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RESEARCH ARTICLE

Next Generation Sequencing in NonsyndromicIntellectual Disability: From a Negative MolecularKaryotype to a Possible Causative MutationDetection

Emmanouil Athanasakis,1 Danilo Licastro,2 Flavio Faletra,1* Antonella Fabretto,1 Savina Dipresa,3

Diego Vozzi,1 Anna Morgan,4 Adamo P. d’Adamo,3 Vanna Pecile,1 Xevi Biarnes,5 andPaolo Gasparini1,3**1Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, Trieste, Italy2CBM S.c.r.l., Area Science Park–Basovizza, Trieste, Italy3University of Trieste, Trieste, Italy4Telethon Institute, Rome, Italy5Institut Quımic de Sarria (IQS), Universitat Ramon Llull (URL), Barcelona, Spain

Manuscript Received: 4 February 2013; Manuscript Accepted: 29 August 201

3

How to Cite this Article:Athanasakis E, Licastro D, Faletra F,

Fabretto A, Dipresa S, Vozzi D, Morgan A,

d’Adamo AP, Pecile V, Biarnes X,

Gasparini P. 2014. Next generation

sequencing in nonsyndromic intellectual

disability: From a negative molecular

karyotype to a possible causative mutation

detection.

Am J Med Genet Part A 164A:170–176.

Emmanouil Athanasakis, Danilo Licastro, and Flavio Faletra contributed

equally to this work.�Correspondence to:

Flavio Faletra, Department of Medical Genetics, Institute for Maternal

and Child Health—IRCCS “Burlo Garofolo”, Via dell’Istria, 65/1, Trieste

34137, Italy.

The identification of causes underlying intellectual disability

(ID) is one of the most demanding challenges for clinical

Geneticists and Researchers. Despite molecular diagnostics

improvements, the vast majority of patients still remain without

genetic diagnosis. Here, we report the results obtained using

Whole Exome and Target Sequencing on nine patients affected

by isolated ID without pathological copy number variations,

which were accurately selected from an initial cohort of 236

patients. Three patterns of inheritance were used to search for:

(1) denovo, (2)X-linked, and (3) autosomal recessive variants. In

three of the nine proband–parent trios analyzed, we identified

andvalidated twodenovo andoneX-linkedpotentially causative

mutations located in three ID-related genes. We proposed three

genes as ID candidate, carrying one de novo and three X-linked

mutations. Overall, this systematic proband–parent trio ap-

proach using next generation sequencing could explain a con-

sistent percentage of patients with isolated ID, thus increasing

our knowledge on the molecular bases of this disease and

opening new perspectives for a better diagnosis, counseling,

and treatment. � 2013 Wiley Periodicals, Inc.

Key words: nonsyndromic; intellectual disability; exome

sequencing; target sequencing; de novo; X-linked; KDM5B;

plexins

E-mail: faletra@burlo.trieste.it��Correspondence to:

Paolo Gasparini, Department of Medical Genetics, Institute for Maternal

and Child Health—IRCCS “Burlo Garofolo”, Via dell’Istria, 65/1, Trieste

34137, Italy.

E-mail: gasparini@burlo.trieste.it

Article first published online in Wiley Online Library

(wileyonlinelibrary.com): 4 December 2013

DOI 10.1002/ajmg.a.36274

INTRODUCTION

Early-onset cognitive impairment, or intellectual disability (ID) is

one of the most common neuropsychiatric disorders and an

unresolved health care problem, whose prevalence ranges from

1% to 3% [Leonard and Wen, 2002]. However, up to 60% of

patients, have no genetic identifiable cause [Rauch et al., 2006].

2013 Wiley Periodicals, Inc.

Most severe forms of ID are due to chromosomal abnormalities or

defects in specific genes. For many years, the research on genetic

causes of IDhas focused onX-chromosome, since the ratio ofmales

170

FIG. 1. Workflow of the present study for the identification of

ATHANASAKIS ET AL. 171

to females with ID ranges in between 1.4 and 1.6:1 [Basel-

Vanagaite, 2008]. Recently, it has been suggested that in outbred

Caucasian populations, a significant proportion of sporadic

patients may be due to de novo mutations [Vissers et al., 2010;

de Ligt et al., 2012]. Although some studies have recently been

published [Abou Jamra et al., 2011; Calıskan et al., 2011;Najmabadi

et al., 2011], up to now, little is known about the role of autosomal

recessive ID in Western societies.

