3q25.31CNV Type: Deletion-Duplication
Largest CNV size: 87537 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
Excess of rare, inherited truncating mutations in autism.
Deletion-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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
krumm_13_ASD_discovery_cases
Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
81.265% Male
12332
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
39089
1
9
10
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)
39060
0
1
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
20676
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
87537
1
10
11
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
krumm_13_ASD_discovery_controls
Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
46.47% Male
12332
0
1
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
12333
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)
12332
0
1
1
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)
20676
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.
28566
2
4
6
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
krumm_13_ASD_discovery_cases
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
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
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
krumm_13_ASD_discovery_controls
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
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
krumm_13_ASD_discovery_cases-case13487.p1
N/A
M
ASD
ASD proband from SSC quad family 13487. SRS score of 56.
Full-scale IQ (FSIQ) score of 96.
155763516
155775848
12333
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_cases-case11257.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case11498.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12007.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12494.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13072.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763517
155802606
39090
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13576.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763516
155775848
12333
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13655.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
155775701
155802606
26906
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case14123.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763516
155775848
12333
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case14231.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155767508
155775848
8341
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case14249.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
155763516
155775848
12333
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case99HI0765
N/A
F
ASD
ASD case from AGRE (AGRE ID AU054805; NDAR ID NDAR_INVHV388WC3)
155763517
155802576
39060
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case85275L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
156552716
156573391
20676
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11113.p1
15
M
Autism
NA
Full-scale IQ, 87; non-verbal IQ, 100; verbal IQ 86
155352676
155372196
19521
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11257.p1
5.5
M
Autism
NA
Full-scale IQ, 129; non-verbal IQ, 128; verbal IQ, 118
155763308
155801046
37739
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11394.p1
5.3
M
Autism
NA
Full-scale IQ, 76; non-verbal IQ, 74; verbal IQ 87
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11498.p1
7.3
M
Autism
NA
Full-scale IQ, 113; non-verbal IQ, 102; verbal IQ, 110
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11634.p1
5.7
M
Autism
NA
Full-scale IQ, 55; non-verbal IQ, 56; verbal IQ, 63
156030905
156118442
87538
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12007.p1
8.7
F
Autism
NA
Full-scale IQ, 64; non-verbal IQ, 54; verbal IQ, 83
155763308
155787808
24501
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12232.p1
7.7
M
Autism
NA
Full-scale IQ, 62; non-verbal IQ, 74; verbal IQ, 51
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12414.p1
4.4
M
ASD
NA
Full-scale IQ, 116; non-verbal IQ, 129; verbal IQ, 90
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12434.p1
5.3
M
Autism
NA
Full-scale IQ, 117; non-verbal IQ, 121; verbal IQ, 106
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12494.p1
7.9
M
Autism
NA
Full-scale IQ, 59; non-verbal IQ, 67; verbal IQ, 56
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-13072.p1
15.5
F
Autism
NA
Full-scale IQ, 94; non-verbal IQ, 94; verbal IQ, 97
155765530
155791874
26345
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
krumm_13_ASD_discovery_controls-control13922.s1
N/A
M
Control
Unaffected sibling from SSC quad family 13922. SRS score of 41.
155763516
155775848
12333
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_controls-control12007.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control12494.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
155763517
155775850
12334
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control13922.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
155763516
155775848
12333
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control14123.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
155763516
155775848
12333
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_controls-control04C27774A
N/A
F
Control
NIMH Control (NIMH ID 62995)
155763517
155775848
12332
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11909.s1
5.7
M
Control (matched sibling)
NA
NA
156660082
156674402
14321
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11909.s1
5.7
M
Control (matched sibling)
NA
NA
156717618
156732802
15185
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12007.s1
10.9
M
Control (matched sibling)
NA
NA
155763308
155787808
24501
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12434.s1
8.8
F
Control (matched sibling)
NA
NA
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12494.s1
11
F
Control (matched sibling)
NA
NA
155763308
155791874
28567
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12682.s1
8.1
M
Control (matched sibling)
NA
NA
155763308
155791874
28567
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_cases-case13487.p1
Paternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case11257.p1
Illumina 1M
Maternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case11498.p1
Illumina 1M
Paternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case12007.p1
Illumina 1MDuo
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
C3orf33
krumm_15_ASD_discovery_cases-case12494.p1
Illumina 1MDuo
Paternal
Simplex
Not segregated (CNV in unaffected sibling)
C3orf33
krumm_15_ASD_discovery_cases-case13072.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case13576.p1
1M-Duov3
Paternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case13655.p1
Omni2.5-4v1
Maternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case14123.p1
Omni2.5-4v1
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
C3orf33
krumm_15_ASD_discovery_cases-case14231.p1
Omni2.5-4v1
Maternal
Simplex
Segregated
C3orf33
krumm_15_ASD_discovery_cases-case14249.p1
Omni2.5-4v1
Maternal
Simplex
Segregated
C3orf33
poultney_13_ASD_discovery_cases-case99HI0765
Unknown
Unknown (likely multiplex/AGRE)
Unknown
C3orf33
prasad_12_ASD_discovery_cases-case85275L
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-11113.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11257.p1
Maternal
Simplex (quad-proband matched)
Segregated
C3orf33
sanders_11_ASD_discovery_cases-11394.p1
Paternal
Simplex (trio)
NA
C3orf33
sanders_11_ASD_discovery_cases-11498.p1
Paternal
Simplex (quad-proband matched)
Segregated
C3orf33
sanders_11_ASD_discovery_cases-11634.p1
Paternal
Simplex (quad-proband matched)
Not segregated
ALG1L15P,MRE11P1,VN2R1P,KCNAB1
sanders_11_ASD_discovery_cases-12007.p1
Maternal
Simplex (quad-proband matched)
Not segregated
C3orf33
sanders_11_ASD_discovery_cases-12232.p1
Paternal
Simplex (trio)
NA
C3orf33
sanders_11_ASD_discovery_cases-12414.p1
Maternal
Simplex (trio)
NA
C3orf33
sanders_11_ASD_discovery_cases-12434.p1
Maternal
Simplex (quad-proband matched)
Not segregated
C3orf33
sanders_11_ASD_discovery_cases-12494.p1
Paternal
Simplex (quad-proband matched)
Not segregated
C3orf33
sanders_11_ASD_discovery_cases-13072.p1
Paternal
Simplex (quad-proband matched)
Not segregated
C3orf33
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control13922.s1
Paternal
Simplex
C3orf33
krumm_15_ASD_discovery_controls-control12007.s1
Illumina 1MDuo
Maternal
C3orf33
krumm_15_ASD_discovery_controls-control12494.s1
Illumina 1MDuo
Paternal
C3orf33
krumm_15_ASD_discovery_controls-control13922.s1
Omni2.5-4v1
Paternal
C3orf33
krumm_15_ASD_discovery_controls-control14123.s1
Omni2.5-4v1
Maternal
C3orf33
poultney_13_ASD_discovery_controls-control04C27774A
Unknown
C3orf33
sanders_11_ASD_discovery_controls-11909.s1
Unknown
Simplex (quad)
NA
TIPARP-AS1,TIPARP
sanders_11_ASD_discovery_controls-11909.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12007.s1
Maternal
Simplex (quad)
NA
C3orf33
sanders_11_ASD_discovery_controls-12434.s1
Maternal
Simplex (quad)
NA
C3orf33
sanders_11_ASD_discovery_controls-12494.s1
Paternal
Simplex (quad)
NA
C3orf33
sanders_11_ASD_discovery_controls-12682.s1
Paternal
Simplex (quad)
NA
C3orf33
No Animal Model Data Available