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Xp11.3CNV Type: Deletion-Duplication


Largest CNV size: 664901 bp

Statistics Box:
Number of Reports: 15



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
Structural variation of chromosomes in autism spectrum disorder.
Duplication
Deletion of MAOA and MAOB in a male patient causes severe developmental delay, intermittent hypotonia and stereotypical hand movements.
Deletion
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
MAOA/B deletion syndrome in male siblings with severe developmental delay and sudden loss of muscle tonus.
Deletion
Excess of rare, inherited truncating mutations in autism.
Duplication
Array-CGH Analysis in a Cohort of Phenotypically Well-Characterized Individuals with Essential Autism Spectrum Disorders.
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Identification of candidate intergenic risk loci in autism spectrum disorder.
Duplication
Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Recurrent copy number variations as risk factors for Autism Spectrum Disorders: analysis of the clinical implications.
Duplication
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 engchuan_15_ASD_discovery_cases
 Samples from the Autism Genome Project (AGP)
 1892
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 N/A
 85.78% Male
 212362
 0
 2
 2
 kaminsky_11_DD/ID/ASD_discovery_cases
 Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium
 15749
 Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome
 NA
 NA
 1081794
 0
 8
 8
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 10267
 0
 1
 1
 kushima_18_ASD_discovery_cases
 Individuals predominantly recruited from the middle of Honshu Island (Japan)
 1108
 Cases were diagnosed with ASD according to DSM-5 criteria, with diagnostic and screening instruments (ADI-R, ADOS, ASQ, and SRS) used to evaluate ASD-related behaviors and symptoms in the majority of cases.
 Median age, 19 years
 78.0% Male
 1900362
 1
 0
 1
 lionel_13_ASD/ADHD/DD/ID_discovery_cases
 Individuals referred for postnatal genetic testing across 10 different sites, including 64,114 subjects with neurodevelopmental disorders, from Alberta Children's Hospital, BBGRE, Boston Children's Hospital, Credit Valley Hospital, the Hospital for Sick Children, Italian diagnostic laboratories, The Mayo Clinic, Odense University Hospital, Signature Genomics, and The Centre for Applied Genomics
 89985
 64,114 cases with neurodevelopmental disorders (including ASD, ADHD, developmental delay, and/or intellectual disability); 25,871 cases with non-neurodevelopmental disorders (multiple congential anomalies, etc.)
 N/A
 N/A
 53420
 0
 2
 2
 marshall_08_ASD_discovery_cases
 Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
 427
 ASD
 
 
 664901
 0
 1
 1
 napoli_17_ASD_discovery_cases
 Children recruited between June 2009 and December 2014 at the Child Neuopsychiatry Unit of Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
 133
 Inclusion criteria included a clinical diagnosis of pervasive developmental disorders (PDD) and of ASD, according to DSM-IV-TR and DSM-5 criteria, respectively, and fewer than six dysmorphic features (children with six or more minor anomalies and/or systemic congenital malformations, such as congenital heart defects, were excluded). Cognitive or developmental level was assessed by the brief intelligence quotient (IQ) from Leiter-R or by the general quotient (GQ) from Griffiths Mental Development Scales Extended Revised for age 2-8, GMDS-ER 2-8 (mean IQ, 73.7 24.3). The calibrated severity score (CSS) index was also calculated to quantify autism symptoms independently (median score of 7, r
 Mean, 6.7 3.0 years
 84.96% Male
 377000
 0
 1
 1
 oikonomakis_16_ASD_discovery_cases
 ASD cases evaluated with chromosomal microarray (CMA) from 2008-2015
 195
 Cases assessed for ASD according to DSM-IV behavioral criteria
 Range, 1-38 yrs.
 64.61% Male
 180000
 0
 1
 1
 pinto_10_ASD_discovery_cases
 Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
 996
 ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
 