Until recently, the most common technology used to investigate

unexplained ID patients was the molecular karyotyping since copy

number variations (CNVs) could explain up to 15% of patients

[Hochstenbach et al., 2011]. The recent introduction of next

generation sequencing technologies has opened new perspectives

in the identification ofmutations related to ID and the discovery of

new causative genes [Zahir and Friedman, 2007; Vissers et al., 2010;

Abou Jamra et al., 2011; Najmabadi et al., 2011]. In this light, to

increase our knowledge on the genetic bases of isolated ID, a whole

exome sequencing (WES) approach, coupled by deep target se-

quencing, has been carried out in nine probands (seven males and

two females) and their parents. Probands, with isolated ID and

without pathological CNVs, were selected from a cohort of 236

patients, and WES data were analyzed with three patterns of

inheritance in order to search for: (1) de novo; (2) X-linked; and

(3) autosomal recessive mutations (Fig. 1).

genetic causes of intellectual disability. Molecular karyotyping

analysis in a cohort of 236 proband detected a proportion of

16.5% with pathological CNVs and 7.6% with an inherited CNV or

an uniparental disomy. After clinical evaluation, nine ID trios

were selected for whole exome and target sequencing. Bioinfor-

matic analysis of exome data outcome three potentially causing

mutations in ID-related genes and three possible ID candidate

genes with four potentially causative mutations.

MATERIALS AND METHODS

Molecular KaryotypingTo detect CNVs, molecular karyotyping study was previously

performed in a cohort of 236 probands using high density SNP

array (HumanOmniExpress BeadChip, Illumina, CA) and the data

were analyzed by GenomeStudio software (Illumina, CA). To

determine the presence of pathological CNVs our data were com-

pared to theDatabase ofGenomicVariants (http://projects.tcag.ca/

variation/). This first step allowed us to exclude polymorphic

structural variations previously identified in healthy control sam-

ples. In case of CNVs with uncertain clinical significance, DECI-

PHER database (http://decipher.sanger.ac.uk/) and the scientific

literature was consulted (NCBI, http://www.ncbi.nlm.nih.gov/).

Additionally, SNP array or targeted analysis of both parents was

performed to determine whether the CNV was inherited or oc-

curred as de novo. In the present study patients with de novo

pathological CNVs and with an inherited CNV or a uniparental

disomy were excluded. Informed consent was obtained from all

participants.

Patients SelectionNine probands were selected from the initial cohort of 236 ID

patients. In particular, we conducted detailed medical record

review and inclusion criteria. In particular, we required: (a) nega-

tive family history for ID, (b) no parental inbreeding, (c) absence of

any dysmorphic feature including absence of micro or macro-

cephaly, hands or foot malformations, (d) normal genitalia, skin,

and annexes, (e) clinical history showing growth parameters range

within the 10th and 90th percentile, (f) absence of any malforma-

tion and seizure assessed using several instrumental exams (i.e.,

abdominal and heart ultrasound, nuclear magnetic resonance, and

electroencephalogram), (g) normal hearing and vision function,

(h) normal karyotype (550 band resolution), negative X-fragile test

and absence of pathologic CNVs using high density SNP array. The

degrees of the ID have been reported in Table I.

Whole Exome Sequencing and VariantsAnnotationExome sequencing has been carried out using Illumina HiScanSQ

platform and TruSeq Exome Enrichment kit (Illumina, CA) target-

ing 62Mb of the human genome, �20.794 genes. Briefly, high-

quality reads were aligned to the human reference genome

(GRCh37/hg19) following GTAK recommendation [McKenna

et al., 2010]. Base calling data of single nucleotide variants

(SNVs) and indels were combined, annotated and inserted in a

local variation database. All nongenic, intronic, and synonymous

variants, except those belonging to canonical splice sites were

excluded. Next, all variants were compared with the dbSNP

(www.ncbi.nlm.nih.gov/projects/SNP/Build137), 1000 Genomes

Project (www.1000genomes.org), NHLBI-ESP project (http://

evs.gs.washigton.edu/EVS/) and our in-house database that ac-

TABLE I. Overview of All WES Variants Detected, Selected, and Confirmed in the Three Different Filtering Pattern(De Novo, X-Linked, Recessive)

