3p12.1CNV Type: Deletion-Duplication
Largest CNV size: 614887 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
Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Convergence of genes and cellular pathways dysregulated in 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-Duplication
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
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
calderoni_20_ASD_discovery_cases
Females referred consecutively to the Autism Spectrum Disorders Unit of the Children Neuropsychiatry Hospital between 2015 and 2016
90
Clinical diagnosis of ASD based on DSM-5 criteria
Range, 21 mos.-17 yrs.
Female
57234
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
244560
4
2
6
girirajan_11_ASD_discovery_cases
ASD cases with sporadic autism from the Simons Simplex Collection (SSC)
336
Diagnosis of ASD based on meeting criteria on ADOS, ADI-R, and expert clinical judgment. 246 cases with no intellectual disability, 90 cases with intellectual disability. Exclusion criteria: significant hearing, vision, or motor problems; significant birth complications; a diagnosis of ASD-related disorders, such as Fragile X; or having a relative (up to 3rd degree) with ASD or sibling showing ASD-related symptoms.
571348
0
1
1
kaminsky_11_DD/ID/ASD_discovery_cases
Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium
15749
Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome
NA
NA
1018860
2
2
4
pinto_14_ASD_discovery_cases
ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
1359
Cases classified according to ADOS and ADI-R
N/A
N/A
89050
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
241851
2
0
2
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
614887
9
2
11
szatmari_07_ASD_discovery_cases
ASD patients from 173 families with at least two affected individuals from AGP
196
Patients diagnosed with ASD based on ADI-R and ADOS
1000
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
158223
3
0
3
girirajan_11_ASD_discovery_controls
Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
337
Control. Individuals screened specifically for eight mental health disorders.
571348
0
0
0
kaminsky_11_DD/ID/ASD_discovery_controls
Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium
10118
Controls
NA
NA
NA
NA
NA
NA
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)
241851
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.
614887
8
2
10
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
calderoni_20_ASD_discovery_cases
Italy
aCGH
Agilent 8x60K
qPCR
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_11_ASD_discovery_cases
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
None
kaminsky_11_DD/ID/ASD_discovery_cases
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
pinto_14_ASD_discovery_cases
Predominantly European
Solid phase hybridization
Illumina 1M (v.1 and v.3)
qPCR, MLPA, long-range PCR
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
szatmari_07_ASD_discovery_cases
Array SNP
Affymetrix 10K (v2)
HMM
dChip
Karyotyping, qPCR, aCGH, array SNP, overlap with Mendelian genotype errors
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_11_ASD_discovery_controls
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
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
calderoni_20_ASD_discovery_cases-caseP14
14 yrs.
F
ASD
ADOS module 3 evaluation: Social Affect score 5, Restricted and Repetitive Behaviors score 5, Calibrated Severity Score 4. Language and communication evaluation: verbal.
IQ > 70
85566418
85623651
57234
GRCh38
Deletion
Yes
engchuan_15_ASD_discovery_cases-case13007_83
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
85144904
85260570
115667
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case20000_1010002
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
85490666
85579715
89050
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case21006_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
84783183
84815966
32784
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case3198_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
85144904
85276120
131217
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4461_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
84336535
84507054
170520
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5549_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
83998645
84243205
244561
GRCh38
Deletion
No
girirajan_11_ASD_discovery_cases-Si128
8
M
Autism
ADOS score: 7. Vineland composite score: 69.
No mental retardation/intellectual disability. Full-scale IQ, 91; Verbal IQ, 83; Non-verbal IQ, 98.
84736288
85307637
571350
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004194
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
85714723
86559429
844707
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004258
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
85269738
86273143
1003406
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004751
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
85714723
86559429
844707
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005253
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
85774706
86793566
1018861
GRCh38
Duplication
Yes
pinto_14_ASD_discovery_cases2-case20000_1010002
N/A
F
ASD
Clinical profile: N/A.
Cognitive profile: N/A.
