DOI: 10.1542/peds.113.5.e472
2004;113;e472-e486 Pediatrics
Rebecca Muhle, Stephanie V. Trentacoste and Isabelle Rapin
The Genetics of Autism
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REVIEW ARTICLE
The Genetics of Autism
Rebecca Muhle, BA*; Stephanie V. Trentacoste, BA*; and Isabelle Rapin, MD‡
ABSTRACT. Autism is a complex, behaviorally de-
fined, static disorder of the immature brain that is of
great concern to the practicing pediatrician because of an
astonishing 556% reported increase in pediatric preva-
lence between 1991 and 1997, to a prevalence higher than
that of spina bifida, cancer, or Down syndrome. This
jump is probably attributable to heightened awareness
and changing diagnostic criteria rather than to new en-
vironmental influences. Autism is not a disease but a
syndrome with multiple nongenetic and genetic causes.
By autism (the autistic spectrum disorders [ASDs]), we
mean the wide spectrum of developmental disorders
characterized by impairments in 3 behavioral domains: 1)
social interaction; 2) language, communication, and
imaginative play; and 3) range of interests and activities.
Autism corresponds in this article to pervasive develop-
mental disorder (PDD) of the Diagnostic and Statistical
Manual of Mental Disorders, Fourth Edition and Interna-
tional Classification of Diseases, Tenth Revision. Except
for Rett syndrome—attributable in most affected indi-
viduals to mutations of the methyl-CpG-binding protein
2 (MeCP2) gene—the other PDD subtypes (autistic disor-
der, Asperger disorder, disintegrative disorder, and PDD
Not Otherwise Specified [PDD-NOS]) are not linked to
any particular genetic or nongenetic cause. Review of 2
major textbooks on autism and of papers published be-
tween 1961 and 2003 yields convincing evidence for mul-
tiple interacting genetic factors as the main causative
determinants of autism. Epidemiologic studies indicate
that environmental factors such as toxic exposures, ter-
atogens, perinatal insults, and prenatal infections such as
rubella and cytomegalovirus account for few cases. These
studies fail to confirm that immunizations with the mea-
sles-mumps-rubella vaccine are responsible for the surge
in autism. Epilepsy, the medical condition most highly
associated with autism, has equally complex genetic/non-
genetic (but mostly unknown) causes. Autism is frequent
in tuberous sclerosis complex and fragile X syndrome,
but these 2 disorders account for but a small minority of
cases. Currently, diagnosable medical conditions, cytoge-
netic abnormalities, and single-gene defects (eg, tuber-
ous sclerosis complex, fragile X syndrome, and other rare
diseases) together account for <10% of cases. There is
convincing evidence that “idiopathic” autism is a herita-
ble disorder. Epidemiologic studies report an ASD prev-
alence of �3 to 6/1000, with a male to female ratio of 3:1.
This skewed ratio remains unexplained: despite the con-
tribution of a few well characterized X-linked disorders,
male-to-male transmission in a number of families rules
out X-linkage as the prevailing mode of inheritance. The
recurrence rate in siblings of affected children is �2% to
8%, much higher than the prevalence rate in the general
population but much lower than in single-gene diseases.
Twin studies reported 60% concordance for classic au-
tism in monozygotic (MZ) twins versus 0 in dizygotic
(DZ) twins, the higher MZ concordance attesting to ge-
netic inheritance as the predominant causative agent.
Reevaluation for a broader autistic phenotype that in-
cluded communication and social disorders increased
concordance remarkably from 60% to 92% in MZ twins
and from 0% to 10% in DZ pairs. This suggests that
interactions between multiple genes cause “idiopathic”
autism but that epigenetic factors and exposure to envi-
ronmental modifiers may contribute to variable expres-
sion of autism-related traits. The identity and number of
genes involved remain unknown. The wide phenotypic
variability of the ASDs likely reflects the interaction of
multiple genes within an individual’s genome and the
existence of distinct genes and gene combinations among
those affected. There are 3 main approaches to identify-
ing genetic loci, chromosomal regions likely to contain
relevant genes: 1) whole genome screens, searching for
linkage of autism to shared genetic markers in popula-
tions of multiplex families (families with >1 affected
family member); 2) cytogenetic studies that may guide
molecular studies by pointing to relevant inherited or de
novo chromosomal abnormalities in affected individuals
and their families; and 3) evaluation of candidate genes
known to affect brain development in these significantly
linked regions or, alternatively, linkage of candidate
genes selected a priori because of their presumptive con-
tribution to the pathogenesis of autism. Data from
whole-genome screens in multiplex families suggest in-
teractions of at least 10 genes in the causation of autism.
