3p11.2CNV Type: Deletion
Largest CNV size: 54080 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Deletion
Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...
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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Global increases in both common and rare copy number load associated with autism.
Duplication
Identification of candidate intergenic risk loci in autism spectrum disorder.
Duplication
Refining analyses of copy number variation identifies specific genes associated with developmental delay.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_cases
Primarily pediatric cases with intellectual disability, developmental delay, and/or ASD (cohort consists of 13,318 previously unpublished cases and 15,767 cases originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
29085
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
320000
9
0
9
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
54079
1
1
2
girirajan_13b_ASD_discovery_cases
Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)
243
Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol
N/A
N/A
609188
0
1
1
lesca_12_EP_discovery_cases
Epilepsy patients collected at four French hospitals from 2009: Strasbourg Univ. Hospital (n=40), Lyons Univ. Hospital (n=18), Henri Gastaut Hospital (St. Paul Centre) in Marseille (n=2), and Reims American Memorial Hospital (n=1).
61
Epilepsy/epileptic encephalopathy. 41 patients with continuous spike and wave during slow-wave sleep syndrome (CSWSS), 20 patients with Landau-Kleffner syndrome (LKS). 12 (out of 57) patients displayed autistic features; ADHD features (hyperactivity, attention deficit and/or aggressiveness) reported in 41/58 patients,
Mean age of diagnosis: 5.6 yrs. (range, 1-14 yrs.)
61% Male
29000
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
54080
1
0
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
53954
1
0
1
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
53167
13
0
13
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
35126
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_controls
Adult population controls (cohort consists of 11,255 new controls and 8329 controls originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
19584
Control
N/A
N/A
320000
0
0
0
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
187352
2
1
3
girirajan_13b_ASD_discovery_controls
Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)
223
Control
N/A
N/A
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)
53954
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.
6763
6
0
6
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
35126
N/A
N/A
N/A
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_cases
N/A
aCGH
N/A
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_13b_ASD_discovery_cases
133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American
aCGH
Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
DNA Copy Number v1.6
None
lesca_12_EP_discovery_cases
France
aCGH
Agilent SurePrint G3 Human CGH Microarray 4x180K
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent Genomic WORKBENCH v5.0.14
qPCR
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
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
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
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_controls
N/A
aCGH, solid phase hybridization
Multiple platforms used (including HumanHap, Illumina, and Human610-Quad)
None
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_13b_ASD_discovery_controls
116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American
aCGH
Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
DNA Copy Number v1.6
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
coe_14_ASD/DD/ID_discovery_cases-case591
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case592
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case593
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case594
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case595
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case596
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case597
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case598
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case599
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
87188160
87508160
320001
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case14032_600
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
87134733
87169859
35127
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5040_5
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
87900583
87954662
54080
GRCh38
Deletion
No
girirajan_13b_ASD_discovery_cases-5903100247
N/A
N/A
Autism
Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Mixed Race
N/A
89212795
89821983
609189
GRCh38
Duplication
No
lesca_12_EP_discovery_cases-case003a
NA
M
Epilepsy + autistic features
Phenotype: i-CSWSS. Seizure Characteristics: FS, CPS, GTCS. Autistic features: Yes. ADHD features: Yes. Other features: None.
Initial cognitive development: Normal. Cognitive regression: Yes. Verbal IQ 112, performance IQ 114 (at 5 years of age).