Trio Gender ID degree

De novo X-Linked Recessive

Called Selected Confirmed Called Selected Confirmed Called Selected Confirmed

1 M Mild 7 1 0 4 1 PLXNB3 5 0 —

2 F Mild 11 3 KDM5B 0 0 — 4 0 —

3 M Mild 13 2 0 2 1 PLXNA3 6 1 0

4 M Moderate 5 2 CIC 1 0 — 8 0 —

5 F Moderate 9 4 KIAA2022 1 0 — 7 0 —

6 M Mild 42 7 0 0 0 — 2 0 —

7 M Moderate 9 1 0 2 1 HUWE1 2 0 —

8 M Moderate 7 2 0 3 1 ZNF41 7 0 —

9 M Mild 15 3 0 1 1 PLXNA3 6 0 —

Called, final output of all 179 annotated variants after filtering with one of the pattern; Selected, all variants selected by prioritization (see text); Confirmed, all confirmed variants by Sanger sequencing.

172 AMERICAN JOURNAL OF MEDICAL GENETICS PART A

count 100 exomes. In this step all SNPs with a MAF >0.01 were

excluded from the de novo and X-linked pattern analysis. For the

recessive pattern were excluded all SNPs with a MAF >0.05.

Target Sequencing and Variants AnnotationA set of primers intended formultiplex PCRwas designed using Ion

AmpliSeq Designer v1.2 (Life Technologies, Foster City, CA). The

corresponding target region covers 71 genes CCDS, sizing 226 kb,

with a total coverage equal to 97.9% of the genomic target region

(Supplemental Table SI in supporting information online). Briefly,

a DNA library was constructed and probands’ indexing was carried

out using barcode adapters, according with Life Technologies

protocols. Template positive Ion Sphere Particles were prepared

and a single 200 base-read sequencing run was performed on Ion

PersonalGenomeMachine system (Life Technologies). Sequencing

data were analyzed in accord to Torrent Suite v3.2 analysis pipeline

and SNVs and indels were annotated using ANNOVAR [Wang

et al., 2010]. Excluding variants present in 1000 Genomes Project

and NHLBI-ESP project with a frequency greater than 0.01, the

most likely disease-causing variants were analyzed by Sanger

sequencing.

Variants PrioritizationVariants identified by each approach (de novo, X-linked and

recessive) have been prioritized according to the following criteria:

(a) known and already candidate ID genes; (b) function and tissue

expression [Hubble et al., 2009; Kapushesky et al., 2010], and (c)

pathogenicity of the variant using web prediction tools [Reese

et al., 1997; Ng and Henikoff, 2003; Desmet et al., 2009; Adzhubei

et al., 2010; Schwarz et al., 2010; Choi et al., 2012].

Sanger Sequencing ValidationAll selected variants were confirmed by direct sequencing on ABI

PRISM 3130� l sequencer (Life Technologies). Amplification of

the corresponding genomic regions was conducted by a general

PCRmethod. Sanger sequencing was performed using ABI PRISM

3.1 Big Dye terminator chemistry (Life Technologies) according to

themanufacturer’s instructions.All theunknownvariantswere also

searched in 100 DNA samples of healthy Italian controls.

Structural Bioinformatics AnalysisThe effect of the mutation on the discovered variants was directly

analyzed on selected protein products in terms of sequence com-

parisons and structural analysis. Protein sequences, alignments,

and structures were retrieved from different databases: UniProt

(http://www.uniprot.org), PFAM (http://pfam.sanger.ac.uk) and

PDB (http://pdb.org), respectively. Protein structures were visual-

ized and graphics representedwith VMD (http://www.ks.uiuc.edu/

Research/vmd/).Homolog sequence searchingwas performedwith

BLAST (http://blast.ncbi.nlm.nih.gov/).

RESULTSFrom an initial cohort of 236 probands analyzed by high density

SNP array, according to the molecular karyotype, we excluded 39

(16.5%) of them with pathological CNVs and 18 (7.6%) with an

inherited CNV or an uniparental disomy. Among the remaining

179 probands we selected nine of them to be analyzed by WES.

Sequencing data show an overall median coverage equal to 31-fold

(Supplemental Fig. S1 in supporting information online).

WES data were analyzed using a custom bioinformatic pipeline

and in accord to three different patterns on inheritance: de novo, X-

linked, and recessive (Supplemental Fig. S2 in supporting informa-

tiononline). The analysis revealed a total amount of 179 variants for

all of the 9 probands (Table I).

