A de novo 2q37.2 deletion encompassing AGAP1 and SH3BP4 in a patient with autism and intellectual disability

Accepted Manuscript A de novo 2q37.2 deletion encompassing AGAP1 and SH3BP4 in a patient with autism and intellectual disability Mathilde Pacault, Mathilde Nizon, Olivier Pichon, Marie Vincent, Cédric Le Caignec, Bertrand Isidor PII:

S1769-7212(18)30243-X

DOI:

https://doi.org/10.1016/j.ejmg.2018.11.020

Reference:

EJMG 3586

To appear in:

European Journal of Medical Genetics

Received Date: 27 March 2018 Revised Date:

19 October 2018

Accepted Date: 22 November 2018

Please cite this article as: M. Pacault, M. Nizon, O. Pichon, M. Vincent, Cé. Le Caignec, B. Isidor, A de novo 2q37.2 deletion encompassing AGAP1 and SH3BP4 in a patient with autism and intellectual disability, European Journal of Medical Genetics (2018), doi: https://doi.org/10.1016/j.ejmg.2018.11.020. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

1

ACCEPTED MANUSCRIPT A de novo 2q37.2 deletion encompassing AGAP1 and SH3BP4 in a patient with autism and intellectual disability

2

CHU Nantes, Service de Génétique Médicale, Nantes, France INSERM, UMR 1238, Bone sarcoma and remodeling of calcified tissue, Nantes, France

Corresponding Author: Mathilde Pacault

M AN U

Affiliation address : Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes 1 place Alexis Ricordeau 44093 Nantes Cedex, France Tel: +33 2 40 08 32 45 Fax: +33 2 40 08 76 47

SC

1

RI PT

Mathilde Pacault1, Mathilde Nizon1, Olivier Pichon1, Marie Vincent1, Cédric Le Caignec1,2, Bertrand Isidor1,2

EP

TE D

Present address: Laboratoire de Génétique Moléculaire et Histocompatibilité Centre Hospitalier Régional Universitaire de Brest 2 avenue Foch 29200 Brest, France Tel : +332 29 02 01 50

AC C

E-mail: [email protected]

1

2

ACCEPTED MANUSCRIPT Abstract

3

Autistic spectrum disorders are complex neurodevelopmental syndromes characterized by

4

phenotypic and genetic heterogeneity. Further identification of causal genes may help in

5

better understanding the underlying mechanisms of the disorder, thus improving the

6

patients’ management. To date, abnormal synaptogenesis is thought to be one of the major

7

underlying causes of autistic spectrum disorders.

8

Here, using oligoarray-based comparative genomic hybridization, we identified a de novo

9

deletion at 2q37.2 locus spanning 1 Mb and encompassing AGAP1 and SH3BP4, in a boy with

M AN U

SC

RI PT

2

autism and intellectual disability. Both genes have been described as being involved in

11

endosomal trafficking, and AGAP1 in particular has been shown to be expressed in the

12

developing brain and to play a role in dendritic spine formation and synapse function,

13

making it a potential causative gene to our patient’s phenotype.

14

TE D

10

Keywords

16

AGAP1; SH3BP4; Intellectual Disability; array CGH; Autistic Spectrum Disorder

AC C

17

EP

15

3

ACCEPTED MANUSCRIPT 18

Introduction Autistic spectrum disorder (ASD) is a neurodevelopmental disorder characterized by a

19

triad of limited or absent verbal communication, a lack of reciprocal social interaction or

21

responsiveness, and restricted, stereotypic, and ritualized patterns of interests and behavior.

22

Intellectual disability (ID) often coexists in patients with ASD suggesting common

23

physiological pathways. The prevalence of ASDs is estimated between 1/500 and 1/1000

24

children, making them one of the most common neurodevelopmental disorder (Geschwind,

25

2009).

