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3q22.3CNV Type: Deletion-Duplication


Largest CNV size: 85418 bp

Statistics Box:
Number of Reports: 16



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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Duplication
Excess of rare, inherited truncating mutations in autism.
Duplication
STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Duplication
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Copy number variation in Han Chinese individuals with autism spectrum disorder.
Duplication
Recurrent copy number variations as risk factors for Autism Spectrum Disorders: analysis of the clinical implications.
Deletion
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
Duplication
The Cognitive and Behavioral Phenotypes of Individuals with CHRNA7 Duplications.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 gai_11_ASD_replication_cases
 Replication case samples derived from AGRE sets 1-3
 593
 Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
 
 
 389864
 0
 1
 1
 gazzellone_14_ASD_discovery_cases
 ASD-affected individuals referred to the Children Development and Behavior Research Center (CDRBC) at Harbin Medical University, China, between January 2007 and June 2011.
 104
 Diagnosis of ASD made using Autism Behavior Checklist (ABC) and Childhood Autism Rating Scale (CARS)
 Mean age at enrollment, 4.31 1.80 yrs.
 87.5% Male
 31227
 0
 1
 1
 gillentine_16_ASD/ADHD/DD/ID_discovery_cases
 18 patients from 17 families evaluated by providers at Texas Children's Hospital and tested by clinical chromosomal microarray (CMA) by the Baylor Genetics Laboratory (BGL) or Signature Genomic Laboratory for CHRNA7 duplications
 18
 7/17 cases met criteira for ASD based on clinical impression; 11/18 cases presented with ADHD. Cognitive and behavioral testing included the Differential Ability Scales, Second Edition (DAS-II), the Autism Diagnostic Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule, Second Edition (ADOS-2), the Adaptive Behavior Assessment System, Second Edition (ABAS-II), and the Behavioral Assessment for Children, Second Edition (BASC-2).
 Average, 9.9 years
 66.67% Male
 261658
 0
 1
 1
 girirajan_13a_ASD_discovery_cases
 1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
 2588
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 NA
 NA
 385000
 0
 1
 1
 iourov_12_ASD/ID/EP_discovery_cases
 Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
 54
 Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
 Range, 3 mos.-11 yrs.
 NA
 153171
 1
 0
 1
 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
 849505
 3
 2
 5
 krumm_13_ASD_discovery_cases
 Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 81.265% Male
 35032
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 79059
 0
 2
 2
 lehalle_17_DD/ID_discovery_cases
 7 individuals from 6 families presenting with 3q22.3 deletion containing the STAG1 gene
 7
 All 7 cases present with developmental delay/intellectual disability; epilepsy observed in 3/7 cases, and autistic features observed in 2/7 cases
 Range, 2-33 yrs.
 57.14% Male
 531000
 7
 0
 7
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 76989
 0
 1
 1
 mosca_16_DCD_discovery_cases
 Participants recruited as part of a multidisciplinary study at the Alberta Children's Hospital (Calgary, Alberta, Canada)
 82
 All cases met diagnostic criteria for developmental coordination disorder (DCD) with or without co-occurring ADHD and/or reading disorder.
 Range, 8-17 years (Mean, 10.06 2.92 yrs.)
 N/A
 66959
 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
 35320
 1
 0
 1
 pinto_14_ASD_discovery_cases
 ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
 1359
 Cases classified according to ADOS and ADI-R
 N/A
 N/A
 366808
 0
 1
 1
 poultney_13_ASD_discovery_cases
 ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
 299
 Cases diagnosed with ASD
 N/A
 79.86% Male (before filtering)
 322223
 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
 117623
 1
 2
 3
 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
 85418
 7
 2
 9

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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_13_ASD_discovery_controls
 Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 46.47% Male
 35032
 0
 2
 2
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 21438
 0
 2
 2
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 76989
 0
 1
 1
 poultney_13_ASD_discovery_controls
 Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
 260
 Control
 N/A
 47.49% Male (before filtering)
 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)
 117623
 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.
 