 
 36986
 0
 1
 1
 prasad_12_ASD_discovery_cases
 Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
 676
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
 NA
 82.84% Male
 412785
 3
 2
 5
 saito_13_ASD_discovery_cases
 Affected male siblings born to healthy parents presenting with ASD, severe developmental delay and sudden loss of muscle tone
 2
 Diagnosis of ASD (n=1) and PDD-NOS (n=1) based on fulfillment of DSM-IV criteria
 Range, 4-5 yrs.
 Male
 800000
 2
 0
 2
 sanders_11_ASD_discovery_cases
 Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
 1124
 ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
 Mean, 9.1 yrs.
 86.1% Male
 27207
 5
 2
 7
 tzetis_12_DD/ID_discovery_cases
 Patients referred for aCGH analysis from 2008-present
 334
 Cases presented with at least one of the following clinical indications: developmental delay (DD), intellectual disability (ID), dysmorphic features, unique or multiple congenital anomalies (MCA), growth disorder, behavior disorder, and/or autism (ASD)
 Range, 1 month-38 years (median age of 4 years)
 
 560000
 1
 0
 1
 walker_13_ASD_discovery_cases
 Unrelated ASD probands previously described in Lionel et al., 2011 and Pinto et al., 2010 CNV reports
 1491
 Diagnosis of ASD based on gold-standard instruments including ADI and ADOS.
 N/A
 N/A
 412998
 0
 1
 1
 whibley_10_DD_discovery_cases
 Two affected brothers born to healthy non-consanguienous Caucasian couple with healthy older sister
 2
 Severe developmental delay, intermittent hypotonia, and autistic behaviors (stereotypical hand movements)
 Range, 5-15 yrs.
 Male
 240000
 2
 0
 2

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 engchuan_15_ASD_discovery_controls
 Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)
 2342
 Controls; subjects had no previous psychiatric history
 N/A
 46.67% Male
 468617
 0
 2
 2
 kaminsky_11_DD/ID/ASD_discovery_controls
 Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium
 10118
 Controls
 NA
 NA
 NA
 NA
 NA
 NA
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 199353
 0
 1
 1
 kushima_18_ASD/SCZ_discovery_controls
 Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
 2095
 Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
 Median age, 37 years
 52.0% Male
 0
 0
 0
 0
 marshall_08_ASD_discovery_controls_1
 German PopGen project and entries from Database of Genomic Variants
 500
 Controls
 
 
 0
 0
 0
 0
 marshall_08_ASD_discovery_controls_2
 Non-disease controls from Ontario population
 1152
 Controls
 
 
 0
 0
 0
 0
 prasad_12_ASD_discovery_controls
 PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
 5139
 Control
 NA
 NA (PDx controls 50.2% male)
 412785
 0
 0
 0
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 27235
 3
 4
 7
 walker_13_ASD_discovery_controls
 Control samples from the SAGE cohort (n=1287), from the Ottawa Heart Institute (n=1234), and from the POPGEN collection (n=1123)
 3644
 Control
 N/A
 N/A
 412998
 N/A
 N/A
 N/A

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 kaminsky_11_DD/ID/ASD_discovery_cases
  NA
 aCGH
  Agilent 44K, Agilent 105K
 
 Feature Extraction, DNA Analytics
 FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 kushima_18_ASD_discovery_cases
  Japanese
 aCGH
  NimbleGen 720K, Agilent 400K
 FASST2
 Nexus Copy Number v.9.0
 N/A
 lionel_13_ASD/ADHD/DD/ID_discovery_cases
  N/A
 aCGH, array SNP, solid phase hybridization
  Multiple platforms (Agilent, Affymetrix, Illumina)
 
 
 None
 marshall_08_ASD_discovery_cases
  90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
 Array SNP, karotyping
  Affymetrix 500K
 dChip, CNAG, GEMCA
 
 qPCR, qmPCR
 napoli_17_ASD_discovery_cases
  Italy
 aCGH
  Agilent Human Genome 4x180K
 ADM-2
 Feature Extraction v.10.5, Agilent Genomic Workbench Lite Edition v.7.4
 RT-PCR
 oikonomakis_16_ASD_discovery_cases
  Greece
 aCGH
  Agilent 244K, 4x180K, or 4x180K (SurePrint G3 arrays)
 