SC

M AN U

26

RI PT

20

During the last decade, several causative variants were identified, such as recurrent Copy Number Variants (CNVs) identified by oligoarray-based comparative genomic

28

hybridization (aCGH) as well as single nucleotide variants in genes, arguing for a large

29

heterogeneity of ASD risk loci. Many evidences have unveiled a remarkable convergence of

30

several of these genes on common cellular pathways that intersect with neuronal

31

development and synaptic structure or function (Pescosolido et al., 2013).

EP

32

TE D

27

Here, we report on a patient presenting with ID and ASD associated with a 1Mb de novo 2q37.2 deletion, which encompasses only two genes: AGAP1 and SH3BP4, both

34

implicated in endocytic process. While SH3BP4 function in neuronal cells has not been fully

35

elucidated yet, the 2q37 region has been already linked to ASD (Wassink et al., 2005). More

36

recently, Leroy et al described a cohort of 14 patients with dysmorphic features,

37

brachydactyly, obesity, and neurodevelopmental disorders, for whom a 2q37 deletion had

38

been identified. Among these patients, one had a 1,1 Mb interstitial deletion also involving

39

AGAP1 and SH3BP4, presenting with obesity and mild developmental delay, but no autistic

AC C

33

4

ACCEPTED MANUSCRIPT features (Leroy et al, 2013). AGAP1 has been involved in dendritic spine morphology and

41

synapse function (Arnold et al., 2016). We suggest that haploinsufficiency of at least one of

42

these two genes might be pathogenic, maybe through a cumulative pathogenic effect on

43

brain development.

44

Clinical Report

The propositus is the second child of a healthy non-consanguineous couple. There

SC

45

RI PT

40

was no family history of major medical or genetic condition. He was born full term after an

47

uneventful pregnancy. His birth weight, length and head circumference (OFC) were 3.570 kg

48

(70th pc), 50 cm (mean) and 34 cm (30th pc), respectively.

49

M AN U

46

At 3 months of age, horizontal nystagmus was noticed. Ophthalmological investigations performed thereafter were normal. Global developmental milestones were

51

delayed, as he sat at 14 months of age, and walking was acquired at 24 months of age. At

52

age 8, he spoke only a few words but with a better level of comprehension. He presented

53

with auto- and heteroaggressive behavior as well as stereotypic patterns and sleeping

54

disorder.

EP

At last evaluation, age 10 years and 6 months, his height, weight and OFC were 131

AC C

55

TE D

50

56

cm (-1SD), 24 kg (-2SD), and 53.5cm (mean), respectively. There were no dysmorphic

57

features, no phenotypic particularities and notably no brachymetacarpy or brachymetatarsy.

58

Clinical examination was normal, and nystagmus was not reported. Special education was

59

required. He could only pronounce a few words. Brain MRI, metabolic analyses and FMR1

60

testing were normal.

61

Cytogenetic analysis

5

ACCEPTED MANUSCRIPT 62

Informed consent for genetic analyses was obtained from the patient and his parents according to local ethical guidelines. Genomic DNA was extracted from peripheral blood

64

using standard protocols. Array comparative genomic hybridization (aCGH) experiments

65

were performed using Agilent Human Genome CGH 60K oligonucleotide arrays (Agilent™,

66

Santa Clara, CA) with the ISCA V2 design (www.iscaconsortium.org). Arrays were scanned

67

with the Agilent scanner and analysed with Cytogenomics 3.0.2.11 software (Agilent™).

RI PT

63

Fluorescence in situ hybridization (FISH) was performed using standard protocol in

69

the patient’s and his parents’ blood cells, with the RP11-93C24 BAC probe targeted to the

70

2q37.2 deleted region and the subtelomeric 2p25.3 892G20 probe as control.

71

Results

M AN U

SC

68

The 60K aCGH experiment showed a single copy loss of the long arm of chromosome

73

2 (2q37.2), spanning approximately 1.06 Mb with estimated breakpoints at chr2:234966458-

74

236025317 (GRCh38/hg38) in a male (Figure 1A). No other pathogenic imbalance was

75

identified. Karyotype was written as arr[GRCh38] 2q37.2(234966458_236025317)x1.

