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Deletion of 4q13.2q21.1 chromosome and autism spectrum disorder

1 IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy; Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
2 IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
3 IRCCS Azienda Ospedaliero-Universitaria di Bologna, UO Genetica Medica, Bologna, Italy
4 IRCCS Azienda Ospedaliero-Universitaria di Bologna, UO Genetica Medica, Bologna, Italy; Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy

Date of Submission29-Apr-2021
Date of Decision22-Oct-2021
Date of Acceptance03-Dec-2021
Date of Web Publication07-Jan-2022

Correspondence Address:
Annio Posar,
IRCCS Istituto delle Scienze Neurologiche di Bologna, via Altura 3, 40139 Bologna.
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jpn.JPN_98_21



We describe a boy with autism spectrum disorder and intellectual disability who presented a de novo interstitial deletion of the long arm of chromosome 4 (4q13.2q21.1), sized approximately 7.5 Mb, identified by array-based comparative genomic hybridization (array-CGH), considered as pathogenic and not described in the literature so far. The phenotype of this child was basically dominated by a severe neurodevelopmental impairment without particular dysmorphisms suggesting a specific genetic diagnosis at first. This case report once again underlines the importance of a genetic screening by array-CGH in individuals with autism spectrum disorder, in particular when associated with intellectual disability, even if no specific dysmorphisms are present.

Keywords: Array-based comparative genomic hybridization, autism spectrum disorder, genetics, intellectual disability

How to cite this URL:
Posar A, Visconti P, Magini P, Ambrosini E, Severi G, Seri M. Deletion of 4q13.2q21.1 chromosome and autism spectrum disorder. J Pediatr Neurosci [Epub ahead of print] [cited 2023 Sep 25]. Available from: https://www.pediatricneurosciences.com/preprintarticle.asp?id=335215

   Introduction Top

Autism spectrum disorder (ASD) represents a clinical condition with early onset and persistent impairment of social-communication abilities as well as restricted and repetitive interests and activities.[1] A clear etiology is found only in a minority of individuals with ASD and mostly consists of genetic conditions, including single-gene mutations, copy number variations, and chromosomal abnormalities.[2] A genetic condition is sometimes shown also in the absence of dysmorphisms suggesting a well-defined syndromic framework.

We report the case of a boy with ASD presenting a de novo interstitial deletion of the long arm of chromosome 4.

   Case Report Top

The boy has come to our evaluation at the age of 3 years and 9 months, already diagnosed with ASD, to perform medical examinations.

Family history was positive for initial slight speech delay (then recovered) in the mother and for amyotrophic lateral sclerosis in a cousin of the mother. Our patient is the only child of nonconsanguineous parents. Prenatal period was normal; delivery was induced with oxytocin and obstetric maneuvers due to lack of uterine contractions. At birth, weight was 2.680 kg (10th percentile) and length was 48 cm (15th percentile); he had a cephalohematoma, then reabsorbed. Since birth, hypotonia was present. Sucking was hypovalid and he did not latch on to the breast. Feeding was selective: he refused meat (if not pureed), fruit, and vegetables. He had several food allergies, including that for cow milk proteins, and suffered from atopic dermatitis and constipation. Screening for celiac disease was negative. Teething was delayed, having started at 2 years of age. Already from the first year of life, a clinical picture characterized by lack of eye contact, lallation, interest for toys, and interaction with others was reported by the parents. Sleep-wake rhythm was disturbed by difficulty falling asleep and nocturnal awakenings, requiring niaprazine. He acquired autonomous walking around 16 months, but never acquired verbal nor gestural communication (including pointing). To ask for something, he used to take a parent by the hand leading him/her to what he wanted. Spoken language understanding was very lacking. He was unable to accept apparently insignificant changes in daily routines and showed an absorbing interest in mobile phones and cartoons. Threshold for pain was high. Behavioral audiometry ruled out deafness. Since the age of 2 years and 9 months, he began to present multi-daily absence-like episodes with fixed gaze and motor arrest, lasting a few seconds. At that time, an electroencephalogram (EEG) during wakefulness and sleep was normal. These episodes gradually spontaneously faded after some months. At 3 years and 6 months, he underwent a neuro-behavioral evaluation. Autism Diagnostic Observation Schedule – Second Edition, the gold standard diagnostic tool for ASD, showed a result largely above the cut-off for autism, with a high level of autistic symptoms (calibrated severity score = 9). An intellectual disability not quantifiable by standardized tests was present. At that time, Applied Behavior Analysis (ABA) intervention was started and then some progress has been noticed: improvement of functional use of objects and appearance of some gestures to make requests.

