3q21.2CNV Type: Deletion-Duplication
Largest CNV size: 211085 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
De novo rates and selection of large copy number variation.
Duplication
Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families.
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
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
itsara_10_ASD_discovery_cases
ASD probands from multiplex (n=1270) and simplex (n=60) families from AGRE collection
1330
ASD: Autism, broad spectrum autism (Spectrum), or NQA (not quite autism)
1289486
0
2
2
leppa_16_ASD_discovery_cases
Children affected with ASD from 1,464 families from the Autism Genetic Resource Exchange (AGRE)
1764
Diagnosis according to ADOS and ADI-R
N/A
N/A
1289000
0
2
2
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)
1304597
0
1
1
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
38650
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
211085
1
4
5
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
134242
0
4
4
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
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
39566
1
1
2
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
itsara_10_ASD_discovery_cases
Solid phase hybridization
Illumina HumanHap550v1 and v3 SNP array
HMM
Illumina GenomeStudio
aCGH (custom NimbleGen 12 X 135)
leppa_16_ASD_discovery_cases
N/A
Solid phase hybridization
Illumina 550v1 and 550v3, Omni-1.0-B and -H, Omni 2.5
PennCNV, QuantiSNP, GNOSIS
GenomeStudio, CNVision
qPCR
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
None (not tested or failure to confirm by 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
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
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
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
itsara_10_ASD_discovery_cases-HI2543
NA
NA
Autism
NA
NA
124765105
126052855
1287751
GRCh38
Duplication
Yes
itsara_10_ASD_discovery_cases-HI2544
NA
NA
Autism
NA
NA
124765105
126054595
1289491
GRCh38
Duplication
Yes
leppa_16_ASD_discovery_cases-AU0911301
N/A
N/A
ASD
124765105
126054595
1289491
GRCh38
Duplication
Yes
leppa_16_ASD_discovery_cases-AU0911302
N/A
N/A
ASD
124765105
126054595
1289491
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case05HI2544A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0911302; NDAR ID NDAR_INVBZ963FL8)
124763621
126068221
1304601
GRCh38
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR01-044
N/A
N/A
PMG
Diagnosis of polymicrogyria (PMG).
126189352
126228001
38650
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
125714187
125925273
211087
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12158.p1
5.7
M
Autism
NA
Full-scale IQ, 86; non-verbal IQ, 81; verbal IQ, 100
125824023
125925273
101251
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12260.p1
5.3
M
Autism
NA
Full-scale IQ, 106; non-verbal IQ, 103; verbal IQ, 109
125824023
125925273
101251
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12691.p1
10.9
F
Autism
NA
Full-scale IQ, 34; non-verbal IQ, 32; verbal IQ, 39
125199910
125202613
2704
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12892.p1
6.3
M
ASD
NA
Full-scale IQ, 69; non-verbal IQ, 79; verbal IQ, 63
125877144
125925273
48130
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
girirajan_13b_ASD_discovery_controls-17203100441
N/A
N/A
Control
Ethnicity: Caucasian
N/A
126046992
126181234
134243
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-40804101794
N/A