 57699
 7
 1
 8

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 gai_11_ASD_replication_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 None
 gazzellone_14_ASD_discovery_cases
  Han Chinese
 Array SNP
  Affymetrix CytoScan HD
 ChAS, iPattern, Nexus, Partek
 
 None
 gillentine_16_ASD/ADHD/DD/ID_discovery_cases
  N/A
 CMA
  Platform N/A
 
 
 None
 girirajan_13a_ASD_discovery_cases
  NA
 aCGH
  Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
 ADM-2
 Agilent Genomic Workbench
 None
 iourov_12_ASD/ID/EP_discovery_cases
  Russian
 aCGH
  BACs aCGH
 
 
 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_13_ASD_discovery_cases
  N/A
 WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
 DNACopy, CGHCall
 CoNIFER
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 lehalle_17_DD/ID_discovery_cases
  N/A
 aCGH, array SNP, WGS
  Agilent Human Genome CGH 180K, Agilent Human Genome CGH 60K, Affymetrix CytoScan 750K, Affymetrix 250K-Nsp1, WGS
 
 Agilent Feature Extraction v.9.1, Agilent CGH Analytics v.4.0
 qPCR, FISH
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 
 mosca_16_DCD_discovery_cases
  Canada
 Solid phase hybridization
  Illumina HumanOmni2.5-Quad BeadChip
 iPattern, PennCNV, QuantiSNP, CNVPartition
 
 None
 oikonomakis_16_ASD_discovery_cases
  Greece
 aCGH
  Agilent 244K, 4x180K, or 4x180K (SurePrint G3 arrays)
 
 
 None
 pinto_14_ASD_discovery_cases
  Predominantly European
 Solid phase hybridization
  Illumina 1M (v.1 and v.3)
 
 
 qPCR, MLPA, long-range PCR
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 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
 
 

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  krumm_13_ASD_discovery_controls
  N/A
  WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
  DNACopy, CGHCall
  CoNIFER
  Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
 
  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
 
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  gai_11_ASDS_replication_cases-AU0881301
 