 
 None
 pinto_10_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium 1M SNP microarray
 QuantiSNP, iPattern
 
 qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 saito_13_ASD_discovery_cases
  Japanese
 aCGH
  Agilent 180K
 
 CGH-Analytics V3.4
 qPCR
 sanders_11_ASD_discovery_cases
  White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
 Solid phase hybridization
  Illumina 1M v1, Illumina 1M v3
 PennCNV, QuantiSNP, GNOSIS
 
 
 tzetis_12_DD/ID_discovery_cases
  Greece
 aCGH
  Agilent 244K, Agilent 4x180K
 ADM-1
 Agilent Feature Extraction V9.1, Agilent CGH Analytics V4.0, Illumina GenomeStudio V2011.1
 None
 walker_13_ASD_discovery_cases
  N/A
 Array SNP, solid phase hybridization
  Illumina 1M, Affymetrix 6.0
 
 QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
 None
 whibley_10_DD_discovery_cases
  Caucasian
 aCGH
  X-chromosome-specific Nimblegen 385K array
 ADM-1
 Agilent CGH Analytics V3.4
 Array SNP (Affymetrix 250K Nsp), FISH, qPCR, long-range PCR

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  None
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  kushima_18_ASD/SCZ_discovery_controls
  Japanese
  aCGH
  NimbleGen 720K, Agilent 400K
  FASST2
  Nexus Copy Number v.9.0
  N/A
  marshall_08_ASD_discovery_controls_1
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  marshall_08_ASD_discovery_controls_2
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  prasad_12_ASD_discovery_controls
  NA
  aCGH
  Agilent 1M
  ADM-2, DNAcopy (R Bioconductor)
  DNA Analytics v4.0.85 (Agilent), DNAcopy
 
  sanders_11_ASD_discovery_controls
 
  Solid phase hybridization
  Illumina 1M v1 or Illumina 1M v3
  PennCNV, QuantiSNP, GNOSIS
 
 
  walker_13_ASD_discovery_controls
  N/A
  Array SNP, solid phase hybridization
  Illumina 1M, Affymetrix 6.0
 
  QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
  None

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  engchuan_15_ASD_discovery_cases-case3240_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 44962513
 45174875
  212363
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case5007_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 46511595
 46548580
  36986
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001846
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46156693
 46636156
  479464
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001872
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46184889
 46582592
  397704
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002271
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46456409
 46476928
  20520
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002438
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46508077
 46548482
  40406
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002722
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46617620
 46973582
  355963
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004897
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46456409
 46476928
  20520
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004916
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 46514093
 46548482
  34390
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005379
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 43573663
 44655459
  1081797
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case11109.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 46462747
 46473014
  10268
 GRCh38
 Duplication
 Yes
  kushima_18_ASD_discovery_cases-caseASD1059
 44 yrs.
 F
 ASD
 No additional clinical information reported for this individual. Family history: unknown.
 
 44209146
 46109507
  1900362
 GRCh38
 Deletion
 N/A
  lionel_13_ASD/ADHD/DD/ID_discovery_cases-case9
 N/A
 M
 Developmental delay and anxiety disorder
 Developmental delay, anxiety disorder, macrocephaly.
 
 44334346
 44387765
  53420
 GRCh38
 Triplication
 No
  marshall_08_ASD_discovery_cases-NA0100-000
 NA
 M
 ASD
 NA
 NA
 44780400
 45445301
  664902
 GRCh38
 Duplication
 Yes
  napoli_17_ASD_discovery_cases-case22
 N/A
 M
 ASD
 Case diagnosed with ASD according to DSM-5 criteria. Congenital anomalies: none. Dysmorphic features: fewer than six. Karyotype: 46,XY
 
 44941786
 45319135
  377350
 GRCh38
 Duplication
 Yes
  oikonomakis_16_ASD_discovery_cases-case342
 5 yrs.
 M
 ASD
 Case was assessed for ASD according to DSM-IV behavioral criteria. Clinical characteristics other than ASD: echolalia, stereotypic movements. Note: CNV start and end points extracted from report are incomplete and do not correlate with gene (MAOA) in Table 1.
 
