6p24.3-p24.2CNV Type: Deletion
Largest CNV size: 68270 bp
Statistics Box:
Number of Reports: 7
Number of Reports: 7
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Gene-network analysis identifies susceptibility genes related to glycobiology in autism.
Deletion
Functional impact of global rare copy number variation in autism spectrum disorders.
Deletion
Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
Deletion
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
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
75803
5
0
5
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
70184
1
0
1
leblond_12_ASD_replication_cases
Dataset featuring ASD patients from the Autism Genome Project carrying de novo SHANK2 deletions previously identified by Pinto et al. 2010. CNV validation information taken from Pinto report.
2
1 patient diagnosed with autism, 1 patient diagnosed with PDD-NOS.
NA
100% Male
61042
1
0
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
61042
1
0
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
60515
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
58968
3
0
3
van_der_zwaag_09_ASD_discovery_cases
Samples and phenotypic data from ASD patients, Dept. of Child & Adolescent Psychiatry, UMC Utrcht
105
53 cases diagnosed with non-complex autism, 52 diagnosed with complex autism
68270
1
0
1
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
62360
6
0
6
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
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.
58968
2
0
2
van_der_zwaag_09_ASD_discovery_controls
Ethnically matched, unrelated, healthy volunteers recruited by Dept. of Neurology, UMC Utrecht
267
Controls
N/A
1
0
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
leblond_12_ASD_replication_cases
1 Canadian, 1 French
Solid phase hybridization
Illumina 1M SNP array
QuantiSNP, PennCNV
aCGH (Agilent 1M)
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)
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
van_der_zwaag_09_ASD_discovery_cases
Dutch
Solid phase hybridization
HumanHap300 Beadchip
BeadStudio genotyping V2.3.41
qPCR
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
van_der_zwaag_09_ASD_discovery_controls
Dutch
Solid phase hybridization
HumanHap300 Beadchip
BeadStudio genotyping V2.3.41
Cases
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_cases-case3102_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
10488368
10564171
75804
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case3177_6
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
10469593
10528561
58969
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4541_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
10439735
10512089
72355
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case5237_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
10467520
10528561
61042
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case8629_201
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
10467520
10531953
64434
GRCh38
Deletion
No
krumm_15_ASD_discovery_cases-case11079.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
10556423
10626607
70185
GRCh38
Deletion
Yes
leblond_12_ASD_replication_cases-Pintocase5237_3
NA
M
Autism
Diagnosis of autism based on ADI-R and ADOS. Language and communication evaluation: below average language (<1st %ile). Epilepsy/seizures: no history of epilepsy. Dysmorphic features: minor, including 5th finger clinodactyly and several curled toes.
Below average non-verbal IQ (<1st %ile)
10467520
10528561
61042
GRCh38
Deletion
Yes
pinto_10_ASD_discovery_cases-case5237_3
NA
M
Autism
Below average language (<1%ile), no epilepsy, 5th finger clinodactyly, several curled toes
Below average nonverbal IQ (1%ile)
10467520
10528561
61042
GRCh38
Deletion
Yes
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR06-278
N/A
N/A
CBLH
Diagnosis of cerebellar hypoplasia (CBLH).
10446472
10506986
60515
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12321.p1
11.2
M
Autism
NA
Full-scale IQ, 96; non-verbal IQ, 108; verbal IQ, 76
10469593
10528561
58969
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12524.p1
6.4
F
Autism
NA
Full-scale IQ, 146; non-verbal IQ, 130; verbal IQ, 166
10469593
10528561
58969
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12532.p1
11.8
M
Autism
NA
Full-scale IQ, 121; non-verbal IQ, 110; verbal IQ, 135
10469593
10528561
58969
GRCh38
Deletion
No
van_der_zwaag_09_ASD_discovery_cases-subject021-003
NA
M
Non-complex autism
NA
NA
10596587
10664858
68270
Unknown
Deletion
Yes
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-controlB334479_1007875807
N/A
N/A
Control
No previous psychiatric history
10469593
10531953
62361
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB497980_1007852882
N/A
N/A
Control
No previous psychiatric history
10469593
10528561
58969
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB828621_0057060997
N/A
N/A
Control
No previous psychiatric history
10469593
10528561
58969
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB867787_1007854142
N/A
N/A
Control
No previous psychiatric history
10469593
10528561
58969
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900131_900131
N/A
N/A
Control
No previous psychiatric history
10467462
10528561
61100
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900197_900197
N/A
N/A
Control
No previous psychiatric history
10467462
10518117
50656
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12321.s1
9.8
F
Control (matched sibling)
NA
NA
10469593
10528561
58969
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12532.s1
9
F
Control (matched sibling)
NA
NA
10469593
10528561
58969
GRCh38
Deletion
No
van_der_zwaag_09_ASD_discovery_controls-control1
NA
Control
NA
NA
N/A
Unknown
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case3102_3
Unknown
GCNT2
engchuan_15_ASD_discovery_cases-case3177_6
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_cases-case4541_1
Unknown
MIR5689,MRPL48P1,LINC02522,MIR5689HG,GCNT2
engchuan_15_ASD_discovery_cases-case5237_3
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_cases-case8629_201
Unknown
LINC02522,GCNT2
krumm_15_ASD_discovery_cases-case11079.p1
Illumina 1M
Paternal
Simplex
Segregated
GCNT2
leblond_12_ASD_replication_cases-Pintocase5237_3
aCGH (Agilent 1M)
Paternal
LINC02522,GCNT2
pinto_10_ASD_discovery_cases-case5237_3
Agilent1M
paternal
Simplex
NA
LINC02522,GCNT2
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR06-278
Not tested by qPCR
Unknown
Unknown
Unknown
MRPL48P1,LINC02522,MIR5689HG,GCNT2
sanders_11_ASD_discovery_cases-12321.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC02522,GCNT2
sanders_11_ASD_discovery_cases-12524.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC02522,GCNT2
sanders_11_ASD_discovery_cases-12532.p1
Maternal
Simplex (quad-proband matched)
Not segregated
LINC02522,GCNT2
van_der_zwaag_09_ASD_discovery_cases-subject021-003
qPCR
Maternal
NA
NA
GCNT2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB334479_1007875807
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_controls-controlB497980_1007852882
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_controls-controlB828621_0057060997
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_controls-controlB867787_1007854142
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_controls-controlHABC_900131_900131
Unknown
LINC02522,GCNT2
engchuan_15_ASD_discovery_controls-controlHABC_900197_900197
Unknown
LINC02522,GCNT2
sanders_11_ASD_discovery_controls-12321.s1
Paternal
Simplex (quad)
NA
LINC02522,GCNT2
sanders_11_ASD_discovery_controls-12532.s1
Maternal
Simplex (quad)
NA
LINC02522,GCNT2
van_der_zwaag_09_ASD_discovery_controls-control1
Unknown
NA
NA
No Animal Model Data Available