 
 Autism
 
 
 137518427
 137908290
  389864
 Unknown
 Duplication
 No
  gazzellone_14_ASD_discovery_cases-case562-3
 N/A
 F
 ASD
 ASD; no other clinical information provided
 N/A
 136914662
 136945889
  31228
 GRCh38
 Duplication
 No
  gillentine_16_ASD/ADHD/DD/ID_discovery_cases-patient10
 10 yrs.
 F
 ASD and developmental delay/intellectual disability
 Case met or exceeded cutoff scores in all behavioral areas on ADI-R and met criteria for being on the autistic spectrum on ADOS (clinical impression of ASD). Original reason for referral: Moderate developmental delay/intellectual disability, dysmorphic features. Developmental milestones: sitting at 12 months, walking at 36 months. Langauge and communication evaluation: language impairment. Motor and musculoskeletal evaluation: no hypotonia. Behavioral/psychiatric evaluation: no ADHD. Epilepsy/seizures: no seizures. Growth parameters: height 50th %ile, weight 80th %ile, OFC 36th %ile. Ethnicity: Vietnamese. Family history: carrier parental phenotype, none; noncarrier parental phenotype, none.
 Full scale ratio IQ (DAS-II): 38.
 138408600
 138670257
  261658
 GRCh38
 Duplication
 No
  girirajan_13a_ASD_discovery_cases-AU0881301
 N/A
 N/A
 ASD
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 N/A
 136338468
 136728468
  390001
 GRCh38
 Duplication
 No
  iourov_12_ASD/ID/EP_discovery_cases-case30
 2 yrs. 11 mos.
 M
 Intellectual disability
 Speech delay, obesity, hypogenitalism
 Mild intellectual disability
 136790230
 136943401
  153172
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000471
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 138946408
 138948348
  1941
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001166
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 137593514
 138443019
  849506
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004959
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 138945182
 138946841
  1660
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005230
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 138945182
 138946841
  1660
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005432
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 138296035
 139015548
  719514
 GRCh38
 Duplication
 Yes
  krumm_13_ASD_discovery_cases-case11067.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 11067. SRS score of 85.
 Full-scale IQ (FSIQ) score of 130.
 138062815
 138097847
  35033
 GRCh38
 Duplication
 No (not tested)
  krumm_15_ASD_discovery_cases-case11333.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 138130848
 138209907
  79060
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case14295.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 138062815
 138084253
  21439
 GRCh38
 Duplication
 Yes
  lehalle_17_DD/ID_discovery_cases-patient1
 8 yrs.
 M
 Intellectual disability
 Birth/neonatal history: pregnancy marked by intrauterine growth retardation; born at 38 weeks; birth weight of 2370 g (1st %ile), length of 48 cm (25th %ile), and OFC of 31 cm (1st %ile); severe gastrointestinal reflux in neonatal period. Developmental milestones: developmental delay noticed from first months; walking at 23 months, spoke a few words at 5 years, made sentences at 7 years. Behavioral/psychiatric evaluation: anxious and quiet behavior. Epilepsy/seizures: none reported. Brain imaging: normal brain MRI and TDM. Dysmorphic features: high nasal bridge, deep-set eyes, wide mouth, widely spaced central incisors, thin eyebrows. Growth parameters: weight -3 SD, length -2 SD, and OFC -3 SD. Family history: sixth child of non-related parents; two siblings with minor learning difficulties, family history otherwise unremarkable.
 Moderate intellectual disability
 136260901
 136791970
  531070
 GRCh38
 Deletion
 Yes
  lehalle_17_DD/ID_discovery_cases-patient2
 12 yrs.
 F
 Intellectual disability, epilepsy, and autistic features
 Birth/neonatal history: born at 39 weeks after normal pregnancy; intrauterine growth retardation; birth weight of 2450 g (1st %ile), length of 47 cm (3rd %ile), and OFC of 30.5 cm (<1st %ile); neonatal feeding difficulties (poor suck, failure to thrive). Developmental milestones: severely delayed development; walking at 3 years, no speech and 12 years. Language and communication evaluation: absent speech. Motor and musculoskeletal evaluation: hypertonia of the lower limbs. Behavioral/psychiatric evaluation: autistic features. Epilepsy/seizures: atypical absence seizures at 5 years. Brain imaging: not performed. Dysmorphic features: high nasal bridge, deep-set eyes, wide mouth, widely spaced central incisors, thin eyebrows. Growth parameters: microcephaly (OFC -4 SD); weight 0 SD, length 0 SD. Family history: negative.
 Severe intellectual disability
 136316680
 136694106
  377427
 GRCh38
 Deletion
 Yes
  lehalle_17_DD/ID_discovery_cases-patient3
 33 yrs.
 F
 Intellectual disability and autistic features