87868660
88729723
861064
GRCh38
Duplication
Yes
pinto_10_ASD_discovery_cases-case5040_5
NA
F
ASD
NA
NA
87900583
87954662
54080
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case62231L
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
88032773
88086726
53954
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11680.p1
8
M
Autism
NA
Full-scale IQ, 71; non-verbal IQ, 82; verbal IQ, 54
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12026.p1
6.6
M
Autism
NA
Full-scale IQ, 51; non-verbal IQ, 72; verbal IQ, 36
89072771
89096190
23420
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12063.p1
8.7
M
Autism
NA
Full-scale IQ, 92; non-verbal IQ, 96; verbal IQ, 82
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12115.p1
12.1
M
Autism
NA
Full-scale IQ, 102; non-verbal IQ, 107; verbal IQ, 94
87657234
87710401
53168
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12219.p1
7.2
M
Autism
NA
Full-scale IQ, 121; non-verbal IQ, 110; verbal IQ, 136
88659184
88660755
1572
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12330.p1
4.5
M
Autism
NA
Full-scale IQ, 59; non-verbal IQ, 62; verbal IQ, 62
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12359.p1
9.3
M
Autism
NA
Full-scale IQ, 78; non-verbal IQ, 87; verbal IQ, 69
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12423.p1
10.1
M
Autism
NA
Full-scale IQ, 104; non-verbal IQ, 115; verbal IQ, 82
89023376
89026905
3530
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12573.p1
17
M
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 70; verbal IQ, 80
88659184
88677722
18539
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12838.p1
4.7
M
Autism
NA
Full-scale IQ, 78; non-verbal IQ, 93; verbal IQ, 50
88659184
88665947
6764
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
89023376
89026905
3530
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13056.p1
4.6
M
Autism
NA
Full-scale IQ, 64; non-verbal IQ, 65; verbal IQ, 58
87076970
87091249
14280
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13175.p1
11.7
M
Autism
NA
Full-scale IQ, 63; non-verbal IQ, 70; verbal IQ, 52
88659184
88665947
6764
GRCh38
Deletion
No
walker_13_ASD_discovery_cases-case8-14032-600
N/A
M
ASD
N/A
N/A
87134733
87169859
35127
GRCh38
Duplication
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
engchuan_15_ASD_discovery_controls-controlB250275_1007874021
N/A
N/A
Control
No previous psychiatric history
87900583
87954662
54080
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB493911_1007842333
N/A
N/A
Control
No previous psychiatric history
87641879
87829231
187353
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900244_900244
N/A
N/A
Control
No previous psychiatric history
87725127
87805127
80001
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11088.s1
14.5
F
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11590.s1
7.9
F
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12063.s1
11.8
F
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12359.s1
6.3
F
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12573.s1
11.7
M
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13175.s1
13.7
F
Control (matched sibling)
NA
NA
88659184
88665947
6764
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
coe_14_ASD/DD/ID_discovery_cases-case591
Inherited
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case592
Inherited
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case593
Inherited
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case594
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case595
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case596
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case597
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case598
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
coe_14_ASD/DD/ID_discovery_cases-case599
Unknown
Unknown
Unknown
MIR4795,KRT8P25,CHMP2B,POU1F1
engchuan_15_ASD_discovery_cases-case14032_600
Unknown
LINC00506
engchuan_15_ASD_discovery_cases-case5040_5
Unknown
RNU6ATAC6P
girirajan_13b_ASD_discovery_cases-5903100247
Unknown
Unknown
Unknown
MTCO2P6,MTCO1P6,EPHA3
lesca_12_EP_discovery_cases-case003a
qPCR
Maternal
Unknown
Unknown
RNU6ATAC6P,HTR1F,CBX5P1,ABCF2P1,NDUFA5P5,C3orf38,CSNKA2IP,CGGBP1,ZNF654
pinto_10_ASD_discovery_cases-case5040_5
Agilent1M
maternal
NA
NA
RNU6ATAC6P
prasad_12_ASD_discovery_cases-case62231L
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-11680.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12026.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12063.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12115.p1
Maternal
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12219.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12330.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12359.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12423.p1
Maternal
Simplex (quad-proband unmatched)
Unknown
sanders_11_ASD_discovery_cases-12573.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12838.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12851.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-13056.p1
Maternal
Simplex (trio)
NA
LINC00506
sanders_11_ASD_discovery_cases-13175.p1
Paternal
Simplex (quad-proband matched)
Not segregated
walker_13_ASD_discovery_cases-case8-14032-600
Unknown
Simplex
Unknown
LINC00506
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB250275_1007874021
Unknown
RNU6ATAC6P
engchuan_15_ASD_discovery_controls-controlB493911_1007842333
Unknown
RNU6-873P
engchuan_15_ASD_discovery_controls-controlHABC_900244_900244
Unknown
RNU6-873P
sanders_11_ASD_discovery_controls-11088.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11590.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12063.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12359.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12573.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-13175.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available