Thus far, a putative speech and language region at 7q31-
q33 seems most strongly linked to autism, with linkages
to multiple other loci under investigation. Cytogenetic
abnormalities at the 15q11-q13 locus are fairly frequent
in people with autism, and a “chromosome 15 pheno-
type” was described in individuals with chromosome 15
duplications. Among other candidate genes are the
FOXP2, RAY1/ST7, IMMP2L, and RELN genes at 7q22-
q33 and the GABAA receptor subunit and UBE3A genes
on chromosome 15q11-q13. Variant alleles of the seroto-
nin transporter gene (5-HTT) on 17q11-q12 are more fre-
quent in individuals with autism than in nonautistic
populations. In addition, animal models and linkage
data from genome screens implicate the oxytocin receptor
at 3p25-p26. Most pediatricians will have 1 or more chil-
dren with this disorder in their practices. They must
diagnose ASD expeditiously because early intervention
increases its effectiveness. Children with dysmorphic
features, congenital anomalies, mental retardation, or
family members with developmental disorders are those
most likely to benefit from extensive medical testing and
genetic consultation. The yield of testing is much less in
From the *Class of 2004, Albert Einstein College of Medicine, Bronx, New
York; and ‡Saul R. Korey Department of Neurology, Department of Pedi-
atrics, and Rose F. Kennedy Center for Research in Mental Retardation and
Human Development, Albert Einstein College of Medicine, Bronx, New
York.
Received for publication Aug 27, 2002; accepted Dec 1, 2003.
Ms Muhle and Ms Trentacoste contributed equally to this work.
Address correspondence to Isabelle Rapin, MD, Albert Einstein College of
Medicine, K 807, 1300 Morris Park Ave, Bronx NY 10461. E-mail:
rapin@aecom.yu.edu
PEDIATRICS (ISSN 0031 4005). Copyright © 2004 by the American Acad-
emy of Pediatrics.
e472 PEDIATRICS Vol. 113 No. 5 May 2004 http://www.pediatrics.org/cgi/content/full/113/5/e472
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high-functioning children with a normal appearance and
IQ and moderate social and language impairments. Ge-
netic counseling justifies testing, but until autism genes
are identified and their functions are understood, prena-
tal diagnosis will exist only for the rare cases ascribable
to single-gene defects or overt chromosomal abnormali-
ties. Parents who wish to have more children must be
told of their increased statistical risk. It is crucial for
pediatricians to try to involve families with multiple
affected members in formal research projects, as family
studies are key to unraveling the causes and pathogene-
sis of autism. Parents need to understand that they and
their affected children are the only available sources for
identifying and studying the elusive genes responsible
for autism. Future clinically useful insights and potential
medications depend on identifying these genes and elu-
cidating the influences of their products on brain devel-
opment and physiology. Pediatrics 2004;113:e472–e486.
URL: http://www.pediatrics.org/cgi/content/full/113/
5/e472; autism, genetic, chromosome, review.
ABBREVIATIONS. ASD, autistic spectrum disorder; PDD, perva-
sive developmental disorder; MMR, measles-mumps-rubella;
DSM-IV, Diagnostic and Statistical Manual of Mental Disorders Fourth
Edition; ICD-10, International Classification of Diseases Tenth Revi-
sion; TSC, tuberous sclerosis complex; FXS, fragile X syndrome;
AS, Angelman syndrome; PWS, Prader-Willi syndrome; MZ,
monozygotic; DZ, dizygotic; LD, linkage disequilibrium; GABA,
�-amino butyric acid; IMGSAC, International Molecular Genetic
Study of Autism Consortium; MLS, multipoint logarithm of the
odds score; DBH, dopamine � hydroxylase; Hox, homeobox; OT,
oxytocin.