 Birth/neonatal history: born at 37 weeks after normal pregnancy; birth weight of 2000 g (3rd %ile), birth length and OFC not available; initially tube-fed. Developmental milestones: poor eye contact noted in first months of life; delayed psychomotor development; walking at 30-36 months; first words at 3.5 years. Behavioral/psychiatric evaluation: autistic features. Epilepsy/seizures: none reported. Brain imaging: central atrophy in the right hemisphere on brain CT scan. Dysmorphic features: high nasal bridge, deep-set eyes, wide mouth, thin eyebrows. Growth parameters: normal (weight 0 SD, length 0 SD, OFC 0 SD). Family history: negative.
 Severe intellectual disability
 136264342
 136664587
  400246
 GRCh38
 Deletion
 No
  lehalle_17_DD/ID_discovery_cases-patient4
 7 yrs.
 M
 Intellectual disability and epilepsy
 Birth/neonatal history: intrauterine growth retardation; born full-term; birth weight 2600 g (<1st-3rd %ile), length and OFC not available. Developmental milestones: severe developmental delay; head control at 6 months; unable to sit at 7 years. Language and communication evaluation: very few words, almost no non-verbal communication skills, fluctuant eye contact. Motor and musculoskeletal evaluation: scoliosis that required orthopedic surgery; spastic tetraparesis. Behavioral/psychiatric evaluation: no autistic features or other behavioral concerns reported. Epilepsy/seizures: generalized epilepsy at 15 months. Brain imaging: global brain atrophy predominant on the cerebellar vermis on brain MRI. Additional medical history: myopia; bilateral inguinal hernia. Dysmorphic features: high nasal bridge, deep-set eyes, wide mouth. Growth parameters: weight -2.5 SD, length -1 SD, OFC -1.5 SD. Family history: only child; parents are first cousins.
 Severe intellectual disability
 136390696
 136591869
  201174
 GRCh38
 Deletion
 Yes
  lehalle_17_DD/ID_discovery_cases-patient5a
 6 yrs.
 M
 Intellectual disability
 Birth/neonatal history: weight 25th-50th %ile, length 75th %ile, and OFC 98th %ile at 2 weeks. Developmental milestones: walking at 11-12 months; speech delay (sentences at 5 years). Behavioral/psychiatric evaluation: no autistic features or other behavioral concerns reported. Epilepsy/seizures: none reported. Brain imaging: not performed. Dysmorphic features: high nasal bridge, deep-set eyes, wide mouth. Growth parameters: weight -1 SD, length 0 SD, OFC -2 SD. Family history: maternal half-brother of patient 5b; family history of intellectual disability on the maternal side of the family (all six members carry the same STAG1 deletion); history of learning difficulties on paternal side of the family.
 Mild intellectual disability
 136535900
 136708991
  173092
 GRCh38
 Deletion
 No
  lehalle_17_DD/ID_discovery_cases-patient5b
 2 yrs.
 F
 Intellectual disability
 Birth/neonatal history: normal pregnancy; birth weight 9th-25th %ile (length and OFC not available); neonatal period marked by early feeding difficulties and suspected gastroesophageal reflux. Behavioral/psychiatric evaluation: no autistic features or other behavioral concerns reported. Epilepsy/seizures: none reported. Brain imaging: not performed. Dysmorphic features: brachycephaly, deep-set eyes, thin eyebrows, straight eyebrows with medial flaring. Growth parameters: microcephaly (OFC -3 SD); weight 0 SD, length not available. Family history: maternal half-sister of patient 5a; family history of intellectual disability on the maternal side of the family (all six members carry the same STAG1 deletion); history of learning difficulties on paternal side of the family.
 Mild intellectual disability
 136535900
 136708991
  173092
 GRCh38
 Deletion
 No
  lehalle_17_DD/ID_discovery_cases-patient6
 6 yrs.
 M
 Intellectual disability and epilepsy
 Birth/neonatal history: pregnancy obtained by in vitro fertilization for paternal infertility; pregnancy complicated by ultrasound diagnosis of increased nuchal translucency, polyhydramnios, ventricular septal defect, and single unbilical artery; developed cardiac failure and underwent surgery to repeat VSD at 4 weeks; birth weight 70th %ile, length 80th %ile, and OFC 80th %ile; gastroesophageal reflux during neonatal period; diagnosed with severe vesicoureteral reflux at 6 weeks (surgery at 2 years); underwent orchidopexy for bilateral cryptorchidism at 2 years. Developmental milestones: developmental delay; walking at 24 months; speech delay. Behavioral/psychiatric evaluation: no autistic features or other behavioral concerns reported. Epilepsy/seizures: partial atonic seizures at 12 months (treated with levetiracetam). EEG: generalized spikes and waves discharges. Brain imaging: symmetric dilatation of the ventricles and pericerebral space, possible partial vermis hypoplasia on brain MRI. Additional medical history: conductive hearing loss. Dysmorphic features: hypertelorism, deep-set eyes, wide mouth, thick eyebrows, high nasal bridge. Growth parameters: weight 0 SD, length -1 SD, OFC + 1 SD. Family history: negative.
 Intellectual disability
 136250913
 136586634
  335722
 GRCh38
 Deletion
 No
  levy_11_ASD_discovery_cases-11067.p1
 NA
 M
 ASD
 NA
 NA
 138049320
 138126308
  76989
 GRCh38
 Duplication
 No
  mosca_16_DCD_discovery_cases-case119903
 N/A
 M
 DCD (with or without ADHD and/or RD)
 Ancestry: unknown. Family history: maternal diagnosis unknown; paternal diagnosis unknown.
 