Under the de novo model 118 variants were called and 25 of

them were excluded from the fellows analysis because in discor-

dance with all the abovementioned criteria of the prioritization

(see Materials and Methods section). The remaining 93 variants

were prioritized and 25 of them were analyzed by Sanger sequenc-

ATHANASAKIS ET AL. 173

ing, which confirmedonly 3 variants. TheX-linkedpattern showed

that 5 variants out of 14 received a high prioritization, and they

were subsequently sequenced and confirmed. In the recessive

pattern analysis, 47 homozygous or compound heterozygous

variants were detected but none of them was considered (Supple-

mental Figs. S3, S4, and Supplemental Table SII in supporting

information online).

Target sequencing on Ion chip-318 generated 887Mb of output,

producing a mean read length equal to 140 bp, a 305-fold total

mean.Amedian of 122 variants per patient have been identified and

after filtering with the above reported database only one missense

variation in FGD1 gene, not detected by previously WES analysis,

was confirmed by Sanger sequencing.

ID Related GenesTwo de novo potentially causative mutations and three X-linked

variantswith uncertain effect have been identified infive out of nine

probands (Patients 4–8): four variants were detected byWES while

the remaining onewas identified by targeted sequencing. A de novo

missense mutation (NM_015125.3, c.680A>G, p.Asn227Ser—trio

4) was identified inCIC gene, a member of a novel subfamily of the

HMG-box superfamily, expressed in the developing mouse brain

[Lee et al., 2002]. Another de novo mutation was a nonsense allele

(NM_001008537.2, c.1882C>T, p.Arg628�—trio 5) in gene

KIAA2022, located on chromosome X. A X-linked nucleotide

change (NM_031407.5, c.3082A>G, p.Thr1028Ala—trio 7) was

detected in HUWE1 gene; mutations affecting this gene have been

reported in several families as ID causing [Froyen et al., 2008; Nava

et al., 2012]. Another X-linked variant affected ZNF41

(NM_007130.2, c.2116C>T, p.Leu706Phe—trio 9), a likely zinc

finger family transcription factor containingKRAB-A andKRAB-B

domains;ZNF41 acts as transcriptional repressor and its function is

related to chromatin remodeling mechanisms, a process defective

in various forms of ID. Finally a nonsynonymous variant in ID-

related gene FGD1 (NM_004463.2, c.2224C>T, p.Pro742Ser) was

identified by targeted sequencing.

ID Candidated GenesIn the remaining four probands (Patients 1–3, 9) were identified

one de novo and three X-linked. A de novo splicing mutation

(NM_006618.3, c.283-2A>G) involving KDM5B was identified in

trio 2. This gene encodes for a Lysine-specific demethylase 5B

protein belonging to the H3K4 demethylase family, involved in

cancer progression and playing a role in cell fate decisions [Dey

et al., 2008; Shackleton, 2010]. Interestingly, in regard to X-linked

variants, three of them were located within members of the Plexins

family, PLAXNA3 (NM_017514.3, c.3712G>A, p.Val1238Met—

trio 3 and c.1298G>A, p.Arg433His—trio 9) and PLXNB3

(NM_005393.2, c.5390C>T, p.Ser1797Leu—trio 1) whose func-

tion is related to neuronal growth.

DISCUSSION

In the last years the emerging high throughput technologies, as next

generation sequencing, have contributed to the identification of

genetics causes in neurological disorders. Until now, several studies

have been performed mainly searching for X-linked and recessive

causative mutations [Hu et al., 2009; Najmabadi et al., 2011]. As

described by Vissers et al. [2010], de novo mutations could be

attributed to ID and possibly to other disorders. In nonsyndromic

cases of ID, causative de novo mutations range from 16% to 55%

[de Ligt et al., 2012; Rauch et al., 2012]. In our study, three potential

causative de novo mutations were identified, two in ID-related

genes (CIC, KIA2022) and one in a possibly ID candidate gene

(KDM5B).

ID Related GenesCIC. Lee et al. [2005], through an in silico SAGE analysis of

human normal and malignant brain, demonstrated that medullo-

blastoma exhibited the highest level of CIC expression and that it

wasmost common in tumors of the CNS in general. More recently,

this gene has been reported as involved in human oligodendro-

glioma [Bettegowda et al., 2011], andmutations in CIC jointly with

IDH mutations, and 1p/19q loss could distinguish oligodendro-

gliomas from other type of cancers [Yip et al., 2012]. Moreover, a

recent studybasedonexome sequencingof IDaffectedprobandand

their parents (trios) detected a CIC mutation in a proband

with isolated ID [Vissers et al., 2010]. Given the expression of

this gene, the pathogenicity of this mutation and mostly the

previously reported patient with ID and CIC mutation, the

c.680A>G nucleotide change could have a role in generating

the proband’s ID of trio 4.