EP

76

TE D

72

FISH analyses confirmed the interstitial deletion and showed its de novo occurrence (Figure 1B). This deletion encompassed 2 genes, namely AGAP1 (MIM*608651) and SH3BP4

78

(MIM*605611). This deletion was submitted to the Decipher database (Firth et al., 2009) as

79

number 251750.

80

AC C

77

Inquiry on Decipher database (Firth et al., 2009) showed no similar deletion, as other

81

patients presented with larger deletions encompassing more genes. A patient was previously

82

reported with a similar 1Mb deletion encompassing SH3BP4 and AGAP1 and showed obesity

83

and isolated ID without ASD (Leroy et al., 2013). Concerning AGAP1, haploinsufficiency score

6

ACCEPTED MANUSCRIPT (Huang et al., 2010) was evaluated between 10 and 20%. Finally, ExAC (Lek et al., 2016)

85

predicted a Z-score on missense variants of 2.28 and a probability of Loss of Function

86

intolerance of 1, making AGAP1 a gene likely intolerant to variation or haploinsufficiency. On

87

the other hand, SH3BP4 showed a haploinsufficiency score of 50 to 60% with predicted Z-

88

score on missense variants of 0.96 and probability of Loss of Function Intolerance of 0.08,

89

making this gene more tolerant to haploinsufficiency. One patient has been reported in

90

Decipher with a SH3BP4 deletion inherited from a healthy parent, as well as a de novo 778

91

kb duplication on chromosome 16 (ID 254671). Unfortunately, no phenotypic features have

92

been reported for this patient.

93

Discussion

SC

M AN U

94

RI PT

84

AGAP1 (MIM*608651), also called CENTG2 (centaurin gamma2) encodes a 857 aminoacid protein belonging to an ADP-ribosylation factor (Arf) GTPase-activating (GAP)

96

family, characterized by a highly conserved Arf-GAP domain (Kahn et al., 2008). These

97

proteins range from relatively small proteins to large, multidomain proteins that are thought

98

to function as scaffolds for cell signaling (Kahn et al., 2008). Within this protein family, the

99

AGAPs proteins form the largest subgroup (Luo et al., 2012). AGAP1 is a ubiquitous

AC C

EP

TE D

95

100

multivalent scaffold protein, characterized by a GTP-binding protein-like domain, a split

101

pleckstrin homology domain, the ArfGAP domain and an ankyrin repeat domain (Nie et al.,

102

2002). It has been shown to be involved in endocytic pathway, membrane trafficking and

103

actin cytoskeleton dynamics (Nie et al., 2002, Luo et al., 2016).

104

AGAP1 is likely involved in neurodevelopmental disorders. Indeed, it was first

105

evaluated as a candidate ASD susceptibility gene in patients with large 2q37 terminal

7

ACCEPTED MANUSCRIPT

deletion identified by standard karyotyping and FlSH analyses (Casas et al., 2004, Wassink et

107

al., 2005) and linked to schizophrenia in a large Genome-Wide Association Study (Shi et al.,

108

2009). To be noted that our patient does not present any dysmorphic features, unlike what

109

was previously described by Falk and Casas (Falk and Casas, 2007). AGAP1 associates in

110

neuronal cells with the endosomal complexes AP-3 (adaptor protein 3) and BLOC-1

111

(Biogenesis of Lysosome related Organelles Complex 1) with a role in dopamine release

112

through endocytic recycling of muscarinic receptor (Bendor et al., 2010). These two proteins

113

have also been identified as risk factors for ASD (O’Roak et al., 2012) and schizophrenia

114

(Greenwood et al., 2011). More recently, AGAP1 has been shown in a mouse model to be

115

expressed in the developing brain starting at embryonic day16.5 and increasing throughout

116

prenatal and postnatal development with highest levels of expression in the hippocampus.

117

AGAP1 was found to modulate dendritic spines morphology and density, with AGAP1

118

deficiency causing dendritic spine abnormalities such as can be seen in intellectual

119

disabilities of other cause (Arnold et al., 2016). Finally, other proteins from the same

120

centaurin family have been involved in PI-3-phosphate and ADP-ribosylation pathways

121

influencing neuronal processes such as cell growth, differentiation, survival, metabolism,

122

transcription, vesicular trafficking and cytoskeletal organization (Jackson et al., 2000).