 136486165
 136553123
  66959
 GRCh38
 Duplication
 No
  oikonomakis_16_ASD_discovery_cases-case3
 8 yrs.
 F
 ASD
 Case was assessed for ASD according to DSM-IV behavioral criteria. Clinical characteristics other than ASD: microotia, microretrognathia, deep philtrum, strabismus, narrow palpebral fissures, hypotonia, contractures
 
 134871229
 134906547
  35319
 GRCh38
 Deletion
 No
  pinto_14_ASD_discovery_cases2-case8587_210
 N/A
 F
 ASD
 Autism (ADI-R and ADOS positive), no language delay (first words 10 mo, first phrases 12 mo), verbal. Family history: N/A.
 Average IQ (WISC-III at 13 y 9 mo: VIQ 92, PIQ 78, FSIQ 84)
 138559364
 138926171
  366808
 GRCh38
 Duplication
 Yes
  poultney_13_ASD_discovery_cases-case01HI2304A
 N/A
 M
 ASD
 ASD case from AGRE (AGRE ID AU0881301; NDAR ID NDAR_INVRE134JKL)
 
 136301028
 136623250
  322223
 GRCh38
 Duplication
 No
  prasad_12_ASD_discovery_cases-case100676L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 138712001
 138723519
  11519
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case115748L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 139255955
 139284652
  28698
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case98105
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 139735559
 139853181
  117623
 Unknown
 Duplication
 No
  sanders_11_ASD_discovery_cases-11067.p1
 11.3
 M
 Autism
 NA
 Full-scale IQ, 130; non-verbal IQ, 128; verbal IQ, 121
 138048231
 138125803
  77573
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11133.p1
 17
 M
 Autism
 NA
 Full-scale IQ, 128; non-verbal IQ, 110; verbal IQ 140
 136626977
 136627771
  795
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11333.p1
 9.8
 M
 Autism
 NA
 Full-scale IQ, 63; non-verbal IQ, 70; verbal IQ, 53
 138131161
 138216579
  85419
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11941.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 85; non-verbal IQ, 87; verbal IQ, 86
 137311751
 137323774
  12024
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12071.p1
 11.7
 F
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 102; verbal IQ, 112
 137311751
 137323774
  12024
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12103.p1
 6.6
 M
 Autism
 NA
 Full-scale IQ, 38; non-verbal IQ, 44; verbal IQ, 31
 136626977
 136627771
  795
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12434.p1
 5.3
 M
 Autism
 NA
 Full-scale IQ, 117; non-verbal IQ, 121; verbal IQ, 106
 137311341
 137323774
  12434
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12445.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 104; non-verbal IQ, 111; verbal IQ, 91
 137311341
 137323774
  12434
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12610.p1
 5.4
 M
 ASD
 NA
 Full-scale IQ, 86; non-verbal IQ, 99; verbal IQ, 71
 137307798
 137323774
  15977
 GRCh38
 Deletion
 No

Controls

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  krumm_13_ASD_discovery_controls-control11067.s1
  N/A
  F
  Control
  Unaffected sibling from SSC quad family 11067. SRS score of 40.
 