Autism, also known as autistic spectrum dis-order (ASD) or pervasive developmentaldisorder (PDD), is of great concern to the
practicing pediatrician. The US Department of De-
velopmental Services reported a 556% increase in the
prevalence of autism from 1991 to 1997,1 a rate that is
higher than the prevalence rates reported for other
pediatric disorders such as spina bifida, cancer, and
Down syndrome.2 Likely explanations for this aston-
ishing increase include the inclusion of broader cri-
teria for the diagnosis of ASD and physicians’ in-
creased awareness of ASD symptoms.3 Although the
media have focused attention on the measles-
mumps-rubella (MMR) vaccine and, more recently,
mercury poisoning as potential causes of autism,
epidemiologic studies to date have shown no correl-
ative associations.4,5 Greater public awareness of
autism has led to increased funding for autism re-
search, yet the cause of ASD remains largely un-
known because of the complex behavioral pheno-
types and multigenic etiology of this disorder.6
According to the Diagnostic and Statistical Manual of
Mental Disorders, Fourth Edition, Text Revision (DSM-
IV-TR)7 and International Classification of Diseases,
Tenth Revision (ICD-10)8 classifications, autism is
characterized by impairments in 3 behavioral do-
mains: 1) social interaction; 2) language, communi-
cation, and imaginative play; and 3) range of inter-
ests and activities.7 Assignment to 1 of 5 subtypes is
based on the number and distribution of endorsed
behavioral descriptors in each of the domains, as
well as on the age at onset. The 5 DSM-IV PDD
subtypes are 1) autistic disorder (classic autism), 2)
Asperger disorder (language development at the ex-
pected age, no mental retardation), 3) disintegrative
disorder (behavioral, cognitive, and language regres-
sion between ages 2 and 10 years after entirely nor-
mal early development, including language), 4) PDD
not otherwise specified (individuals who have autis-
tic features and do not fit any of the other subtypes),
and 5) Rett disorder (a genetic disorder of postnatal
brain development, caused by a single-gene defect
predominantly affecting girls).
The highly variable cognitive manifestations of the
ASDs range from a nonverbal child with severe men-
tal retardation and self-injury9 to a high-functioning
college student with an above-average IQ despite
impaired language use and inadequate social skills.10
Mental retardation thus is not a defining criterion for
autism (albeit certain cognitive abilities are charac-
teristically affected), but the mean distribution of IQs
is lower than average,11 and the likelihood of retar-
dation increases with more widespread brain dys-
function.12 Mental retardation is itself a behaviorally
defined disorder of complex human abilities with
many genetic and nongenetic causes. The more se-
vere the retardation, the more likely the underlying
brain dysfunction will affect the widely distributed
networks responsible for sociability, language, and
cognitive flexibility.
Like mental retardation, autism is a behaviorally
defined syndrome with a wide variety of both ge-
netic and nongenetic causes. With the exception of
Rett syndrome, which is caused in the majority of
cases by de novo mutations or microdeletions of the
methyl-CpG-binding protein 2 (MeCP2) gene on
Xq28,13 there is no current evidence that the other
DSM-IV subtypes of autism are linked to any partic-
ular genetic or nongenetic disorder. Therefore, when
we refer in this article to autism, we are referring to
the entire spectrum of behaviorally defined autism
with the exception of Rett syndrome. Current evi-
dence indicates that multiple genetic factors are the
causative determinants of the majority of cases of
autism.14
METHODS
We performed a comprehensive search of Medline using the
terms “autism,” “autistic,” “gene,” “genome,” ”genomic,“ ”ge-
netic,“ ”chromosome,“ ”chromosomal,“ and ”loci“ in various
combinations. These queries returned �500 citations. We re-
viewed papers published between 1961 and 2003, focusing on
scientific articles published between 1995 and 2003. After study of
these papers, we performed additional searches to examine spe-
cific topics (eg, ”autism, oxytocin“) not included in the initial set.