123

Altogether, these data strongly suggest an involvement of AGAP-1-dependant endosomal

124

trafficking in neurodevelopmental disorders (Ryder and Faundez, 2009, Arnold et al., 2016).

125

AC C

EP

TE D

M AN U

SC

RI PT

106

The other gene involved, SH3BP4, encodes a ubiquitous 963 aminoacid protein,

126

SH3BP4 (SH3-domain binding protein 4), that was first identified in cultured human corneal

127

fibroblasts (Dunlevy et al., 1999). It has been shown to be a negative regulator of the mTOR

128

signaling pathway (Kim et al., 2012). It contains repeat motifs for binding to the Eps15

8

ACCEPTED MANUSCRIPT homology domain as well as binding sites for proteins involved in endocytosis such as

130

clathrin (Kim et al. 2013). Perturbation of SH3BP4 levels have been shown to impair

131

transferrin receptor endocytosis (Tosoni et al., 2005), but mechanisms have not been

132

described further since the first report. Overall, it seems that SH3BP4 is a part of cargo

133

complex that regulates endocytosis by interacting directly via clathrin and dynamin2 but to

134

date, little is known about its neuronal functions.

Interestingly, 2q37 microdeletion has been previously individualized as a specific

SC

135

RI PT

129

syndrome (Wilson et al., 1995, Doherty et al., 2007) with a broad clinical spectrum, including

137

mild to moderate ID, ASD, short stature, obesity, facial dysmorphism and skeletal

138

abnormalities such as brachymetaphalangism (Brachydactyly-Mental Retardation Syndrome,

139

BDMR, OMIM #600430). Phenotypical heterogeneity and important clinical variability have

140

been described, as some patients carrying the deletion did not show developmental delay

141

(Wheeler et al., 2014, Jean-Marçais et al., 2015), whereas other have been described

142

without brachydactyly (Villavicencio-Lorini et al., 2013, Ogura et al., 2014). To our

143

knowledge, no recurrent breakpoints have been identified (Aldred et al., 2004, Leroy et al,

144

2013). The critical region has been narrowed to a 200 kb region containing HDAC4 (Williams

145

et al., 2010), although this gene alone may not be responsible for ID (Wheeler et al., 2014).

146

Interestingly, an atypical 2q37 microdeletion syndrome phenotype has already been

147

reported by Leroy et al (Leroy et al., 2013), where the patient presented with ID but no

148

skeletal involvement, and an interstitial deletion encompassing SH3BP4 and AGAP1. As this

149

patient was obese, the authors suggested AGAP1 involvement in obesity, but our

150

observation does not support this hypothesis. To be noted that this patient did not present

151

with 2q37-deletion syndrome associated facial dysmorphism either (Leroy et al., 2013, Falk

AC C

EP

TE D

M AN U

136

9

ACCEPTED MANUSCRIPT and Casas, 2007). A patient was also reported in Decipher (ID 254671) with a 767 kb CNV

153

leading to SH3BP4 deletion, inherited from a healthy parent, as well as a small duplication on

154

chromosome 16 that was considered pathogenic. Although no associated phenotype was

155

described, this description is in favor of AGAP1 role in our patient’s phenotype.

156

RI PT

152

As our patient’s deletion disrupts two genes, we cannot completely rule out that it would result in a fusion transcript between exon 1 of SH3BP4 and exons 14 to 18 of AGAP1.

158

This mechanism was previously suggested as another mechanism for ASD susceptibility (Holt

159

et al., 2012, Ceroni et al., 2014), but the authors emphasized the need for further studies.

160

Unfortunately, because of lack of our patient’s RNA and lymphoblastoid cell lines, we could

161

not conduct any further functional study for this deletion.