KIAA2022. In vitro experiments showed that this gene is highly

expressed in fetal and adult murine brain and that it plays an

important role in postmitotic maturing neurons [Cantagrel

et al., 2009]. Ishikawa et al. [2012] studying the transient expression

ofKIAA2022 concluded that itwas involved in theneurite extension

and disturbances of this neuronal circuit formation and it could

play a role in the pathogenesis ofmental retardation.Moreover, this

genewas found interrupted in twomale patients with severemental

retardation [Cantagrel et al., 2004]. Since our patient is a 13-year-

old girl presenting amild ID,wedecided to study the inactivation of

chromosome X. Experiments carried out by amplification of poly-

morphic regions demonstrated a 65–35% values of inactivation.

Considering the above data reported, the stop codonmutation and

the skewed X-inactivation, we supposed that the KIAA2022muta-

tion could cause the proband’s ID.

We also report on two X-linked uncommon variants identified

by WES. Even if they are classified as polymorphisms, nevertheless

their occurrence in genes related to ID (HUWE1, ZNF41) makes

them very interesting to be reported.

HUWE1mutations were reported in several families as ID cause

[Froyen et al., 2008;Nava et al., 2012]; despite variationwe found in

this gene was included in dbSNP, it has been reported in 1 out of

4,548 analyzed chromosomes,without any information concerning

the gender of carrier. ZNF41 is a known ID gene reported and is

interrupted in a proband with a t(X;7)(p11.3;q11.21) translocation

and mutated in other unrelated patients [Shoichet et al., 2003].

To corroborate our study we performed target sequencing using

a custom ID panel. Target sequencing (305-fold average coverage)

174 AMERICAN JOURNAL OF MEDICAL GENETICS PART A

shows the following advantage, in comparison to WES (31-fold

average coverage): investigation of a large number of ID-related

genes with higher coverage in the proband (trio 6) previously

reported as negative to possibly causative mutations through

WES analysis. We also applied target sequencing of the remaining

probands, with the purpose to exclude any possibly other potential

mutations in the large set of our custom ID-related genes panel.

In the proband (trio 6), we identified a possibly causative variant

in the ID-related gene FGD1, hence a “false negative” inWES. This

missing was due to very low WES coverage across corresponding

FGD1 gene region. Mutations in this gene were reported both as

syndormic, associated with the Aarskog–Scott syndrome [Orrico

et al., 2010], and nonsyndromic, linked to ID [Lebel et al., 2002;

Martınez-Castellano, 2006].

FGD1 encodes a cytoplasmatic protein involved in actin cyto-

skeleton regulation and cell shape. FGD1 activates a membrane

anchored Ras-like RhoGTPase (CDC42). It is formed by one Dbl

homology (DH) domain, two pleckstrin homology (PH)-like

domains and one FYVE-type zinc finger. The novel mutation

(Pro742Ser) is actually located in the zinc finger. This proline is

notably conserved in all members of the FYVE-type zinc finger

family, and it is actually located just before a highly conservedmotif

of six hydrophobic aminoacids. Several structural and biophysical

studies reveal that this motif actually forms a hydrophobic loop

insertion that interacts with the inner cellular membrane in a non-

specific manner [Misra and Hurley, 1999; Kutateladze and

Overduin, 2001]. Since FGD1 needs to target the membrane for

further association with CDC42, it is presumable that Pro742Ser

may alter the membrane localization of FGD1, affecting the regu-

lation process. Since alterations in this gene have already been

reported as related to ID, it is quite plausible thatmutations in other

regions of the gene, such as theonewehave confirmedhere by target

sequencing, may have comparable effect (Supplemental Fig. S5 in

supporting information online).

ID Candidated GenesKDM5B. Given the homology with KDM5A and KDM5C and

the role of H3K4 demethylases in generating complex neurodeve-

lopmental diseases [Wynder et al., 2010], we decided to candidate

this gene as a new possibly ID-related. Indeed, the first one,

KDM5A, has been recently demonstrated as involved in autosomal

recessive ID [Najmabadi et al., 2011], while KDM5C has been

recently reported mutated in a syndromic form of X-linkedmental

retardation. It is characterized by moderate short stature, ID,

clumsy gait, ataxia, increased muscle tone, and hyperreflexia

[Ounap et al., 2012]. Considering the homology between these

genes and the pathogenicity of the nucleotide change insisting on

the splicing site, we suppose that this KDM5B splicing mutation

could have a causative role in the proband’s phenotype.