We also reviewed 2 current definitive textbooks concerned with
autism: Cohen and Volkmar15 and Gillberg and Coleman.9
RESULTS
Defined Nongenetic and Genetic Medical Conditions
Associated With Autism
Autism has been linked to a wide variety of pre-
natal and postnatal insults but predominantly in in-
dividual case reports or short series. In the aggregate,
they account for only a small percentage of cases.9,16
Obstetric complications (eg, an increased incidence
of uterine bleeding) have often been blamed for au-
tism17 despite that many studies show no significant
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causal relationship.18,19 Intrauterine exposure to the
teratogenic drugs thalidomide and valproate have
been implicated as the cause of autism in a few
affected children.20,21 Mean levels of some of the
neuropeptides substance P, vasoactive intestinal
peptide, pituitary adenylate cyclase-activating
polypeptide, calcitonin gene-related peptide, and
neurotrophin nerve growth factor, the concentration
of all of which is under genetic control, were elevated
in the cord blood of children who later received a
diagnosis of autism or mental retardation22; they
were normal in nonautistic children with cerebral
palsy, which generally results from an abnormal in-
trauterine environment or peri-/postnatal insult
rather than a genetic condition. Maternal factors
have also been examined as potential causes of au-
tism; antibodies in the sera of a mother of 2 children,
one with autism and another with severe language
impairment, were shown to bind to the cerebellar
cells of developing fetal mice.23 There is no evidence
in population surveys of any association between
autism and immigrant status, socioeconomic status,
or ethnicity.16
Various epidemiologic studies have reported that
cerebral palsy, defined as a static motor deficit of
brain origin present from early life, is present in 2.1%
to 2.9% of individuals with autism and mental retar-
dation.24–27 Congenital rubella infection, initially
found to be highly associated with autism,28 is
present in only 0.75% of recent autistic populations,24
thanks to the near eradication of rubella after the
introduction of quasi-universal immunization in
Western countries. Other pre- and postnatal infec-
tions by organisms such as Haemophilus influenzae
and cytomegalovirus can cause autism when they
significantly damage the immature brain.9
In a review of several epidemiologic studies of
autism, Fombonne24 found no association between
autism and inflammatory bowel disease or with a
live MMR vaccination. This contradicts an earlier
publication by Wakefield et al.29 Large surveys that
have examined the prevalence of autism before and
after the initiation of widespread MMR vaccination
have also failed to corroborate an association with
autism4,5 but have not reassured a skeptical public of
the safety of the vaccine.30 Some investigators pos-
tulate that it is the mercury-based preservative
thimerosal in vaccines, rather than the vaccines
themselves, that poses a risk to the developing in-
fant.31 This theory has also met with significant crit-
icism.32
Epilepsy has the highest association with autism,
reported in up to a third of individuals with an ASD
by adulthood.25–27,33–35 The epilepsy may be subclin-
ical, yielding an electroencephalogram that is epilep-
tiform but without clinical seizures, and is particu-
larly frequent in disintegrative disorder.36 Like
autism, epilepsy is a disorder of the brain with mul-
tiple genetic and nongenetic causes and a broad
range of phenotypes. Infantile spasms are particu-
larly likely to result in autism with nondevelopment
of language and mental retardation, especially when
the epileptiform activity involves both temporal
lobes.37 An occasional nonverbal child with mental
retardation, autism, and epilepsy has exhibited early
bilateral hippocampal sclerosis.38,39
Behavioral symptoms of autism are frequent in
tuberous sclerosis complex (TSC) and fragile X syn-
drome (FXS), but these 2 disorders nevertheless ac-
count for only a minority of the total cases of au-
tism.40,41 Given the high rate of epilepsy in children
with TSC and the association between autism and
epilepsy, it is perhaps not surprising that as many as
25% of patients with TSC have autism.42,43 An auto-
somally dominant neurocutaneous disorder, TSC
arises from genetic mutations of either TSC1 on 9q or
TSC2 on 16p and is characterized by ash-leaf depig-
mented or other cutaneous manifestations and
hamartomatous lesions in multiple organs. In the
brain, these lesions are termed tubers, and they are
thought to cause the epilepsy seen in more than three
quarters of children with TSC.44,45 Furthermore, it is
the haphazard distribution of these tubers, together
with other metabolic changes, that influences the
phenotype of TSC, giving rise in some individuals to
autism or epilepsy (often infantile spasms).37 In the
population of patients with autism, numerous stud-
ies have quoted TSC rates of 1.1% to 1.3%,25–27,46
rates that, although low, are 30% higher than the
prevalence of TSC in the general population.
FXS is an X-linked genetic disorder that is signifi-
cantly associated with autism and that is denoted by
unusual facial features, macro-orchidism in adult-
hood, and cognitive impairment of variable severity.
It is caused by an increased number of trinucleotide
(CGG) repeats in the gene coding for the fragile X
mental retardation protein. Approximately 30% of
individuals with FXS are on the autistic spec-
trum.47,48 There is disagreement, however, over the
degree of FXS prevalence in patients with autism.
Some early studies reported little or no association
between FXS and autism,24,49 whereas others found a
high association50 (see41 for additional review). More
recent epidemiologic studies have documented rates
of FXS between 7% and 8% in populations with
autism.26,33,51,52 The discrepancies regarding the
prevalence of FXS among individuals with autism
may reflect the limited reliability of the cytogenetic
tests used in the past compared with the more sen-
sitive molecular tests currently used; as such, the
number of girls who receive a diagnosis of FXS has
increased.6
Genetic mutations that give rise to a number of
additional diagnosable