M AN U

162

SC

157

As a conclusion, we present here a patient presenting with ASD caused by a 2q37.2 deletion encompassing AGAP1 and SH3BP4. This deletion is smaller than the ones previously

164

reported, which may explain the absence of obesity and skeleton involvement in our patient

165

compared to the 2q37-deletion syndrome. We cannot conclude on a unique causative gene

166

as, although AGAP1 is most likely involved in the pathogenesis of ASD in our patient, we

167

cannot exclude a participation of SH3BP4 haploinsufficiency. However, with this report, we

168

hope to further delineate the role of AGAP1 and SH3BP4 in the phenotype associated with a

169

2q37.2 deletion.

170

Acknowledgments

171

The authors thank the family described in this report.

172

The authors have no conflict of interest to declare.

AC C

EP

TE D

163

10

ACCEPTED MANUSCRIPT This research did not receive any specific grant from funding agencies in the public,

174

commercial, or not-for-profit sectors.

AC C

EP

TE D

M AN U

SC

RI PT

173

11

ACCEPTED MANUSCRIPT Legend of figure: A:

Map

of

the

patient’s

deletion

adapted

from

UCSC

genome

browser

(https://genome.ucsc.edu/index.html). Our patient’s deletion is depicted as the red

RI PT

rectangle. Overlapping deletions as described in Decipher (https://decipher.sanger.ac.uk/) and Patient 5 from Leroy’s report (Leroy et al, Eur J Hum Genet, 2013) are depicted as grey

SC

rectangles.

All patients reported here present with ID or developmental delay except for patients

M AN U

285992 and 266258. Patients 248985 and 294708 also presented with ASD. Only patients 248985 and 278203 presented with brachydactyly.

B: In situ hybridization confirmation of the deletion and transmission study. The specific

AC C

EP

proband.

TE D

probe (RP11-93C24, red) is detected on both chromosomes in the parents but deleted in the

12

ACCEPTED MANUSCRIPT References

Aldred, M.A., Sanford, R.O., Thomas, N.S., Barrow, M.A., Wilson, L.C., Brueton, L.A., Bonaglia, M.C., Hennekam, R.C., Eng, C., Dennis, N.R., Trembath, R.C., 2004. Molecular analysis of 20

RI PT

patients with 2q37.3 monosomy: definition of minimum deletion intervals for key phenotypes. J Med Genet, 41:433–9.

Arnold, M., Cross, R., Singleton, K.S., Zlatic, S., Chapleau, C., Mullin, A.P., Rolle, I., Moore,

SC

C.C., Theibert, A., Pozzo-Miller, L., Faundez, V., Larimore, J., 2016. The Endosome Localized

M AN U

Arf-GAP AGAP1 Modulates Dendritic Spine Morphology Downstream of the Neurodevelopmental Disorder Factor Dysbindin. Front Cell Neurosci, 22, 10-218. Bendor, J., Lizardi-Ortiz, J.E., Westphalen, R.I., Brandstetter, M., Hemmings, H.C. Jr, Sulzer, D., Flajolet, M., Greengard, P., 2010. AGAP1/AP-3-dependent endocytic recycling of M5

TE D

muscarinic receptors promotes dopamine release. EMBO J, 29, 2813-26. Casas, K.A., Mononen, T.K., Mikail, C.N., Hassed, S.J., Li, S., Mulvihill, J.J., Lin, H.J., Falk, R.E., 2004. Chromosome 2q terminal deletion: report of 6 new patients and review of phenotype-

EP

breakpoint correlations in 66 individuals. Am J Med Genet A, 130A, 331-9.

AC C

Ceroni, F., Sagar, A., Simpson, N.H., Gawthrope, A.J., Newbury, D.F., Pinto, D., Francis, S.M., Tessman, D.C., Cook, E.H., Monaco, A.P., Maestrini, E., Pagnamenta, A.T., Jacob, S.. 2014. A deletion involving CD38 and BST1 results in a fusion transcript in a patient with autism and asthma. Autism Res, 7, 254-63. doi: 10.1002/aur.1365. Doherty, E.S., Lacbawan, F.L, 2007. 2q37 Microdeletion Syndrome. [updated 2013 Jan 31]. GeneReviews®

13

ACCEPTED MANUSCRIPT Dunlevy, J.R., Berryhill, B.L., Vergnes, J.P., SundarRaj, N., Hassell, J.R., 1999. Cloning, chromosomal localization, and characterization of cDNA from a novel gene, SH3BP4, expressed by human corneal fibroblasts. Genomics, 62, 519-24.

