are estimated to cause 10-
20% of all inherited cases of ID/MR. There is a
higher prevalence of ID/MR among males
relative to females (1.8 in 1000 males; carrier
females 2.4 in 1000). However, female carriers
may manifest mild symptoms, due to a skewed
X-inactivation (25).
Based on symptoms’ presentation, XLMR can be
divided into three groups: 1) syndromes -
characterized by multiple congenital anomalies
(phenotypic dysmorphy, organ anomalies); 2)
neuromuscular disorders - epilepsy, dystonia,
spasticity, muscle weakness and so on without
malformations and 3) nonspecific conditions
(MRX) – isolated ID/MR is the only clinical
manifestation. There are 215 XLMR conditions
divided according to their clinical presentation:
149 with specific clinical findings, including 98
syndromes and 51 neuromuscular conditions,
and 66 nonspecific forms (26).
Fragile X syndrome (FRAXA, OMIM 309550) is
the most common form of syndromic XLMR (20
% of all XLMR cases), with a prevalence of
approximately 1:5000 males, and causes
intellectual disability in about 1 in 8000 females
(27). Affected individuals have a folate-sensitive
fragile site in the region Xq27.3, associated with
an expansion of a trinucleotide repeat (CGG) in
the 5'-noncoding region of a gene that encodes
an RNA binding protein termed FMR1.
Individuals with fragile X syndrome have a loss-
of-function variant of FMR1 caused by an
increased number of CGG trinucleotide repeats
(typically >200) accompanied by aberrant CpG
methylation of FMR1 (28).
Another common gene is MECP2 (methyl CpG
binding protein 2 (OMIM 300005) on
chromosome Xq28, which causes Rett
syndrome, affecting approximately 1 in every
10,000–15,000 females worldwide (29). But it is
also identified in the clinical spectrum seen in
males with severe neonatal-onset
encephalopathy or with X-linked intellectual
disability associated with psychosis, pyramidal
signs, parkinsonian features and macro-
orchidism (PPM-X syndrome; OMIM 300055)
(30).
Evaluation and Testing
The clinical geneticist has an important role in
the evaluation of patients with intellectual
disability and in making decisions about further
genetic testing. Evaluation includes physical
examination and the collection of family history
information. The physical exam should focus on
dysmorphological and neurological evaluation,
congenital malformations, somatometric
measurements and behavioral evaluations. In all
patients with neurological symptoms, such as
epilepsy and macro/microcephaly,
neuroimaging studies - MRI (magnetic
resonance imaging) should be performed for
evaluation of brain malformations. If there are
signs of metabolic disease, metabolic tests
should be done (organic acid in urine, amino
acids in serum, lactate, pyruvate) (31).
When investigating a patient with ID/MR, with or
without dysmorphic features, the initial analysis
several years ago usually began with
cytogenetic testing (GTG-banding).
GTG banding (G-banding with Trypsin/Giemsa)
is used for the detection of aneuploidy
(abnormal number of chromosomes) and the
identification of structural aberrations: deletions
and translocations in chromosomal
rearrangements only larger than 5–10 Mb. The
overall yield of routine cytogenetic testing is 3.7
% (32).
Fluorescent in situ hybridization (FISH), using
location specific probes, detects

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submicroscopic alterations less than 5 Mb that
cannot be observed using standard cytogenetic
tests (GTG-banding). Today this method is used
when a specific syndrome is suspected with
high frequency in the general population (e.g.,
DiGeorge/velocardiofacial syndrome, Williams
Beuren syndrome). The yield of FISH screening
on patients with moderate to severe ID/MR is 6.8
% (33).
Candidates for subtelomere screening are
patients with ID/MR and two or more
dysmorphic features (mostly facial), congenital
organ abnormalities, skeletal abnormalities,
positive family history and pre/postnatal poor
growth/overgrowth (34).
Several assays are currently available to detect
subtelomeric rearrangements, but subtelomeric
FISH and subtelomeric MLPA have been the
most frequently used. MLPA results needed to
be confirmed using other more accurate
techniques such as FISH or aCGH (35).
With the introduction of comparative genomic
hybridization on microarrays it is possible to
screen the entire genome for evaluation of
deletions and duplications of specific DNA
sequences. Comparative genomic hybridization
on microarrays (Array Comparative Genomic
Hybridization - aCGH) and the technical basis of
the method was first published in 1997 (36).
Detection of subtle submicroscopic changes in
a number of copies of DNA less than 1Mb is
possible using different platforms. With the
application of aCGH in patients with ID/MR it is
possible to determine etiology in 20% of patients
with normal karyotype and subtelomere
screening with MLPA (36).
Copy number variations (CNVs) are the most
prevalent structural variations in the human
genome, which appear largely in the
subtelomeric regions and can be detected by
aCGH. ID/MR is associated with variable sizes of
CNVs (18).
A disadvantage of the aCGH is that the
identification of de novo CNVs of uncertain
significance and unreported CNVs can be
challenging to interpret. CNVs should be listed
as benign or pathogenic, or reported as variants
of unknown clinical significance (37). Pathogenic
variants are detected in 15 % to 20 % of ID/MR
patients (37, 38). Not all CNVs are fully
penetrated or cause a spectrum of phenotypes,
including intellectual disability, autism,
schizophrenia, and dimorphisms. Such CNVs
can pose challenges to genetic counseling.
More variants of uncertain significance are found
with higher density arrays (38). Sometimes,
variants of unknown significance can be
resolved by trio testing (mother, father and
proband). Interpretation of those variants is very
comprehensive and challenging, and demands
bioinformatics and clinical knowledge.
Next-generation sequencing (NGS) is DNA
sequencing technology that sequences all
genes in one genetic test. Exome sequencing
analyzes all exons of protein coding genes in the
genome known as a cause of the diseases
(clinical exome sequencing) or all of the genes in
the genome (whole genome sequencing). NGS
in a clinical setting opens up possibilities for
discovering the genetic contribution for a large
percentage of ID/MR individuals at the first
onset of symptoms and the possible opening up
of pathways for therapeutic interventions (37).
NGS is progressively being set up in clinical
laboratories for the diagnosis of ID/MR because
of a higher diagnostic yield and devaluation in
costs. Many studies revealed the usefulness of
using an integrative approach to examine
genotype-phenotype variability (37, 39, 40).
Whole exome sequencing (WES) is an
impressive tool for identifying clinically
undefined forms of ID/MR, especially when
aCGH identified a de novo CNV of uncertain
significance (37).
The vast majority of benign variants are single
base pair substitutions. With better coverage
depth, WES is adequate for the detection for
close to all (99.7 %) pathogenic variants (41). CNV
analysis is still an active area of research in NGS
variant analysis and has long been important in
ID research. CGH microarrays can only detect
unbalanced structural variants, while apparently
balanced chromosomal rearrangements occur
in 1.54 % of live births and contribute to 6 % of
abnormal phenotypes including ID (42). Whole