At our first observation (age 3 years and 9 months), physical and neurological examination showed normal head circumference (≈ 50th percentile), short stature (<3rd percentile), absent speech, joint laxity, mild generalized hypotonia, stereotypies, bruxism, clumsiness, and tendency to internally rotate the feet while walking. No significant dysmorphic features were observed. A medical workup to establish the etiology was performed. EEG during wakefulness was normal, as well as brain magnetic resonance imaging (1.5 Tesla). Molecular analysis for Fragile X syndrome was negative. Array-based comparative genomic hybridization (array-CGH) (mean actual resolution: approximately 120 kb) showed an interstitial deletion of the long arm of one chromosome 4 sized approximately 7.5 Mb, considered pathogenic: arr[GRCh37] 4q13.2q21.1(69536031_76911551)×1 [Figure 1]A. The copy number of this region was evaluated in the DNA of both parents through quantitative polymerase chain reaction (PCR), revealing that the deletion occurred de novo in the proband [Figure 1]B.
Figure 1: Array-CGH and quantitative PCR results. (A) Array-CGH profile of the deleted region in the proband with OMIM genes and disease associated genes indicated in light blue and orange, respectively. (B) Histogram of the copy number ratio between each family member (proband, father, and mother) and control individuals disomic at 4q13.2q21.1

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At our last observation, the boy was 5 years and 11 months old and his clinical picture was stable, characterized by severe autism, intellectual disability, and absent speech.

   Discussion Top

With the increasing number of array-CGH studies, new information continues to emerge regarding the contribution of copy-number variants (CNVs) in ASD. The 2013 guidelines revisions state that the frequency of clinically relevant CNVs in patients with ASD is approximately 10%.[3] Given this diagnostic yield, Chromosomal Microarray Analysis was moved to the first-tier test, displacing karyotype. More than 100 different genomic changes have been reported in individuals with ASD, with some loci involved more frequently. For example, the 16p11.2 region has been reported to have CNVs occurring in 0.5–1% of all individuals with ASD,[4] considering both deletions and duplications. Almost every chromosome has at least one locus that has been someway related to ASD.[3]

Deletions involving the proximal portion of the long arm of chromosome 4 are rare and variable in size and breakpoint position, complicating the definition of precise genotype-phenotype correlations and the interpretation of their clinical consequences. So far, in literature no ASD individuals have been described with the same interstitial deletion identified in our patient. Nevertheless, we classified this deletion as pathogenic for different reasons. First, the deletion arose de novo, as confirmed by quantitative PCR in both his healthy parents DNA. Second, in the literature, deletions partially overlapping that of our patient and considered as pathogenic have been described in cases with language delay, mild to severe intellectual disability, short stature, aspecific dysmorphisms, feeding problems, and behavior disorder.[5],[6],[7] Third, the deletion spans a large genomic region (about 7.5 Mb) and over 70 genes, including nine known disease genes (AMTN, PROL1, AMBN, ENAM, SLC4A4, ADAMTS3, ALB, AFP, ODAPH), most of which, however, are associated with recessive disorders. Haploinsufficiency of the ENAM gene, associated with an autosomal dominant type of amelogenesis imperfecta (MIM 104500), could have contributed to delayed teeth eruption.[8] The AFP (alpha-fetoprotein) gene encodes the plasma protein considered as the fetal equivalent of serum albumin and higher levels in amniotic fluid suggest the presence of neural tube defects (including anencephaly and open spina bifida). In addition, a possible involvement of AFP in ASD pathophysiology has been hypothesized. During critical periods of intrauterine life, AFP could avert the inappropriate stimulation of gene expression caused by retinoic acid and maternal estradiol in sensitive developing brain regions.[9] In literature, significantly higher levels of serum AFP were found in mothers of ASD children compared to controls,[10],[11] suggesting that increased AFP levels may have a compensatory significance. In this perspective, the lack of one AFP allele in our patient could have reduced the available amount of AFP and its protective effect during crucial phases of intrauterine development, ultimately favoring some pathogenetic mechanisms leading to ASD. Also Yang et al.[12] found the AFP precursor among the possible ASD biomarkers.

Comparing all the deletions with defined or assumed genomic positions,[5],[7],[13] a very small (approximately 52 kb) minimal overlapping region emerges, including only part of the UGT2B15 gene [Figure 2], involved in the metabolism and elimination of toxic compounds and unlikely responsible for the neurodevelopmental condition observed in patients. We cannot exclude that this region contains some regulatory elements controlling genes relevant for brain development and function and located elsewhere,[14] such as the UBA6 gene proposed by Quintela et al.[7] as candidate for cognitive and behavioral phenotypes, but not deleted in our patient [Figure 2]. Excluding the patient described by Shimada et al.,[13] with a confounding Saethre-Chotzen-like phenotype due to a concurrent pathogenic 7p15.3p21.1 deletion, a gene involved in the regulation of stature should map within the deleted region shared by our patient and patient 2 reported by Quintela et al.[7]
Figure 2: Comparison of overlapping deletions in 4q13.1q21.1. The genomic positions of the deletions are indicated by red bars. UCSC (University of California, Santa Cruz) genes and OMIM (Online Mendelian Inheritance in Man) disease-associated genes are shown. The minimal overlapping deleted region and the locus potentially associated with short stature are green and yellow colored, respectively. This figure has been modified from the UCSC genome browser view

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The collection of additional patients with similar deletions is needed to clarify genotype-phenotype correlations and to possibly identify genes mainly implicated in growth and cognitive development.

