3q13.2CNV Type: Deletion-Duplication
Largest CNV size: 139186 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
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
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
celestino-soper_11_ASD_discovery_cases
ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
99
ASD
87.88% Male
5001
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
44857
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
21399
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
139186
12
1
13
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
kanduri_15_ASD_discovery_controls
Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
269
Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
N/A
N/A
10195
1
0
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
44857
1
0
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)
11732
1
0
1
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)
21399
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.
12525
8
0
8
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
celestino-soper_11_ASD_discovery_cases
aCGH
Agilent 1M
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
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
kanduri_15_ASD_discovery_controls
Finnish
Solid phase hybridization
Illumina Infinium HD Human610-Quad BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
qPCR
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
celestino-soper_11_ASD_discovery_cases-11418
NA
M
ASD
NA
NA
113659384
113664385
5002
GRCh38
Deletion
No
krumm_15_ASD_discovery_cases-case14343.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
112974790
113019647
44858
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case110408
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
113499766
113521164
21399
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11604.p1
17.2
F
Autism
NA
Full-scale IQ, 18; non-verbal IQ, 23; verbal IQ 13
111743113
111750527
7415
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11773.p1
13.1
M
Autism
NA
Full-scale IQ, 43; non-verbal IQ, 50; verbal IQ, 28
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11800.p1
13.3
M
Autism
NA
Full-scale IQ, 34; non-verbal IQ, 34; verbal IQ, 35
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11941.p1
10.9
M
Autism
NA
Full-scale IQ, 85; non-verbal IQ, 87; verbal IQ, 86
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12074.p1
6.3
F
Autism
NA
Full-scale IQ, 75; non-verbal IQ, 82; verbal IQ, 79
112383718
112394487
10770
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12086.p1
14.5
M
Autism
NA
Full-scale IQ, 118; non-verbal IQ, 108; verbal IQ, 131
111743113
111762099
18987
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12437.p1
10.1
M
Autism
NA
Full-scale IQ, 75; non-verbal IQ, 78; verbal IQ, 72
112383718
112394487
10770
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12534.p1
7
F
Autism
NA
Full-scale IQ, 81; non-verbal IQ, 83; verbal IQ, 84
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12631.p1
17.2
M
Autism
NA
Full-scale IQ, 80; non-verbal IQ, 87; verbal IQ, 76
112383718
112395969
12252
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12794.p1
8.3
M
Autism
NA
Full-scale IQ, 96; non-verbal IQ, 96; verbal IQ, 97
113326368
113465554
139187
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12809.p1
5.6
M
ASD
NA
Full-scale IQ, 86; non-verbal IQ, 88; verbal IQ, 88
112383718
112395969
12252
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12961.p1
4.4
M
Autism
NA
Full-scale IQ, 115; non-verbal IQ, 125; verbal IQ, 93
112384293
112394487
10195
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13065.p1
5.6
M
Autism
NA
Full-scale IQ, 91; non-verbal IQ, 101; verbal IQ, 81
113536296
113536968
673
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
kanduri_15_ASD_discovery_controls-control_split286
N/A
N/A
Control
Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
112103140
112113334
10195
Unknown
Deletion
No
krumm_15_ASD_discovery_controls-control14343.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
112974790
113019647
44858
GRCh38
Deletion
Yes
poultney_13_ASD_discovery_controls-control05C45305
N/A
F
Control
NIMH Control (NIMH ID 26586)
111638077
111649808
11732
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_controls-11665.s1
12.9
M
Control (matched sibling)
NA
NA
113524443
113536968
12526
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11809.s1
8.4
F
Control (matched sibling)
NA
NA
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11941.s1
8.7
F
Control (matched sibling)
NA
NA
113536296
113536968
673
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12345.s1
12.9
F
Control (matched sibling)
NA
NA
112383718
112395969
12252
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12437.s1
14.1
M
Control (matched sibling)
NA
NA
112383718
112394487
10770
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12517.s1
11.7
M
Control (matched sibling)
NA
NA
113536296
113546147
9852
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12631.s1
18.8
M
Control (matched sibling)
NA
NA
112383718
112395969
12252
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12780.s1
5.9
M
Control (matched sibling)
NA
NA
112383718
112394487
10770
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
celestino-soper_11_ASD_discovery_cases-11418
Unknown
Simplex
NA
USF3
krumm_15_ASD_discovery_cases-case14343.p1
Omni2.5-4v1
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
CD200R1,GTPBP8,NEPRO
prasad_12_ASD_discovery_cases-case110408
Unknown
Multiplex
Unknown
0 genes
sanders_11_ASD_discovery_cases-11604.p1
Maternal
Simplex (trio)
NA
PLCXD2,PHLDB2
sanders_11_ASD_discovery_cases-11773.p1
Unknown
Simplex (quad-proband matched)
Not segregated
SIDT1
sanders_11_ASD_discovery_cases-11800.p1
Unknown
Simplex (quad-proband unmatched)
Unknown
SIDT1
sanders_11_ASD_discovery_cases-11941.p1
Unknown
Simplex (quad-proband matched)
Not segregated
SIDT1
sanders_11_ASD_discovery_cases-12074.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12086.p1
Maternal
Simplex (quad-proband matched)
Segregated
PLCXD2,PHLDB2
sanders_11_ASD_discovery_cases-12437.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12534.p1
Unknown
Simplex (quad-proband matched)
Not segregated
SIDT1
sanders_11_ASD_discovery_cases-12631.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12794.p1
Unknown
Simplex (quad-proband matched)
Not segregated
MIR8076,CFAP44-AS1,CFAP44,SPICE1
sanders_11_ASD_discovery_cases-12809.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12961.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-13065.p1
Unknown
Simplex (trio)
NA
SIDT1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kanduri_15_ASD_discovery_controls-control_split286
Unknown
Intergenic CNV: nearest genes, CD200(dist=21482),BTLA(dist=69479)
krumm_15_ASD_discovery_controls-control14343.s1
Omni2.5-4v1
Maternal
CD200R1,GTPBP8,NEPRO
poultney_13_ASD_discovery_controls-control05C45305
qPCR
Unknown
CD96
sanders_11_ASD_discovery_controls-11665.s1
Unknown
Simplex (quad)
NA
SIDT1
sanders_11_ASD_discovery_controls-11809.s1
Unknown
Simplex (quad)
NA
SIDT1
sanders_11_ASD_discovery_controls-11941.s1
Unknown
Simplex (quad)
NA
SIDT1
sanders_11_ASD_discovery_controls-12345.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12437.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12517.s1
Paternal
Simplex (quad)
NA
SIDT1
sanders_11_ASD_discovery_controls-12631.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12780.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available