RI PT

Falk, R.E., Casas, K.A., 2007. Chromosome 2q37 deletion: Clinical and molecular aspects. Am J Med Genet C Semin Med Genet, 145C, 357–371.

Firth, H.V., Richards, S.M., Bevan, A.P., Clayton, S., Corpas, M., Rajan, D., Van Vooren, S.,

SC

Moreau, Y. Pettett, R.M., Carter, N.P., 2009. DECIPHER: Database of Chromosomal

Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet, 84, 524-

M AN U

33.

Geschwind, D.H., 2009. Advances in autism. Ann Rev Med, 60, 367-80. Greenwood, T.A., Lazzeroni, L.C., Murray, S.S., Cadenhead, K.S., Calkins, M.E., Dobie, D.J., Green, M.F, Gur, R.E., Hardiman, G., Kelsoe, J.R., Leonard, S., Light, G.A., Nuechterlein, K.H.,

TE D

Olincy, A., Radant, A.D., Schork, N.J., Seidman, L.J., Siever, L.J., Silverman, J.M., Stone, W.S., Swerdlow, N.R., Tsuang, D.W., Tsuang, M.T., Turetsky, B.I., Freedman, R., Braff, D.L., 2011.

EP

Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia. Am J Psychiatry, 168, 930-46. doi:

AC C

10.1176/appi.ajp.2011.10050723.

Huang, N., Lee, I., Marcotte, E.M., Hurles, M.E., 2010. Characterising and predicting haploinsufficiency in the human genome. PLoS Genet, 6, e1001154. Jackson, T.R., Kearns, B.G., Theibert, A.B., 2000. Cytohesins and centaurins: mediators of PI3kinase-regulated Arf signaling. Trends Biochem Sci, 25, 489-95. Jean-Marçais, N., Decamp, M., Gérard, M., Ribault, V., Andrieux, J., Kottler, M.L., Plessis, G., 2015. The first familial case of inherited 2q37.3 interstitial deletion with isolated skeletal

14

ACCEPTED MANUSCRIPT abnormalities including brachydactyly type E and short stature. Am J Med Genet A, 167A(1):185-9. doi: 10.1002/ajmg.a.36428. Kahn, R.A., Bruford, E., Inoue, H., Logsdon, J.M. Jr, Nie, Z., Premont, R.T., Randazzo, P.A.,

RI PT

Satake, M., Theibert, A.B., Zapp, M.L., Cassel, D., 2008. Consensus nomenclature for the human ArfGAP domain-containing proteins. J Cell Biol, 182, 1039-44.

Kim, Y.M., Stone, M., Hwang, T.H., Kim, Y.G., Dunlevy, J.R., Griffin, T.J., Kim, D.H., 2012.

833-46. doi:10.1016/j.molcel.2012.04.007.

SC

SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Mol Cell, 46,

M AN U

Kim, Y.M., Kim, D.H., 2013. dRAGging amino acid-mTORC1 signaling by SH3BP4. Mol Cells, 35, 1-6. doi: 10.1007/s10059-013-2249-1.