  138062815
  138097847
  35033
  GRCh38
  Duplication
  No (not tested)
  krumm_13_ASD_discovery_controls-control12106.s1
  N/A
  F
  Control
  Unaffected sibling from SSC quad family 12106. SRS score of 56.
 
  138062815
  138084253
  21439
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control12106.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  138062815
  138084253
  21439
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control14295.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  138062815
  138084253
  21439
  GRCh38
  Duplication
  Yes
  levy_11_ASD_discovery_controls-11067.s1
  NA
  F
  Control
  NA
  NA
  138049320
  138126308
  76989
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11067.s1
  16.7
  F
  Control (matched sibling)
  NA
  NA
  138048231
  138105930
  57700
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11235.s1
  4.8
  M
  Control (matched sibling)
  NA
  NA
  137311751
  137323774
  12024
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11239.s1
  15.1
  M
  Control (matched sibling)
  NA
  NA
  137311751
  137323774
  12024
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11941.s1
  8.7
  F
  Control (matched sibling)
  NA
  NA
  137311751
  137323774
  12024
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12360.s1
  7.9
  F
  Control (matched sibling)
  NA
  NA
  137296645
  137323774
  27130
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12434.s1
  8.8
  F
  Control (matched sibling)
  NA
  NA
  137311341
  137323774
  12434
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12445.s1
  6.6
  M
  Control (matched sibling)
  NA
  NA
  137311341
  137328545
  17205
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12894.s1
  4.9
  F
  Control (matched sibling)
  NA
  NA
  136626977
  136627771
  795
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gai_11_ASDS_replication_cases-AU0881301
 
 
 Inherited
 
 
 PCCB, STAG1
 
 gazzellone_14_ASD_discovery_cases-case562-3
 
 
 Unknown
 Unknown
 Unknown
 NCK1
 
 gillentine_16_ASD/ADHD/DD/ID_discovery_cases-patient10
 
 
 Paternal
 Simplex
 Unknown
 PPIAP72,ESYT3,FAIM,CEP70,PIK3CB
 
 girirajan_13a_ASD_discovery_cases-AU0881301
 
 
 Unknown
 Multiplex
 Unknown
 RNU6-1284P,HMGN1P10,RNU6-789P,STAG1
 
 iourov_12_ASD/ID/EP_discovery_cases-case30
 
 
 Unknown
 Unknown
 Unknown
 RAD51AP1P1,NCK1-DT,NCK1,SLC35G2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000471
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 FOXL2,FOXL2NB
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001166
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 SOX14,HSPA8P9,KRT8P36,A4GNT,NPM1P17,LINC01210,DZIP1L,DBR1,MRAS,ESYT3,CLDN18,ARMC8,NME9
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004959
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 FOXL2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005230
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 FOXL2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005432
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 PPIAP72,GAPDHP39,RPL23AP40,EEF1A1P25,ATP5MC1P3,FOXL2,PRR23A,MRAS,ESYT3,FAIM,FOXL2NB,ARMC8,NME9,CEP70,PIK3CB,LINC01391,MRPS22
 
 krumm_13_ASD_discovery_cases-case11067.p1
 
 
 Maternal
 Simplex
 Not segregated
 DZIP1L
 
 krumm_15_ASD_discovery_cases-case11333.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 A4GNT,DBR1,ARMC8
 