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genome sequencing (WGS) has the potential to
uncover all forms of genetic variation in one test,
and offers a higher diagnostic yield (43). In the
study of Harripaul et al. of patients with severe
ID, a diagnostic yield of 42 % was observed (42)
which is a significant improvement over the
diagnostic yield obtained by microarray, gene
panels or WES (44). A summary of genetic
methods used in diagnosing ID/MR is presented
in Table 2.
Discussion
Defining the cause of intellectual
disability/mental retardation (ID/MR) presents a
diagnostic challenge. Mental retardation is
present in about 1 % to 3 % of individuals in the
general population, but there are many cases
that cannot be explained despite novel
technology and clinical investigations (24).
Genetic factors are involved in many of the
idiopathic cases of ID/MR. This conclusion is
based on the fact that these patients often show
signs such as dysmorphic features, growth
retardation and malformations, or have a family
history of mental retardation (6,7).
The genetic heterogeneity of intellectual
disability requires genome wide approaches,
including the detection of chromosomal
aberrations by chromosomal microarrays and
whole exome sequencing adequate for
discovering single gene mutations (45).
For individuals with idiopathic ID/MR, autism
spectrum disorders, or multiple congenital
anomalies, chromosomal microarray analysis
(CMA) is recommended as the first-line
diagnostic test since it offers a much higher
diagnostic yield (15 % to 20 %) compared with G-
banded karyotype analysis (3 %) (38,42).
Despite those modern technologies, the genetic
etiology of 80 % to 85 % of patients still remains
unknown. NGS-based testing (targeted
Table 2. Advantages and disadvantages of genetic methods for diagnosing intellectual disability
Method
Advantages
Disadvantages
GTG
(G banding with Trypsin and
Giemsa)
Whole genome analysis
Detection of unbalanced and
apparently balanced
chromosomal rearrangements
Time consuming
Small resolution (5 to 10 Mb)
FISH
(fluorescent in situ hybridization)
Detection of unbalanced and
apparently balanced
chromosomal rearrangements and
mosaicism
Detection of small deletions and
duplications
Time consuming
Small resolution (depend on the
size of FISH probe, 30 to 100 kb)
MLPA
(multiplex ligation probe
amplification)
High-throughput
Simultaneously analyses of
several samples
Multiplex technique (study of
several regions of the human
genome in a single reaction)
Low cost
Not whole genome analysis
Sensitive to PCR inhibitors
aCGH
(microarray comparative genomic
hybridization)
Whole genome analysis
High resolution (up to 40 kb)
Impossibility of detection of
apparently balanced
chromosomal rearrangements and
mosaicism
CNVs of unknown significance in
clinic
NGS
(next generation sequencing)
Whole genome analysis
High resolution (covering all
coding variation)
Single strand sequencing
CNVs of unknown significance in
clinic
Expensive

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multigene panels, whole exome sequencing or
whole genome sequencing) for these cases, has
a great potential to obtain diagnosis (44).
The vast majority of individuals with ID/MR
currently receive no molecular diagnosis, which
is a shortcoming that significantly impacts health
and life span. There is also a strongly negative
correlation of survival with the severity of ID (46).
It is important to emphasize that knowing which
genes carry mutations that cause ID/MR can
have huge benefits for diagnosis in clinics, and
can lead to better understanding of each
patient’s health issues, more appropriate care
and treatment, improved overall health and life
span, and appropriate counseling and planning
for families.
Abbreviations
ID/MR - intellectual disability/mental
retardation; GTG- G-banding with
Trypsin/Giemsa; FISH - Fluorescent in situ
hybridization; MLPA-Multiplex Ligation
dependant Probe Amplification; aCGH - Array
Comparative Genomic Hybridization; NGS –
Next generation sequencing; CNVs - copy
number variations; XLMR – X linked mental
retardation; XLID – X linked intellectual disability;
IQ- intelligence quotient test; FRAXA-fragile X
syndrome; MRI - Magnetic resonance imaging;
CA - congenital anomalies.
Funding
This work was supported by the scientific project
VIF2015-MEFOS-11 ‘Etiology of mental
retardation in pediatric population’ Faculty of
Medicine, J. J. Strossmayer University in Osijek
Transparency declaration
Competing interests: None to declare
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