Lek, M., Karczewski, K.J., Minikel, E.V., Samocha, K.E., Banks, E., Fennell, T., O’Donnell-Luria, A.H., Ware, J.S., Hill, A.J., Cummings, B.B., Tukiainen, T., Birnbaum, D.P., Kosmicki, J.A.,

TE D

Duncan, L.E., Estrada, K., Zhao, F., Zou, J., Pierce-Hoffman, E., Berghout, J., Cooper, D.N., Deflaux, N., DePristo, M., Do, R., Flannick, J., Fromer, M., Gauthier, L., Goldstein, J., Gupta,

EP

N., Howrigan, D., Kiezun, A., Kurki, M.I., Moonshine, A.L., Natarajan, P., Orozco, L., Peloso, G.M., Poplin, R., Rivas, M.A., Ruano-Rubio, V., Rose, S.A., Ruderfer, D.M., Shakir, K., Stenson,

AC C

P.D., Stevens, C., Thomas, B.P., Tiao, G., Tusie-Luna, M.T., Weisburd, B., Won, H.H., Yu, D., Altshuler, D.M., Ardissino, D., Boehnke, M., Danesh, J., Donnelly, S., Elosua, R., Florez, J.C., Gabriel, S.B., Gets, G., Glatt, S.J., Hultman, C.M., Kathiresan, S., Laakso, M., McCarroll, S., McCarthy, M.I., McGovern, D., McPherson, R., Neale, B.M., Palotie, A., Purcell, S.M., Saleheen, D., Scharf, J.M., Sklar, P., Sullivan, P.F., Tuomilehto, J., Tsuang, M.T., Watkins, H.C., Wilson, J.G., Daly, M.J., MacArthur, D.G., Exome Aggregation Consortium, 2016. Analysis of

15

ACCEPTED MANUSCRIPT protein-coding genetic variation in 60,706 humans. Nature, 536, 285-91. doi: 10.1038/nature19057. Leroy, C., Landais, E., Briault, S., David, A., Tassy, O., Gruchy, N., Delobel, B., Grégoire, M.J.,

RI PT

Leheup, B., Taine, L., Lacombe, D., Delrue, M.A., Toutain, A., Paubel, A., Mugneret, F., Thauvin-Robinet, C., Arpin, S., Le Caignec, C., Jonveaux, P., Beri, M., Leporrier, N., Motte, J., Fiquet, C., Brichet, O., Mozelle-Nivoix, M., Sabouraud, P., Golovkine, N., Bednarek, N.,

SC

Gaillard, D., Doco-Fenzy, M., 2013. The 2q37-deletion syndrome: an update of the clinical spectrum including overweight, brachydactyly and behavioural features in 14 new patients.

M AN U

Eur J Hum Genet, 21(6):602-12. doi: 10.1038/ejhg.2012.230.

Holt, R., Sykes, N.H., Conceição, I.C., Cazier, J.B., Anney, R.J., Oliveira, G., Gallagher, L., Vicente, A., Monaco, A.P., Pagnamenta, A.T.. 2012. CNVs leading to fusion transcripts in

10.1038/ejhg.2012.73.

TE D

individuals with autism spectrum disorder. Eur J Hum Genet, 20, 1141-7. doi:

Luo, R., Akpan, I.O., Hayashi, R., Sramko, M., Barr, V., Shiba, Y., Randazzo, P.A., 2012. GTP-

EP

binding protein-like domain of AGAP1 is protein binding site that allosterically regulates ArfGAP protein catalytic activity. J Biol Chem, 287, 17176-85. doi: 10.1074/jbc.M111.334458.

AC C

Luo, R., Chen, P.W., Wagenbach, M., Jian, X., Jenkins, L., Wordeman, L., Randazzo, P.A., 2016. Direct Functional Interaction of the Kinesin-13 Family Membrane Kinesin-like Protein 2A (Kif2A) and Arf GAP with GTP-binding Protein-like, Ankyrin Repeats and PH Domains1 (AGAP1). J Biol Chem, 291, 21350-21362. doi:10.1074/jbc.M116.732479. Nie, Z., Stanley, K.T., Stauffer, S., Jacques, K.M., Hirsch, D.S., Takei, J., Randazzo, P.A., 2002. AGAP1, an endosome-associated, phosphoinositide-dependent ADP-ribosylation factor GTPase-activating protein that affects actin cytoskeleton. J Biol Chem , 277, 48965-75.