In conclusion, this case report supports further the core phenotype of deletions involving chromosomal bands 4q13 and 4q21, causing essentially intellectual disability, language/speech delay, behavioral problems and short stature, and once again underlines the importance of the array-CGH in all cases with ASD, in particular when associated with intellectual disability, even if no specific dysmorphisms are present. Much remains to be discovered regarding the pathogenetic mechanisms by which a genetic alteration can cause ASD. A better understanding of these mechanisms is fundamental as it could suggest important insights regarding the prevention and treatment of ASD and could provide to parents and other relatives a more precise estimation of risk from a preconceptional point of view.


The authors would like to thank Cecilia Baroncini for linguistic support.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

   References Top

American Psychiatric Association. Diagnostic and statistical manual of mental disorders. 5th ed. Arlington, VA: American Psychiatric Association; 2013.  Back to cited text no. 1
Sztainberg Y, Zoghbi HY. Lessons learned from studying syndromic autism spectrum disorders. Nat Neurosci 2016;19:1408-17.  Back to cited text no. 2
Schaefer GB, Mendelsohn NJ; Professional Practice and Guidelines Committee. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. Genet Med 2013;15:399-407.  Back to cited text no. 3
Weiss LA, Shen Y, Korn JM, Arking DE, Miller DT, Fossdal R, et al; Autism Consortium. Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med 2008;358:667-75.  Back to cited text no. 4
Eggermann K, Bergmann C, Heil I, Eggermann T, Zerres K, Schüler HM. Rare proximal interstitial deletion of chromosome 4q, del(4)(q13.2q21.22): new case and comparison with the literature. Am J Med Genet A 2005;134A:226-8.  Back to cited text no. 5
Utine GE, Haliloğlu G, Volkan-Salancı B, Çetinkaya A, Kiper PÖ, Alanay Y, et al. Etiological yield of SNP microarrays in idiopathic intellectual disability. Eur J Paediatr Neurol 2014;18:327-37.  Back to cited text no. 6
Quintela I, Barros F, Fernandez-Prieto M, Martinez-Regueiro R, Castro-Gago M, Carracedo A, et al. Interstitial microdeletions including the chromosome band 4q13.2 and the UBA6 gene as possible causes of intellectual disability and behavior disorder. Am J Med Genet A 2015;167A:3113-20.  Back to cited text no. 7
Aren G, Ozdemir D, Firatli S, Uygur C, Sepet E, Firatli E. Evaluation of oral and systemic manifestations in an amelogenesis imperfecta population. J Dent 2003;31:585-91.  Back to cited text no. 8
King CR. A novel embryological theory of autism causation involving endogenous biochemicals capable of initiating cellular gene transcription: a possible link between twelve autism risk factors and the autism “epidemic”. Med Hypotheses 2011;76:653-60.  Back to cited text no. 9
Abdallah MW, Grove J, Hougaard DM, Nørgaard-Pedersen B, Ibrahimov F, Mortensen EL. Autism spectrum disorders and maternal serum α-fetoprotein levels during pregnancy. Can J Psychiatry 2011;56:727-34.  Back to cited text no. 10
Windham GC, Lyall K, Anderson M, Kharrazi M. Autism spectrum disorder risk in relation to maternal mid-pregnancy serum hormone and protein markers from prenatal screening in California. J Autism Dev Disord 2016;46:478-88.  Back to cited text no. 11
Yang J, Chen Y, Xiong X, Zhou X, Han L, Ni L, et al. Peptidome analysis reveals novel serum biomarkers for children with autism spectrum disorder in China. Proteomics Clin Appl 2018;12:e1700164.  Back to cited text no. 12
Shimada S, Okamoto N, Nomura S, Fukui M, Shimakawa S, Sangu N, et al. Microdeletions of 5.5 Mb (4q13.2-q13.3) and 4.1 Mb (7p15.3-p21.1) associated with a Saethre-Chotzen-like phenotype, severe intellectual disability, and autism. Am J Med Genet A 2013;161A:2078-83.  Back to cited text no. 13
Spielmann M, Mundlos S. Looking beyond the genes: the role of non-coding variants in human disease. Hum Mol Genet 2016;25:R157-65.  Back to cited text no. 14


  [Figure 1], [Figure 2]


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