3p25.2CNV Type: Deletion
Largest CNV size: 17815 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
Transmission disequilibrium of small CNVs in simplex autism.
Deletion-Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
Paternally inherited cis-regulatory structural variants are associated with 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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
47049
1
1
2
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
292067
3
0
3
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
130950
0
1
1
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
315935
1
3
4
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
315935
1
3
4
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
164401
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
17815
2
0
2
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
159035
0
2
2
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
159035
0
2
2
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)
164401
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.
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
brandler_18_ASD_replication_cases
N/A
WGS
Illumina HiSeq X10
ForestSV, Lumpy, Manta, Mobster, SV2
None
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
None
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
Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
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)
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
brandler_18_ASD_discovery_cases-caseSSC06431
N/A
M
ASD
Case from SSC_phase1 cohort
12655208
12702257
47050
GRCh38
Duplication
Yes
brandler_18_ASD_discovery_cases-caseSSC07144
N/A
M
ASD
Case from SSC_phase1 cohort
12659300
12661441
2142
GRCh38
Deletion
Yes
brandler_18_ASD_replication_cases-caseAU050603
N/A
M
ASD
Case from MSSNG cohort
12654239
12660565
6327
GRCh38
Deletion
No
brandler_18_ASD_replication_cases-caseAU060004
N/A
M
ASD
Case from MSSNG cohort
13073369
13073483
115
GRCh38
Deletion
No
brandler_18_ASD_replication_cases-caseSSC05077
N/A
F
ASD
Case from SSC_phase2 cohort
12887075
13179140
292066
GRCh38
Deletion
No
gai_11_ASD_replication_cases-AU046503
Autism
11738001
11868950
130950
Unknown
Duplication
No
krumm_13_ASD_discovery_cases-case11905.p1
N/A
M
ASD
ASD proband from SSC quad family 11905. SRS score of 90.
Full-scale IQ (FSIQ) score of 53.
12433897
12749832
315936
GRCh38
Duplication
No (not tested)
krumm_13_ASD_discovery_cases-case12481.p1
N/A
M
ASD
ASD proband from SSC quad family 12481. SRS score of 63.
Full-scale IQ (FSIQ) score of 42.
12590797
12749832
159036
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case12534.p1
N/A
F
ASD
ASD proband from SSC quad family 12534. SRS score of 90.
Full-scale IQ (FSIQ) score of 81.
12899389
12936697
37309
GRCh38
Deletion
No (not tested)
krumm_13_ASD_discovery_cases-case12727.p1
N/A
M
ASD
ASD proband from SSC quad family 12727. SRS score of 78.
Full-scale IQ (FSIQ) score of 90.
12899389
12941865
42477
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_cases-case11680.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
12590797
12749832
159036
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case11905.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
12433897
12749832
315936
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12481.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
12590797
12749832
159036
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12534.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
12899389
13073014
173626
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case146448L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
11705609
11870009
164401
Unknown
Duplication
No
sanders_11_ASD_discovery_cases-11025.p1
4.6
F
ASD
NA
Full-scale IQ, 98; non-verbal IQ, 102; verbal IQ, 92
12122713
12140528
17816
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11700.p1
6.5
M
Autism
NA
Full-scale IQ, 88; non-verbal IQ, 96; verbal IQ, 80
12122713
12132512
9800
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
krumm_13_ASD_discovery_controls-control12481.s1
N/A
M
Control
Unaffected sibling from SSC quad family 12481. SRS score of 34.
12590797
12749832
159036
GRCh38
Duplication
No (not tested)
krumm_13_ASD_discovery_controls-control12727.s1
N/A
M
Control
Unaffected sibling from SSC quad family 12727. SRS score of 58.
12900982
12941865
40884
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_controls-control12481.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
12590797
12749832
159036
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control13829.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
12590797
12749832
159036
GRCh38
Duplication
Yes
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC06431
PCR or SNP data validation
Maternal
CRIP1P1,RAF1
brandler_18_ASD_discovery_cases-caseSSC07144
PCR or SNP data validation
Paternal
RAF1
brandler_18_ASD_replication_cases-caseAU050603
No validation step reported
Maternal
RAF1
brandler_18_ASD_replication_cases-caseAU060004
No validation step reported
Paternal
IQSEC1
brandler_18_ASD_replication_cases-caseSSC05077
No validation step reported
Maternal
IQSEC1
gai_11_ASD_replication_cases-AU046503
Inherited
C3orf31
krumm_13_ASD_discovery_cases-case11905.p1
Maternal
Simplex
Segregated
RNA5SP123,RNU6-377P,CRIP1P1,TSEN2,MKRN2OS,RAF1,TMEM40,PPARG,MKRN2
krumm_13_ASD_discovery_cases-case12481.p1
Solid phase hybridization (Illumina 1M)
Maternal
Simplex
Not segregated
CRIP1P1,RAF1,TMEM40
krumm_13_ASD_discovery_cases-case12534.p1
Maternal
Simplex
Segregated
IQSEC1
krumm_13_ASD_discovery_cases-case12727.p1
Maternal
Simplex
Not segregated
IQSEC1
krumm_15_ASD_discovery_cases-case11680.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
CRIP1P1,RAF1,TMEM40
krumm_15_ASD_discovery_cases-case11905.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
RNA5SP123,RNU6-377P,CRIP1P1,TSEN2,MKRN2OS,RAF1,TMEM40,PPARG,MKRN2
krumm_15_ASD_discovery_cases-case12481.p1
Illumina 1MDuo
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
CRIP1P1,RAF1,TMEM40
krumm_15_ASD_discovery_cases-case12534.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
IQSEC1
prasad_12_ASD_discovery_cases-case146448L
Unknown
Unknown
Unknown
C3orf31,VGLL4
sanders_11_ASD_discovery_cases-11025.p1
Paternal
Simplex (trio)
NA
SYN2
sanders_11_ASD_discovery_cases-11700.p1
Unknown
Simplex (quad-proband matched)
Segregated
SYN2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control12481.s1
Maternal
Simplex
CRIP1P1,RAF1,TMEM40
krumm_13_ASD_discovery_controls-control12727.s1
Maternal
Simplex
IQSEC1
krumm_15_ASD_discovery_controls-control12481.s1
Illumina 1MDuo
Maternal
CRIP1P1,RAF1,TMEM40
krumm_15_ASD_discovery_controls-control13829.s1
Omni2.5-4v1
Maternal
CRIP1P1,RAF1,TMEM40
No Animal Model Data Available