16

ACCEPTED MANUSCRIPT

O'Roak, B.J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B.P., Levy, R., Ko, A., Lee, C., Smith, J.D., Turner, E.H., Stanaway, I.B., Vernot, B., Malig, M., Baker, C., Reilly, B., Akey, J.M., Borenstein, E., Rieder, M.J., Nickerson, D.A., Bernier, R., Shendure, J., Eichler, E.E., 2012.

mutations. Nature, 485, 246-50. doi: 10.1038/nature10989.

RI PT

Sporadic autism exomes reveal a highly interconnected protein network of de novo

Ogura, K., Takeshita, K., Arakawa, C., Shimojima, K., Yamamoto, T., 2014.

SC

Neuropsychological profiles of patients with 2q37.3 deletion associated with developmental

doi:10.1002/ajmg.b.32274.

M AN U

dyspraxia. Am J Med Genet B Neuropsychiatr Genet. 165B(8):684-90.

Pescosolido, M.F., Gamsiz, E.D., Nagpal, S., Morrow, E.M., 2013. The Distribution of DiseaseAssociated Copy Number Variants Across Distinct Disorders of Cognitive Development. J Am Acad Child Adolesc Psychiatry, 52, 414-430.

TE D

Ryder, P.V., Faundez, V., 2009. Schizophrenia: the "BLOC" may be in the endosomes. Sci Signal, 2, pe66. doi: 10.1126/scisignal.293pe66.

EP

Shi, J., Levinson, D.F., Duan, J., Sanders, A.R., Zheng, Y., Pe'er, I., Dudbridge, F., Holmans, P.A., Whittemore, A.S., Mowry, B.J., Olincy, A., Amin, F., Cloninger, C.R., Silverman, J.M.,

AC C

Buccola, N.G., Byerley, W.F., Black, D.W., Crowe, R.R., Oksenberg, J.R., Mirel, D.B., Kendler, K.S., Freedman, R., Gejman, P.V., 2009. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature, 460, 753-7. doi:10.1038/nature08192. Tosoni, D., Puri, C., Confalonieri, S., Salcini, A.E., De Camilli, P., Tacchetti, C., Di Fiore, P.P., 2005. TTP specifically regulates the internalization of the transferring receptor. Cell, 123, 875-88.

17

ACCEPTED MANUSCRIPT Villavicencio-Lorini, P., Klopocki, E., Trimborn, M., Koll, R., Mundlos, S., Horn, D., 2013. Phenotypic variant of Brachydactyly-mental retardation syndrome in a family with an inherited interstitial 2q37.3 microdeletion including HDAC4. Eur J Hum Genet, 21:743–8.

RI PT

Wassink, T.H., Piven, J., Vieland, V.J., Jenkins, L., Frantz, R., Bartlett, C.W., Goedken, R., Childress, D., Spence, M.A., Smith, M., Sheffield, V.C., 2005. Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene. Am J Med Genet B Neuropsychiatr

SC

Genet, 136B, 36-44.

Wheeler, P.G., Huang, D., Dai, Z., 2014. Haploinsufficiency of HDAC4 does not cause

M AN U

intellectual disability in all affected individuals. Am J Med Genet A, 164A(7):1826-9. doi: 10.1002/ajmg.a.36542.

Williams, S.R., Aldred, M.A., Der Kaloustian, V.M., Halal, F., Gowans, G., McLeod, D.R., Zondag, S., Toriello, H.V., Magenis, R.E., Elsea, S.H., 2010. Haploinsufficiency of HDAC4

TE D

causes brachydactyly mental retardation syndrome, with brachydactyly type E, developmental delays, and behavioral problems. Am J Hum Genet, 87:219–28.

EP

Wilson, L.C., Leverton, K., Oude Luttikhuis, M.E., Oley, C.A., Flint, J., Wolstenholme, J., Duckett, D.P., Barrow, M.A., Leonard, J.V., Read, A.P., et Trembath, R.C., 1995. Brachydactyly

AC C

and mental retardation: an Albright hereditary osteodystrophy-like syndrome localized to 2q37. Am J Hum Genet, 56(2):400-7.

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT