1p12CNV Type: Deletion-Duplication
Largest CNV size: 484103 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
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Duplication
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.
Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion-Duplication
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
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
141
0
1
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
349228
2
7
9
gai_11_ASD_replication_cases
Replication case samples derived from AGRE sets 1-3
593
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
444262
0
1
1
girirajan_13a_ASD_discovery_cases
1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
2588
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
NA
NA
1034000
1
1
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
255913
1
1
2
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
39683
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
484103
6
3
9
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
812138
4
1
5
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
22705
0
1
1
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
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)
18633
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.
39682
4
1
5
stamouli_18_ASD/NDD_discovery_controls
Unaffected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
100 twin pairs
Control (unaffected) individual following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities and
N/A
N/A
10884
0
2
2
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
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
None
girirajan_13a_ASD_discovery_cases
NA
aCGH
Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
ADM-2
Agilent Genomic Workbench
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
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)
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
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
stamouli_18_ASD/NDD_discovery_controls
Swedish
Solid phase hybridization
Illumina Infinium PsychArray-24 v1.1
PennCNV, QuantiSNP, iPattern, iPsychCNV
None
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-11303
NA
M
ASD
NA
NA
117952231
117952372
142
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case14042_730
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119572256
119603260
31005
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case3612_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119572761
119603260
30500
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4027_100
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119580556
119688200
107645
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4027_100
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
118859151
119208379
349229
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4519_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119564979
119603260
38282
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5107_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119557357
119597039
39683
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5271_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119572761
119603260
30500
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case6375_6
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119557357
119597039
39683
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case8421_201
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
119572256
119607829
35574
GRCh38
Deletion
No
gai_11_ASD_replication_cases-AU0875301
Autism
119511865
119956126
444262
Unknown
Duplication
No
girirajan_13a_ASD_discovery_cases-13327.p1
N/A
N/A
ASD
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
N/A
119125854
119625854
500001
GRCh38
Duplication
No
girirajan_13a_ASD_discovery_cases-13568.p1
N/A
N/A
ASD
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
N/A
118275854
119305854
1030001
GRCh38
Deletion
No
krumm_15_ASD_discovery_cases-case12548.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
119381085
119626102
245018
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13568.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
118884731
119140644
255914
GRCh38
Deletion
Yes
pinto_10_ASD_discovery_cases-case5107_3
NA
M
ASD
NA
NA
119557357
119597039
39683
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-11073.p1
9.7
M
Autism
NA
Full-scale IQ, 100; non-verbal IQ, 100; verbal IQ, 101
119564860
119603260
38401
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11263.p1
13.2
M
Autism
NA
Full-scale IQ, 97; non-verbal IQ, 100; verbal IQ, 92
119594822
119609459
14638
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11599.p1
6.6
M
Autism
NA
Full-scale IQ, 105; non-verbal IQ, 106; verbal IQ, 99
119594822
119603260
8439
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12367.p1
9.4
M
ASD
NA
Full-scale IQ, 114; non-verbal IQ, 111; verbal IQ, 117
119584367
119611980
27614
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12367.p1
9.4
M
ASD
NA
Full-scale IQ, 114; non-verbal IQ, 111; verbal IQ, 117
117647245
117648126
882
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12548.p1
11.9
M
Autism
NA
Full-scale IQ, 100; non-verbal IQ, 113; verbal IQ, 76
119141627
119625730
484104
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-13152.p1
7.3
M
Autism
NA
Full-scale IQ, 77; non-verbal IQ, 79; verbal IQ, 78
119580556
119603260
22705
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13166.p1
9.1
M
Autism
NA
Full-scale IQ, 46; non-verbal IQ, 47; verbal IQ, 45
119328584
119340989
12406
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13166.p1
9.1
M
Autism
NA
Full-scale IQ, 46; non-verbal IQ, 47; verbal IQ, 45
119564860
119597039
32180
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
engchuan_15_ASD_discovery_controls-controlB147560_1007872587
N/A
N/A
Control
No previous psychiatric history
119572761
119609459
36699
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB259917_1007874661
N/A
N/A
Control
No previous psychiatric history
117956431
118768569
812139
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB525694_1007854064
N/A
N/A
Control
No previous psychiatric history
119557357
119603260
45904
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900283_900283
N/A
N/A
Control
No previous psychiatric history
119572256
119609459
37204
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900360_900360
N/A
N/A
Control
No previous psychiatric history
119572256
119603260
31005
GRCh38
Deletion
No
kanduri_15_ASD_discovery_controls-control_split390
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
120123179
120145883
22705
Unknown
Duplication
No
poultney_13_ASD_discovery_controls-control05C46370
N/A
F
Control
NIMH Control (NIMH ID 48570)
119986958
120005590
18633
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11073.s1
7.8
F
Control (matched sibling)
NA
NA
119557357
119597039
39683
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11152.s1
8.8
F
Control (matched sibling)
NA
NA
118563989
118574544
10556
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11339.s1
11.2
M
Control (matched sibling)
NA
NA
119556421
119584367
27947
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12367.s1
9.3
F
Control (matched sibling)
NA
NA
119584367
119611980
27614
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12367.s1
9.3
F
Control (matched sibling)
NA
NA
117647245
117648126
882
GRCh38
Deletion
No
stamouli_18_ASD/NDD_discovery_controls-family65_Twin_1
N/A
N/A
Control
Control is from a monozygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
119382926
119393809
10884
GRCh38
Duplication
No
stamouli_18_ASD/NDD_discovery_controls-family65_Twin_2
N/A
N/A
Control
Control is from a monozygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
119382926
119393809
10884
GRCh38
Duplication
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-11303
Unknown
Simplex
NA
WDR3
engchuan_15_ASD_discovery_cases-case14042_730
Unknown
GAPDHP33,LINC00622,HSD3BP5
engchuan_15_ASD_discovery_cases-case3612_3
Unknown
GAPDHP33,LINC00622,HSD3BP5
engchuan_15_ASD_discovery_cases-case4027_100
Unknown
GAPDHP33,LINC00622,HSD3BP5,ZNF697,PHGDH
engchuan_15_ASD_discovery_cases-case4027_100
Unknown
RBMX2P3,RPS3AP12,TBX15,WARS2,WARS2-IT1
engchuan_15_ASD_discovery_cases-case4519_1
Unknown
GAPDHP33,LINC00622,HSD3BP4,HSD3BP5
engchuan_15_ASD_discovery_cases-case5107_3
Unknown
GAPDHP27,GAPDHP33,HSD3BP4
engchuan_15_ASD_discovery_cases-case5271_3
Unknown
GAPDHP33,LINC00622,HSD3BP5
engchuan_15_ASD_discovery_cases-case6375_6
Unknown
GAPDHP27,GAPDHP33,HSD3BP4
engchuan_15_ASD_discovery_cases-case8421_201
Unknown
GAPDHP33,LINC00622,HSD3BP5
gai_11_ASD_replication_cases-AU0875301
Inherited
HAO2, HSD3B2, HSD3B1
girirajan_13a_ASD_discovery_cases-13327.p1
Unknown
Simplex
Unknown
RPS3AP12,RPL6P2,RNU1-75P,HAO2-IT1,GAPDHP74,GAPDHP23,GAPDHP58,HSD3B1,GAPDHP32,HSD3BP3,GAPDHP27,GAPDHP33,LINC00622,WARS2,LINC01780,HAO2,HSD3B2,HSD3BP2,HSD3BP1,HSD3BP4,HSD3BP5,ZNF697
girirajan_13a_ASD_discovery_cases-13568.p1
Unknown
Simplex
Unknown
PSMC1P12,RBMX2P3,RPS3AP12,RPL6P2,TBX15,WARS2,WARS2-IT1
krumm_15_ASD_discovery_cases-case12548.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
GAPDHP74,GAPDHP23,GAPDHP58,HSD3B1,GAPDHP32,HSD3BP3,GAPDHP27,GAPDHP33,LINC00622,HAO2,HSD3B2,HSD3BP2,HSD3BP1,HSD3BP4,HSD3BP5,ZNF697
krumm_15_ASD_discovery_cases-case13568.p1
1M-Duov3
Maternal
Simplex
Segregated
RBMX2P3,RPS3AP12,TBX15,WARS2,WARS2-IT1
pinto_10_ASD_discovery_cases-case5107_3
Agilent1M
maternal
NA
NA
GAPDHP27,GAPDHP33,HSD3BP4
sanders_11_ASD_discovery_cases-11073.p1
Paternal
Simplex (quad-proband matched)
Not segregated
GAPDHP33,LINC00622,HSD3BP4,HSD3BP5
sanders_11_ASD_discovery_cases-11263.p1
Paternal
Simplex (quad-proband matched)
Segregated
GAPDHP33,LINC00622,HSD3BP5
sanders_11_ASD_discovery_cases-11599.p1
Maternal
Simplex (quad-proband matched)
Not segregated
GAPDHP33,LINC00622,HSD3BP5
sanders_11_ASD_discovery_cases-12367.p1
Paternal
Simplex (quad-proband matched)
Not segregated
GAPDHP33,LINC00622,HSD3BP5
sanders_11_ASD_discovery_cases-12367.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12548.p1
Maternal
Simplex (quad-proband matched)
Not segregated
RPL6P2,RNU1-75P,HAO2-IT1,GAPDHP74,GAPDHP23,GAPDHP58,HSD3B1,GAPDHP32,HSD3BP3,GAPDHP27,GAPDHP33,LINC00622,LINC01780,HAO2,HSD3B2,HSD3BP2,HSD3BP1,HSD3BP4,HSD3BP5,ZNF697
sanders_11_ASD_discovery_cases-13152.p1
Paternal
Simplex (quad-proband unmatched)
Unknown
GAPDHP33,LINC00622,HSD3BP5
sanders_11_ASD_discovery_cases-13166.p1
Unknown
Simplex (quad-proband matched)
Segregated
RNU1-75P,LINC01780
sanders_11_ASD_discovery_cases-13166.p1
Maternal
Simplex (quad-proband matched)
Not segregated
GAPDHP33,HSD3BP4
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB147560_1007872587
Unknown
GAPDHP33,LINC00622,HSD3BP5
engchuan_15_ASD_discovery_controls-controlB259917_1007874661
Unknown
RNA5SP56,PSMC1P12,WDR3,SPAG17
engchuan_15_ASD_discovery_controls-controlB525694_1007854064
Unknown
GAPDHP27,GAPDHP33,LINC00622,HSD3BP4,HSD3BP5
engchuan_15_ASD_discovery_controls-controlHABC_900283_900283
Unknown
GAPDHP33,LINC00622,HSD3BP5
engchuan_15_ASD_discovery_controls-controlHABC_900360_900360
Unknown
GAPDHP33,LINC00622,HSD3BP5
kanduri_15_ASD_discovery_controls-control_split390
Unknown
LINC00622 (non-coding RNA, exonic)
poultney_13_ASD_discovery_controls-control05C46370
Unknown
NOTCH2
sanders_11_ASD_discovery_controls-11073.s1
Paternal
Simplex (quad)
NA
GAPDHP27,GAPDHP33,HSD3BP4
sanders_11_ASD_discovery_controls-11152.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11339.s1
Maternal
Simplex (quad)
NA
GAPDHP27,HSD3BP4
sanders_11_ASD_discovery_controls-12367.s1
Paternal
Simplex (quad)
NA
GAPDHP33,LINC00622,HSD3BP5
sanders_11_ASD_discovery_controls-12367.s1
Paternal
Simplex (quad)
NA
stamouli_18_ASD/NDD_discovery_controls-family65_Twin_1
Unknown
N/A (both twins typically developing)
HAO2
stamouli_18_ASD/NDD_discovery_controls-family65_Twin_2
Unknown
N/A (both twins typically developing)
HAO2
No Animal Model Data Available