 43573288
 3580109
  180000
 NCBI36
 Duplication
 No
  pinto_10_ASD_discovery_cases-case5007_3
 NA
 M
 Autism
 Anxiety, language delay, no epilepsy, no dysmorphic features
 Below average IQ
 46511595
 46548580
  36986
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case47607
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 46247933
 46295289
  47357
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case58294L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 44380414
 44386744
  6331
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case70106L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 44803831
 45216615
  412785
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case96241
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 47251534
 47263177
  11644
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-caseL656
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 44861727
 44894573
  32847
 Unknown
 Deletion
 No
  saito_13_ASD_discovery_cases-case1
 5 yrs.
 M
 ASD
 Diagnosis of ASD based on fulfilling DSM-IV criteria. Birth/neonatal history: born at 39 weeks of gestation with low birth weight for gestational age (2426 g); phototherapy provided for neonatal jaundice. Developmental milestones: sudden loss of muscle tone at 4-18 months of age; sitting on own around 13 months; no meaningful words at 3 years of age; walking with support at 4 years of age. Langauge and communication evaluation: Several meaningful words at 5 years of age. Motor and musculoskeletal evaluation: Capable of walking several meters by himself at 5 years of age. Beahvioral/psychiatric evaluation: at 3 years of age, patient did not make eye contact, had little interest in other people, and was attached to spinning toys and shiny things; no stereotypic hand movements; hand flapping and lip smacking; abnormal and self-injurious behavior (which included head-banging, hand chewing, and scratching himself) after waking; abnormal behavior disappeared at 3 years of age following risperidone treatment. Sleep disturbances: disturbed sleep patterns observed around 13 months (repeated sleeping for half an hour at a time and screaming during waking); sleep disturbances disappeared at 3 years of age following risperidone treatment. EEG: normal. Brain imaging: normal brain MRI. Other features: elevated CSF serotonin levels. Dysmorphic features: polydactyly of right thumb (operated on at 14 months), bilateral cryptorchidism (operated on at 2 years), long eyelashes, thin upper lip, intermittent internal strabismus. Growth parameters: weight of 15.0 kg (-1.3 SD) and height of 93.7 cm (-3.5 SD) at 5 years of age. Family history: younger male sibling (saito_13_ASD_discovery_cases-case2) with PDD-NOS, severe developmental delay, and sudden loss of muscle tone; healthy parents (mother with heterozygous Xp11.3 deletion is unaffected).
 Severe developmental delay
 43140751
 43940754
  800004
 GRCh38
 Deletion
 Yes
  saito_13_ASD_discovery_cases-case2
 4 yrs.
 M
 PDD-NOS
 Diagnosis of PDD-NOS based on fulfilling DSM-IV criteria. Birth/neonatal history: born at 38 weeks of gestation with birth weight normal for gestational age (2750 g). Developmental milestones: frequent loss of muscle tone around 7 months of age; unassisted sitting at 1 year; some eye gaze but no verbal or non-verbal methods to express requests at 2 years. Langauge and communication evaluation: Spoke some meaningful words. Motor and musculoskeletal evaluation: capable of standing with support. Behavioral/psychiatric evaluation: self-injurious and lip-smacking behaviors; no stereotypic hand movements. Sleep disturbances: none. EEG: unremarkable. Brain imaging: unremarkable brain MRI. Other features: elevated CSF serotonin levels; risperidone treatment started at 3 years of age. Dysmorphic features: bilateral cryptorchidism, long eyelashes, thin upper lip, intermittent strabismus. Growth parameters: weight of 13.2 kg (-1.0 SD) and height of 87.7 cm (-2.9 SD) at 4 years of age. Family history: older male sibling (saito_13_ASD_discovery_cases-case1) with ASD, severe developmental delay, and sudden loss of muscle tone; healthy parents (mother with heterozygous Xp11.3 deletion is unaffected).
 Severe developmental delay
 43140751
 43940754
  800004
 GRCh38
 Deletion
 Yes
  sanders_11_ASD_discovery_cases-11109.p1
 4.5
 F
 Autism
 NA
 Full-scale IQ, 86; non-verbal IQ, 96; verbal IQ 71
 46458899
 46476574
  17676
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11558.p1
 7.4
 M
 Autism
 NA
 Full-scale IQ, 94; non-verbal IQ, 100; verbal IQ, 89
 47471692
 47474107
  2416
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11857.p1
 6.7
 M
 Autism
 NA
 Full-scale IQ, 99; non-verbal IQ, 101; verbal IQ, 96
 47471692
 47474107
  2416
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12543.p1
 8.9
 M
 ASD
 NA
 Full-scale IQ, 86; non-verbal IQ, 99; verbal IQ, 67
 42905490
 42932697
  27208
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12621.p1
 5.8
 M
 Autism
 NA
 Full-scale IQ, 113; non-verbal IQ, 120; verbal IQ, 96
 47471692
 47474107
  2416
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12851.p1
 4.7
 M
 Autism
 NA
 Full-scale IQ, 37; non-verbal IQ, 49; verbal IQ, 14
 42905490
 42932697
  27208
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13023.p1
 4.3
 F
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 118; verbal IQ, 106
 44442415
 44445096
  2682
 GRCh38
 Duplication
 No
  tzetis_12_DD/ID_discovery_cases-case61
 
 M
 DD/ID
 Mild dysmorphic features, hypotonia, severe speech delay
 
 43463947
 44021580
  557634
 GRCh38
 Deletion
 No
  walker_13_ASD_discovery_cases-case3-0100-000
 N/A
 M
 ASD
 N/A
 N/A
 45060991
 45473988
  412998
 GRCh38
 Duplication
 No
  whibley_10_DD_discovery_cases-caseIV:2
 5 yrs.
 M
 Developmental delay
 Patient died unexpectedly at 5 years of age. Birth/neonatal history: born by normal delivery with birth weight of 2.38 kg at about 36 weeks of gestation after normal pregnancy; neonatal hypotonia and feeding difficulties, which required tube feeding, noted; several attacks of sudden hypotonia in first 6 months, which continued in spite of phenobarbital and sodium valproate treatment (started at 9 months of age). Developmental milestones: significantly delayed development; sitting at 20 months, walking with support at 2 years 6 months. Motor and musculoskeletal evaluation: no independent walking achieved at time of death. Behavioral/psychiatric evaluation: recurrent screaming episodes with head banging and hand flapping; additional behaviors of head scratching and hand chewing. EEG: short-wave activity in occipital area noted following onset of hypotonic episodes. Brain imaging: CT scan following onset of hypotonic episodes showed widening of the ventricles and basal spaces. Other features: following patient's death, autopsy did not reveal any abnormalities of internal organs except for brain, which was mildly underweight and showed small foci of perivascular calcification, occasional haemosiderin granules in the Virchow-Robin spaces, and loss of cerebellar Purkinje cells and some cortical neurons. Dysmorphic features: inner canthal folds, long eyelashes, extra upper lateral incisor, unusual hair whorl on posterior hairline. Growth parameters: weight <3rd %ile, lenght <3rd %ile, and OFC 3rd-10th %ile at 4 years of age. Family history: born to healthy non-consanguineous Caucasian parents; healthy older sister; affected brother with similar phenotype (severe developmental delay, intermittent hypotonia, etc.).
 Severe developmental delay
 43682038
 43922394
  240357
 GRCh38
 Deletion
 Yes
  whibley_10_DD_discovery_cases-caseIV:3
 15 yrs.
 M
 Developmental delay
 Birth/neonatal history: born by vertex delivery at 38 weeks gestation after normal pregnancy and weighed 2.5 kg; noted to have jerky movements when falling asleep or walking up; episodes of sudden profound hypotonia (definite axial hypotonia at 13 weeks). Developmental milestones: sitting at 15 months, bottom shuffling at 2 years 8 months, independent walking at 4 years. Language and communication evaluation: able to communicate with many single words and British sign language. Motor and musculoskeletal evaluation: independent walking, clumsy running, continued episodes of hypotonia. Behavioral/psychiatric evaluation: early-onset pursuing and smacking of lips, development of writhing hand movements from 10 months; patient enjoys social events and company. EEG: recent EEG performed during a hypotonic episode showed no focal signs or paroxysmal features. Brain imaging: brain MRI revealed no abnormalities. Other features: lamotrigine treatment tried between 6 and 8 years of age; initial decrease in episode frequency and subsequent increase to 20-30 times/day led to stop of treatment. Dysmorphic features: inner canthal folds, long eyelashes, intermittent convergent strabismus. Growth parameters: height 0.4th %ile, weight 25th %ile, and OFC 3rd-10th %ile at 15 years of age. Family history: born to healthy non-consanguineous Caucasian parents; healthy older sister; affected brother with similar phenotype (severe developmental delay, intermittent hypotonia, etc.) who died unexpectedly at age fo 5 years.
 Severe developmental delay
 43682038
 43922394
  240357
 GRCh38
 Deletion
 Yes