Interestingly, wedetected threemutations in two genes encoding

for Plexins proteins. Plexins are a group of transmembrane recep-

tors expressed in the central nervous system and involvedmainly in

the patterning of neural connections together with semaphorins

[Winberg et al., 1998]. The domains organization in this family of

genes is quite conserved: an extracellular receptor domain is con-

nected throw a single transmembrane alpha helix to the intracellu-

lar domain. The extracellular domain is formed by a semaphorin-

like receptor, a cysteine rich repeat characteristic of plexins and a Ig-

like fold domain found in cell surface receptors. The intracellular

domain is formed by a single Ras-like RhoGTPase activation

domain involved in downstream signaling pathways, acting by

interaction with many signaling proteins and other plexins. The

three novel mutations related to ID discovered for this family of

genes are located in three different regions of this domain organi-

zation (Supplemental Fig. S6 in supporting information online).

PLXNA3. Using null mice studies it has been demonstrated

that PLXNA3 contribute to Sema3A-induced cell death in vitro

[Ben-Zvi et al., 2008]. In this experiment, Ben-Zvi et al. demon-

strated that thePLXNA3was absolutely required for theprocess and

it provided the first evidence implicating semaphoring/

plexin signaling in neuronal survival. In fact, the plexins interacting

with the secreted class 3 semaphorins form complex co-

receptor structures with neuropilins in function to axon guidance

[Takahashi et al., 1999].

The discovered mutation Arg433His is located in the sema-

phorin-like receptor domain, thus suggesting that it may affect the

initiationof theplexin signalingmechanism.Very recently, the low-

resolution crystal structure of a mouse semaphorin-plexin-Nrp

ternary complex has been solved (PDB accession code: 4GZA)

[Janssen et al., 2012]. Mouse Plxna2 in this structure is homolog to

human PLXNA3 in the semaphorin receptor domain (52% se-

quence identity). Looking at this structure, the equivalent

position that corresponds to the discovered mutation (Lys451 in

mouse Plxna2) participates in defining the plexin-neuropilin

interface. Thus, it can be inferred from the structure that

modifications in this position will affect the formation of the

co-receptor structure (Supplemental Fig. S7 in supporting

information online).

A second ID related mutation has been discovered in the same

gene. In this case, Val1238Met is one of the 21 aminoacids

that defines the trans-membrane helix segment in human

PLXNA3. Since this helix is the only structural element that

spans both the extracellular medium and the intracellular one, it

is quite advisable that alterations in the structure of this helix will

affect the signal transduction capacity of the plexin through the

membrane (Supplemental Fig. S7 in supporting information

online).

PLXNB3. The protein encoded by this gene presents a high-

affinity to SEMA5A and this protein complex also plays an impor-

tant role in the axon-guidance-pathway, a key process in brain

development [Lin et al., 2009]. PLXNB3 actually interacts with a

RhoGTPase (Rac1) through the intracellular domain. The discov-

ered mutation in this gene (Ser1797Leu) is located in the cyto-

plasmic Ras GTPase activation domain. Recently, the crystal

structure of the paralog human PLXNB1 in complex with a

constitutively active RhoGTPase (Rac1) has been solved (PDB

accession code: 3SUA) [Bell et al., 2011]. Both genes are close

homologs in the intracellular domain (69% sequence identity).

Looking at this structure, the equivalent position that corresponds

to the discovered mutation (Ala2023 in human PLXNB1) partic-

ipates in direct interactions between the plexin and Rac1. Although

the structure is not fully resolved in this region, it can be inferred

from it that modifications in this position will affect the formation

ATHANASAKIS ET AL. 175

of the plexin-Rac1 complex. This will prevent the activation of Rac1

activity altering in the intracellular signaling processes (Supple-

mental Fig. S7 in supporting information online).

CONCLUSIONS

In summary, high-throughput sequencing in nine ID trios, through

a three steps analysis, might explain several cases of isolated ID.

However, the identification of plausible genetic causes, de novo,

andX-linkedmutations in ID-related genes andnot, request further

analysis.

ACKNOWLEDGMENTS

The authors thank patients and their parents who participated in

the study for their continuous support. Moreover, the authors

deeply appreciate Federico Fornasier and Marco Mocenigo of

Medical Genetics of Institute for Maternal and Child Health—

IRCCS “Burlo Garofolo,” for helping for timely completion of

Sanger sequencing.

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