N/A
Control
Ethnicity: Hispanic
N/A
126053044
126155638
102595
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-54305104360
N/A
N/A
Control
Ethnicity: Mixed Race
N/A
126058283
126181234
122952
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_controls-66705104892
N/A
N/A
Control
Ethnicity: Caucasian
N/A
126062483
126147038
84556
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12691.s1
23.8
M
Control (matched sibling)
NA
NA
125199910
125202613
2704
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13050.s1
6.9
M
Control (matched sibling)
NA
NA
125885707
125925273
39567
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
itsara_10_ASD_discovery_cases-HI2543
aCGH (custom NimbleGen 12 X 135)
De novo
Multiplex
ITGB5-AS1,RNA5SP137,RNU6-230P,MIR5092,DUTP1,RNU6-232P,OR7E130P,OR7E29P,OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,ALG1L,ENO1P3,SNX4,OR7E97P,ENPP7P4,FAM86JP,ROPN1B,MUC13,HEG1,SLC12A8,ZNF148,OSBPL11,SLC41A3,ITGB5
itsara_10_ASD_discovery_cases-HI2544
aCGH (custom NimbleGen 12 X 135)
De novo
Multiplex
ITGB5-AS1,RNA5SP137,RNU6-230P,MIR5092,DUTP1,RNU6-232P,OR7E130P,OR7E29P,OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,ALG1L,ENO1P3,SNX4,OR7E97P,ENPP7P4,FAM86JP,ROPN1B,MUC13,HEG1,SLC12A8,ZNF148,OSBPL11,SLC41A3,ITGB5
leppa_16_ASD_discovery_cases-AU0911301
qPCR
De novo
Unknown
Possibly segregated
ITGB5-AS1,RNA5SP137,RNU6-230P,MIR5092,DUTP1,RNU6-232P,OR7E130P,OR7E29P,OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,ALG1L,ENO1P3,SNX4,OR7E97P,ENPP7P4,FAM86JP,ROPN1B,MUC13,HEG1,SLC12A8,ZNF148,OSBPL11,SLC41A3,ITGB5
leppa_16_ASD_discovery_cases-AU0911302
qPCR
De novo
Unknown
Possibly segregated
ITGB5-AS1,RNA5SP137,RNU6-230P,MIR5092,DUTP1,RNU6-232P,OR7E130P,OR7E29P,OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,ALG1L,ENO1P3,SNX4,OR7E97P,ENPP7P4,FAM86JP,ROPN1B,MUC13,HEG1,SLC12A8,ZNF148,OSBPL11,SLC41A3,ITGB5
poultney_13_ASD_discovery_cases-case05HI2544A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
ITGB5-AS1,RNA5SP137,RNU6-230P,MIR5092,DUTP1,RNU6-232P,OR7E130P,OR7E29P,OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,ALG1L,ENO1P3,SNX4,OR7E97P,ENPP7P4,FAM86JP,ROPN1B,MUC13,HEG1,SLC12A8,ZNF148,OSBPL11,SLC41A3,ITGB5
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR01-044
Not tested by qPCR
Unknown
Unknown
Unknown
ALDH1L1,ALDH1L1-AS2
sanders_11_ASD_discovery_cases-11333.p1
Both parents
Simplex (quad-proband matched)
Segregated
OR7E93P,OR7E53P,MIR548I1,RPS3AP14,SNRPCP11,OR7E97P,ENPP7P4,FAM86JP
sanders_11_ASD_discovery_cases-12158.p1
Maternal
Simplex (trio)
NA
ENPP7P4,FAM86JP
sanders_11_ASD_discovery_cases-12260.p1
Both parents
Simplex (trio)
NA
ENPP7P4,FAM86JP
sanders_11_ASD_discovery_cases-12691.p1
Maternal
Simplex (quad-proband matched)
Not segregated
SLC12A8
sanders_11_ASD_discovery_cases-12892.p1
Both parents
Simplex (quad-proband matched)
Not segregated
ENPP7P4,FAM86JP
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
girirajan_13b_ASD_discovery_controls-17203100441
Unknown
RNU1-30P,ALDH1L1,ALDH1L1-AS1,ALDH1L1-AS2,SLC41A3
girirajan_13b_ASD_discovery_controls-40804101794
Unknown
ALDH1L1,ALDH1L1-AS1,SLC41A3
girirajan_13b_ASD_discovery_controls-54305104360
Unknown
RNU1-30P,ALDH1L1,ALDH1L1-AS1,ALDH1L1-AS2,SLC41A3
girirajan_13b_ASD_discovery_controls-66705104892
Unknown
ALDH1L1,ALDH1L1-AS1,SLC41A3
sanders_11_ASD_discovery_controls-12691.s1
Maternal
Simplex (quad)
NA
SLC12A8
sanders_11_ASD_discovery_controls-13050.s1
Unknown
Simplex (quad)
NA
ENPP7P4,FAM86JP
No Animal Model Data Available