Controls

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  engchuan_15_ASD_discovery_controls-controlB746449_1007844499
  N/A
  N/A
  Control
  No previous psychiatric history
 
  45129175
  45597792
  468618
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900337_900337
  N/A
  N/A
  Control
  No previous psychiatric history
 
  46499154
  46548580
  49427
  GRCh38
  Duplication
  No
  krumm_15_ASD_discovery_controls-control14172.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  44343517
  44542870
  199354
  GRCh38
  Duplication
  Yes
  sanders_11_ASD_discovery_controls-11064.s1
  10
  F
  Control (matched sibling)
  NA
  NA
  44442415
  44445096
  2682
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11198.s1
  8.8
  F
  Control (matched sibling)
  NA
  NA
  44442415
  44445096
  2682
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11694.s1
  6.6
  F
  Control (matched sibling)
  NA
  NA
  44322283
  44346751
  24469
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11839.s1
  4
  F
  Control (matched sibling)
  NA
  NA
  43762162
  43767234
  5073
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12063.s1
  11.8
  F
  Control (matched sibling)
  NA
  NA
  44442415
  44445096
  2682
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12162.s1
  11
  F
  Control (matched sibling)
  NA
  NA
  44169676
  44196911
  27236
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12650.s1
  4.7
  F
  Control (matched sibling)
  NA
  NA
  47471692
  47474107
  2416
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 engchuan_15_ASD_discovery_cases-case3240_3
 
 
 Unknown
 
 
 KDM6A
 
 engchuan_15_ASD_discovery_cases-case5007_3
 
 
 Unknown
 
 
 RNU6-50P,ZNF674-AS1,ZNF674
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001846
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 ACTBP1,LINC01186,GAPDHP65,RNU6-50P,MKI67P1,KRBOX4,ZNF674-AS1,CHST7,ZNF674,SLC9A7
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001872
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 ACTBP1,LINC01186,GAPDHP65,RNU6-50P,MKI67P1,KRBOX4,ZNF674-AS1,CHST7,ZNF674
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002271
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 KRBOX4
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002438
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 RNU6-50P,ZNF674-AS1,ZNF674
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002722
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 PGAM1P7,YBX1P8,RP2,LINC01545,SLC9A7,JADE3
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004897
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 KRBOX4
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004916
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 RNU6-50P,ZNF674-AS1,ZNF674
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005379
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 RRM2P3,FDPSP5,CHTF8P1,RPL19P20,MAOA,NDP,NDP-AS1,TATDN2P1,FUNDC1,MAOB,EFHC2
 
 krumm_15_ASD_discovery_cases-case11109.p1
 Illumina 1M
 
 Paternal
 Simplex
 Segregated
 KRBOX4
 
 kushima_18_ASD_discovery_cases-caseASD1059
 While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
 