 krumm_15_ASD_discovery_cases-case14295.p1
 Omni2.5-4v1
 
 Paternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 DZIP1L
 
 lehalle_17_DD/ID_discovery_cases-patient1
 qPCR
 
 De novo
 Simplex
 Likely segregated
 RNU6-1284P,HMGN1P10,RNU6-789P,STAG1,PCCB
 
 lehalle_17_DD/ID_discovery_cases-patient2
 FISH
 
 De novo
 Simplex
 Likely segregated
 RNU6-1284P,HMGN1P10,STAG1,PCCB
 
 lehalle_17_DD/ID_discovery_cases-patient3
 
 
 De novo
 Simplex
 Likely segregated
 RNU6-1284P,HMGN1P10,STAG1,PCCB
 
 lehalle_17_DD/ID_discovery_cases-patient4
 qPCR
 
 Unknown (not maternal
 
 Unknown
 RNU6-1284P,STAG1
 
 lehalle_17_DD/ID_discovery_cases-patient5a
 
 Maternal
 Maternal
 Multi-generational
 Segregated
 HMGN1P10,STAG1
 
 lehalle_17_DD/ID_discovery_cases-patient5b
 
 Maternal
 Maternal
 Multi-generational
 Segregated
 HMGN1P10,STAG1
 
 lehalle_17_DD/ID_discovery_cases-patient6
 
 
 Unknown
 Simplex
 Unknown
 RNU6-1284P,STAG1,PCCB
 
 levy_11_ASD_discovery_cases-11067.p1
 
 
 Maternal
 Simplex
 Not segregated
 KRT8P36,A4GNT,DZIP1L
 
 mosca_16_DCD_discovery_cases-case119903
 
 
 Unknown
 Unknown
 Unknown
 STAG1
 
 oikonomakis_16_ASD_discovery_cases-case3
 
 
 De novo
 
 
 EPHB1
 
 pinto_14_ASD_discovery_cases2-case8587_210
 qPCR
 
 De novo
 Unknown
 Unknown (not tested)
 PPIAP72,GAPDHP39,RPL23AP40,EEF1A1P25,ATP5MC1P3,FAIM,CEP70,PIK3CB
 
 poultney_13_ASD_discovery_cases-case01HI2304A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 RNU6-1284P,HMGN1P10,STAG1,PCCB
 
 prasad_12_ASD_discovery_cases-case100676L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-case115748L
 
 
 Unknown
 Unknown
 Unknown
 DZIP1L
 
 prasad_12_ASD_discovery_cases-case98105
 
 
 Unknown
 Unknown
 Unknown
 FAIM,CEP70
 
 sanders_11_ASD_discovery_cases-11067.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 KRT8P36,A4GNT,DZIP1L
 
 sanders_11_ASD_discovery_cases-11133.p1
 
 
 Maternal
 Simplex (trio)
 NA
 STAG1
 
 sanders_11_ASD_discovery_cases-11333.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 A4GNT,DBR1,ARMC8
 
 sanders_11_ASD_discovery_cases-11941.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12071.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-12103.p1
 
 
 Both parents
 Simplex (quad-proband unmatched)
 Unknown
 STAG1
 
 sanders_11_ASD_discovery_cases-12434.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12445.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12610.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control11067.s1
 
 
  Maternal
  Simplex
 
  DZIP1L
 
krumm_13_ASD_discovery_controls-control12106.s1
  aCGH (Agilent SurePrint G3 4x180K)
 
  Maternal
  Simplex
 
  DZIP1L
 
krumm_15_ASD_discovery_controls-control12106.s1
  Illumina 1MDuo
 
  Maternal
 
 
  DZIP1L
 
krumm_15_ASD_discovery_controls-control14295.s1
  Omni2.5-4v1
 
  Paternal
 
 
  DZIP1L
 
levy_11_ASD_discovery_controls-11067.s1
 
 
  Maternal
  Simplex
  NA
  KRT8P36,A4GNT,DZIP1L
 
sanders_11_ASD_discovery_controls-11067.s1
 
 
  Maternal
  Simplex (quad)
  NA
  KRT8P36,DZIP1L
 
sanders_11_ASD_discovery_controls-11235.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11239.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11941.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12360.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12434.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12445.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12894.s1
 
 
  Maternal
  Simplex (quad)
  NA
  STAG1
 

No Animal Model Data Available
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