4q28.2CNV Type: Deletion-Duplication
Largest CNV size: 155570 bp
Statistics Box:
Number of Reports: 6
Number of Reports: 6
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
No Major Reports
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
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder.
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_replication_cases
Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
1979
Cases diagnosed with ASD
N/A
N/A
356
1
0
1
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
153477
1
1
2
hnoonual_17_ASD_discovery_cases
Cohort of 114 Thai ASD probands (68 retrospective ASD cases with the use of chromosomal microarray/CMA as a second line test; 46 prospective ASD and developmental delay cases with the use of CMA as the first-tier test)
114
68 cases with non-syndromic ASD (61 of which also presented with intellectual disability) were diagnosed with ASD based on meeting DSM-IV criteria for ASD, whereas an additional 46 prospective ASD and DD cases were given a clinical diagnosis of ASD based on DSM-5 criteria.
Range, 1-18 years (at time of recruitment)
79.82% Male
1260000
0
1
1
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
155570
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
153430
0
1
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
153477
3
1
4
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
149728
3
1
4
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
153430
0
2
2
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
59139
1
0
1
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
155570
0
1
1
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
153477
3
1
4
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_replication_cases
N/A
WGS
Illumina HiSeq X10
ForestSV, Lumpy, Manta, Mobster, SV2
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
hnoonual_17_ASD_discovery_cases
Thai
Solid phase hybridization
Illumina Infinium CytoSNP-850K v1.1 BeadChip
BlueFuse Multi v4.3, GenomeStudio Data Analysis v.2011.1
None
levy_11_ASD_discovery_cases
aCGH
NimbleGen HD2
HMM
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
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
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)
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
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
brandler_18_ASD_replication_cases-case3-0209-000
N/A
M
ASD
Case from MSSNG cohort
128811418
128811773
356
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case20068_1324001
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
128853220
129006697
153478
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case6340_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
130062450
130131794
69345
GRCh38
Deletion
No
hnoonual_17_ASD_discovery_cases-caseTM35-3
N/A
F
ASD
No additional clinical features
127980247
129242409
1262163
GRCh38
Duplication
No
levy_11_ASD_discovery_cases-11977.p1
NA
M
ASD
NA
NA
128852435
129008004
155570
GRCh38
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR00-120
N/A
N/A
CBLH-PMG
Diagnosis of cerebellar hypoplasia (CBLH) and polymicrogyria (PMG).
128853220
129006649
153430
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11059.p1
6.6
M
Autism
NA
Full-scale IQ, 111; non-verbal IQ, 103; verbal IQ, 119
130027717
130094957
67241
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11393.p1
8.2
M
Autism
NA
Full-scale IQ, 28; non-verbal IQ, 37; verbal IQ, 17
130053048
130068334
15287
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11464.p1
4.5
M
Autism
NA
Full-scale IQ, 92; non-verbal IQ, 103; verbal IQ, 78
129791418
129793613
2196
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11977.p1
10.2
M
ASD
NA
Full-scale IQ, 74; non-verbal IQ, 74; verbal IQ, 80
128853220
129006697
153478
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-controlB679348_1007851283
N/A
N/A
Control
No previous psychiatric history
128856921
129006649
149729
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900443_900443
N/A
N/A
Control
No previous psychiatric history
130041108
130082450
41343
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900547_900547
N/A
N/A
Control
No previous psychiatric history
130041108
130082450
41343
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_901236_901236
N/A
N/A
Control
No previous psychiatric history
130061900
130139904
78005
GRCh38
Deletion
No
kanduri_15_ASD_discovery_controls-control_split1764
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
129774375
129927804
153430
Unknown
Duplication
No
kanduri_15_ASD_discovery_controls-control_split216
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
129774375
129927804
153430
Unknown
Duplication
No
krumm_15_ASD_discovery_controls-control14155.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
127930682
127989821
59140
GRCh38
Deletion
Yes
levy_11_ASD_discovery_controls-11977.s1
NA
F
Control
NA
NA
128852435
129008004
155570
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11059.s1
9.3
F
Control (matched sibling)
NA
NA
129974373
130094957
120585
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11393.s1
9.1
M
Control (matched sibling)
NA
NA
130053048
130068334
15287
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11977.s1
13.3
F
Control (matched sibling)
NA
NA
128853220
129006697
153478
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12015.s1
9
F
Control (matched sibling)
NA
NA
129597231
129659873
62643
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_replication_cases-case3-0209-000
No validation step reported
De novo
JADE1
engchuan_15_ASD_discovery_cases-case20068_1324001
Unknown
JADE1,SCLT1
engchuan_15_ASD_discovery_cases-case6340_3
Unknown
hnoonual_17_ASD_discovery_cases-caseTM35-3
Paternal
JADRR,ABHD18,FOSL1P1,PGRMC2,ZSWIM5P3,LARP1B,JADE1,C4orf33,SCLT1
levy_11_ASD_discovery_cases-11977.p1
Maternal
Simplex
Not segregated
JADE1,SCLT1
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR00-120
Not tested by qPCR
Unknown
Unknown
Unknown
JADE1,SCLT1
sanders_11_ASD_discovery_cases-11059.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11393.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11464.p1
Paternal
Simplex (trio)
NA
LINC02465
sanders_11_ASD_discovery_cases-11977.p1
Maternal
Simplex (quad-proband matched)
Not segregated
JADE1,SCLT1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB679348_1007851283
Unknown
JADE1,SCLT1
engchuan_15_ASD_discovery_controls-controlHABC_900443_900443
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900547_900547
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_901236_901236
Unknown
kanduri_15_ASD_discovery_controls-control_split1764
Unknown
JADE1,SCLT1
kanduri_15_ASD_discovery_controls-control_split216
Unknown
JADE1,SCLT1
krumm_15_ASD_discovery_controls-control14155.s1
Omni2.5-4v1
Maternal
ABHD18,MFSD8
levy_11_ASD_discovery_controls-11977.s1
Maternal
Simplex
NA
JADE1,SCLT1
sanders_11_ASD_discovery_controls-11059.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11393.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11977.s1
Maternal
Simplex (quad)
NA
JADE1,SCLT1
sanders_11_ASD_discovery_controls-12015.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available