85490666
85579715
89050
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case114954L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
84128784
84370634
241851
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case56040
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
84977957
85023843
45887
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11088.p1
5.7
M
Autism
NA
Full-scale IQ, 92; non-verbal IQ, 102; verbal IQ, 80
84747499
84773261
25763
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11088.p1
5.7
M
Autism
NA
Full-scale IQ, 92; non-verbal IQ, 102; verbal IQ, 80
83633236
83683236
50001
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11090.p1
11.7
M
Autism
NA
Full-scale IQ, 56; non-verbal IQ, 67; verbal IQ, 53
84804628
84824842
20215
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11301.p1
9.8
M
Autism
NA
Full-scale IQ, 101; non-verbal IQ, 104; verbal IQ, 96
84804628
84824842
20215
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11573.p1
8.6
M
ASD
NA
Full-scale IQ, 68; non-verbal IQ, 85; verbal IQ, 51
84804628
84824842
20215
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11601.p1
6.3
M
Autism
NA
Full-scale IQ, 91; non-verbal IQ, 98; verbal IQ, 83
84713633
85328521
614889
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
84804628
84824842
20215
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11888.p1
4
M
ASD
NA
Full-scale IQ, 81; non-verbal IQ, 89; verbal IQ, 75
86857058
86860518
3461
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12275.p1
4.4
M
Autism
NA
Full-scale IQ, 111; non-verbal IQ, 111; verbal IQ, 107
83568338
83585301
16964
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12310.p1
9.5
M
Autism
NA
Full-scale IQ, 59; non-verbal IQ, 71; verbal IQ, 35
86860304
86860518
215
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12376.p1
12.2
M
Autism
NA
Full-scale IQ, 101; non-verbal IQ, 100; verbal IQ, 104
85441797
85514696
72900
GRCh38
Deletion
No
szatmari_07_ASD_discovery_cases-NAAR025-D4-3081.005
NA
ASD
NA
NA
85486860
85487360
501
GRCh38
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-controlB627204_1007846383
N/A
N/A
Control
No previous psychiatric history
85421492
85579715
158224
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB968409_1007873505
N/A
N/A
Control
No previous psychiatric history
85260570
85365141
104572
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900675_900675
N/A
N/A
Control
No previous psychiatric history
85073473
85119284
45812
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11090.s1
14.8
M
Control (matched sibling)
NA
NA
84804628
84824842
20215
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11135.s1
12.9
F
Control (matched sibling)
NA
NA
86936903
86937670
768
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11141.s1
5.2
F
Control (matched sibling)
NA
NA
84729928
84773261
43334
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11456.s1
11.3
M
Control (matched sibling)
NA
NA
84757652
84760199
2548
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11601.s1
9.3
F
Control (matched sibling)
NA
NA
84713633
85328521
614889
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12015.s1
9
F
Control (matched sibling)
NA
NA
86860304
86860518
215
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12211.s1
11.2
F
Control (matched sibling)
NA
NA
86860304
86860518
215
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12275.s1
8.4
M
Control (matched sibling)
NA
NA
83568338
83585301
16964
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12345.s1
12.9
F
Control (matched sibling)
NA
NA
84579710
84598555
18846
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12376.s1
14.7
F
Control (matched sibling)
NA
NA
85427867
85514696
86830
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
calderoni_20_ASD_discovery_cases-caseP14
qPCR
Paternal
CADM2
engchuan_15_ASD_discovery_cases-case13007_83
Unknown
CADM2
engchuan_15_ASD_discovery_cases-case20000_1010002
Unknown
CADM2
engchuan_15_ASD_discovery_cases-case21006_1
Unknown
LINC00971
engchuan_15_ASD_discovery_cases-case3198_3
Unknown
CADM2
engchuan_15_ASD_discovery_cases-case4461_1
Unknown
engchuan_15_ASD_discovery_cases-case5549_3
Unknown
girirajan_11_ASD_discovery_cases-Si128
Paternal
Simplex
LINC02025,LINC00971,CADM2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004194
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
THAP12P2,RNU6-1129P,RN7SKP284,CADM2-AS2,CADM2-AS1,LINC02070,CADM2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004258
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR5688,THAP12P2,RNU6-1129P,CADM2-AS2,CADM2-AS1,CADM2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004751
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
THAP12P2,RNU6-1129P,RN7SKP284,CADM2-AS2,CADM2-AS1,LINC02070,CADM2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005253
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
THAP12P2,RNU6-1129P,RN7SKP284,CADM2-AS2,CADM2-AS1,LINC02070,CADM2
pinto_14_ASD_discovery_cases2-case20000_1010002
qPCR
Maternal
Simplex
(not tested)
CADM2
prasad_12_ASD_discovery_cases-case114954L
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case56040
Unknown
Unknown
Unknown
LOC440970
sanders_11_ASD_discovery_cases-11088.p1
Unknown
Simplex (quad-proband matched)
Not segregated
LINC00971
sanders_11_ASD_discovery_cases-11088.p1
Unknown
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-11090.p1
Maternal
Simplex (quad-proband matched)
Not segregated
LINC00971
sanders_11_ASD_discovery_cases-11301.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC00971
sanders_11_ASD_discovery_cases-11573.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC00971
sanders_11_ASD_discovery_cases-11601.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC02025,LINC00971,CADM2
sanders_11_ASD_discovery_cases-11773.p1
Paternal
Simplex (quad-proband matched)
Not segregated
LINC00971
sanders_11_ASD_discovery_cases-11888.p1
Unknown
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12275.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12310.p1
Both parents
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12376.p1
Maternal
Simplex (quad-proband matched)
Not segregated
CADM2
szatmari_07_ASD_discovery_cases-NAAR025-D4-3081.005
Karyotyping, qPCR, aCGH, array SNP, or overlap with Mendelian genotype errors
Unknown
NA
NA
CADM2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB627204_1007846383
Unknown
CADM2
engchuan_15_ASD_discovery_controls-controlB968409_1007873505
Unknown
CADM2
engchuan_15_ASD_discovery_controls-controlHABC_900675_900675
Unknown
CADM2
sanders_11_ASD_discovery_controls-11090.s1
Maternal
Simplex (quad)
NA
LINC00971
sanders_11_ASD_discovery_controls-11135.s1
Maternal
Simplex (quad)
NA
VGLL3
sanders_11_ASD_discovery_controls-11141.s1
Paternal
Simplex (quad)
NA
LINC00971
sanders_11_ASD_discovery_controls-11456.s1
Paternal
Simplex (quad)
NA
LINC00971
sanders_11_ASD_discovery_controls-11601.s1
Paternal
Simplex (quad)
NA
LINC02025,LINC00971,CADM2
sanders_11_ASD_discovery_controls-12015.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12211.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12275.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12345.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12376.s1
Maternal
Simplex (quad)
NA
CADM2
No Animal Model Data Available