 Unknown
 Unknown
 Unknown
 RRM2P3,FDPSP5,CHTF8P1,RPL19P20,RPSAP61,RN7SL291P,DUSP21,KRT8P14,MIR221,MIR222,LINC02595,MED28P4,KRT18P68,PCNAP3,TATDN2P1,FUNDC1,MIR222HG,EFHC2,LINC01204,KDM6A
 
 lionel_13_ASD/ADHD/DD/ID_discovery_cases-case9
 
 
 Unknown
 
 
 EFHC2
 
 marshall_08_ASD_discovery_cases-NA0100-000
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 DUSP21,KDM6A
 
 napoli_17_ASD_discovery_cases-case22
 RT-PCR
 
 Maternal
 
 
 KDM6A
 
 oikonomakis_16_ASD_discovery_cases-case342
 
 
 Unknown
 
 
 MAOB (intronic)
 
 pinto_10_ASD_discovery_cases-case5007_3
 qPCR-Maternal,Agilent1M
 
 maternal
 Multiplex
 Not segregated
 RNU6-50P,ZNF674-AS1,ZNF674
 
 prasad_12_ASD_discovery_cases-case47607
 
 
 Unknown
 Unknown
 Unknown
 ZNF674,LOC401588
 
 prasad_12_ASD_discovery_cases-case58294L
 
 
 Unknown
 Simplex
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-case70106L
 
 
 Unknown
 Unknown
 Unknown
 CXorf36,KDM6A
 
 prasad_12_ASD_discovery_cases-case96241
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-caseL656
 
 
 Unknown
 Unknown
 Unknown
 CXorf36
 
 saito_13_ASD_discovery_cases-case1
 qPCR
 
 Maternal
 Multiplex
 Segregated
 IMPDH1P4,NANOGP10,PINCR,MAOA,MAOB
 
 saito_13_ASD_discovery_cases-case2
 qPCR
 
 Maternal
 Multiplex
 Segregated
 IMPDH1P4,NANOGP10,PINCR,MAOA,MAOB
 
 sanders_11_ASD_discovery_cases-11109.p1
 
 
 Paternal
 Simplex (quad-proband unmatched)
 Unknown
 KRBOX4
 
 sanders_11_ASD_discovery_cases-11558.p1
 
 
 Maternal
 Simplex (quad-proband unmatched)
 Unknown
 ZNF41
 
 sanders_11_ASD_discovery_cases-11857.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 ZNF41
 
 sanders_11_ASD_discovery_cases-12543.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12621.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 ZNF41
 
 sanders_11_ASD_discovery_cases-12851.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-13023.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 tzetis_12_DD/ID_discovery_cases-case61
 
 
 Maternal
 Unknown
 
 MAOA,NDP,NDP-AS1,MAOB
 
 walker_13_ASD_discovery_cases-case3-0100-000
 
 
 Unknown
 Simplex
 Unknown
 KDM6A
 
 whibley_10_DD_discovery_cases-caseIV:2
 Array SNP (Affymetrix 250K Nsp), FISH, qPCR, long-range PCR
 
 Maternal
 Multiplex
 Segregated
 MAOA,MAOB
 
 whibley_10_DD_discovery_cases-caseIV:3
 Array SNP (Affymetrix 250K Nsp), FISH, qPCR, long-range PCR
 
 Maternal
 Multiplex
 Segregated
 MAOA,MAOB
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB746449_1007844499
 
 
  Unknown
 
 
  LINC01204
 
engchuan_15_ASD_discovery_controls-controlHABC_900337_900337
 
 
  Unknown
 
 
  RNU6-50P,ZNF674-AS1,ZNF674
 
krumm_15_ASD_discovery_controls-control14172.s1
  Omni2.5-4v1
 
  Paternal
 
 
  FDPSP5,FUNDC1,EFHC2
 
sanders_11_ASD_discovery_controls-11064.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11198.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11694.s1
 
 
  Paternal
  Simplex (quad)
  NA
  EFHC2
 
sanders_11_ASD_discovery_controls-11839.s1
 
 
  Paternal
  Simplex (quad)
  NA
  MAOB
 
sanders_11_ASD_discovery_controls-12063.s1
 
 
  Both parents
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12162.s1
 
 
  Paternal
  Simplex (quad)
  NA
  EFHC2
 
sanders_11_ASD_discovery_controls-12650.s1
 
 
  Both parents
  Simplex (quad)
  NA
  ZNF41
 

No Animal Model Data Available
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