3q26.33CNV Type: Deletion-Duplication
Largest CNV size: 102364 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
Structural variation of chromosomes in autism spectrum disorder.
Duplication
Identification of a functional rare variant in autism using genome-wide screen for monoallelic expression.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population.
Deletion
Large-scale discovery of novel genetic causes of developmental disorders.
Deletion
Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
Retrospective chart review of patients (n=584) with a neurocognitive phenotype (mainly referred from pediatric neurology clinics) seen by a single clinical geneticist from September 2007 to July 2013
584
Inclusion criteria: presence of a neurocognitive phenotype (i.e., syndromic and non-syndromic cases of developmental delay, autism, intellectual disability, and epilepsy) with a normal karyotype
N/A
N/A
793582
1
0
1
ben-david_11_ASD_discovery_cases
Lymphoblastoid cell lines (LCLs) from a subset of ASD subjects previously used in Yirmiya et al. 2006 AVPR1a association study.
17
Diagnosis of DSM IV autistic disorder (n=14) or PDD-NOS (n=3) using ADI-R and ADOS-G; average IQ 51.2 28.3
70.59% Male
130000
0
1
1
fitzgerald_14_ASD/DD/ID_discovery_cases
Children recruited through all 24 regional genetics services of the UK National Health Service and Republic of Ireland as part of the Deciphering Developmental Disorders Study
1133
Cases affected by severe, undiagnosed developmental disorders; most common phenotypes include developmental delay, intellectual disability, specific learning disability, autism, seizures, microcephaly, and dysmorphic features.
Median age, 5.5 years
N/A
1116500
1
0
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
783235
2
0
2
marshall_08_ASD_discovery_cases
Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
427
ASD
102364
0
1
1
pfundt_16_NDD_discovery_cases
Subset of a cohort of 2,603 patients affected by genetic disorders for which exome seqeuncing was performed in a diagnostic setting
1215
Neurodevelopmental disorders
N/A
N/A
2522
0
1
1
pfundt_16_nonNDD_discovery_cases
Subset of a cohort of 2,603 patients affected by genetic disorders for which exome seqeuncing was performed in a diagnostic setting
1430
Craniofacial anomalies (n=31), disorders of sexual development (n=38), immunodeficiency (n=24), metabolic disorders (n=34), hereditary cancer (n=74), renal disorders (n=56), complex phenotypes (n=183), mitochondrial disorders (n=142), muscle disorders (n=171), deafness (n=223), movement disorders (n=217), or blindness (n=237)
N/A
N/A
3594
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
20616
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
21926
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
117808
0
1
1
marshall_08_ASD_discovery_controls_1
German PopGen project and entries from Database of Genomic Variants
500
Controls
0
0
0
0
marshall_08_ASD_discovery_controls_2
Non-disease controls from Ontario population
1152
Controls
0
0
0
0
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)
20616
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.
17474
1
0
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
Saudi Arabia
Array SNP
Affymetrix 6.0, Affymetrix Cyto-V2, Affymetrix CytoScan HD
HMM
Affymetrix GeneChip Command Console v.1.2, Affymetrix ChAS version Cyto 2.0.0.195
None
ben-david_11_ASD_discovery_cases
Array SNP
Affymetrix 6.0
Canary, PennCNV
Affymetrix Genotyping Console
MLPA
fitzgerald_14_ASD/DD/ID_discovery_cases
UK and Ireland
aCGH, WES
Agilent 2x1M, Agilent Exome+
Cnsolidate, CoNVex
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
marshall_08_ASD_discovery_cases
90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
qPCR, qmPCR
pfundt_16_NDD_discovery_cases
N/A
WES
Solid5500xl, IlluminaHiSeq2000
CoNIFER
None
pfundt_16_nonNDD_discovery_cases
N/A
WES
Solid5500xl, IlluminaHiSeq2000
CoNIFER
No
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
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
marshall_08_ASD_discovery_controls_1
European
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
marshall_08_ASD_discovery_controls_2
European
Array SNP, karotyping
Affymetrix 500K
dChip, CNAG, GEMCA
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
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case13DG0963
N/A
N/A
Developmental delay
Global developmental delay, right microphthalmia and left anophthalmia, acquired microcephaly, and micropenis (SOX2 anophthalmia syndrome). Non-consanguineous parents.
Global developmental delay
180960868
181754449
793582
GRCh38
Deletion
No
ben-david_11_ASD_discovery_cases-proband13
NA
NA
ASD
NA
NA
180619034
180748723
130000
Unknown
Duplication
Yes
fitzgerald_14_ASD/DD/ID_discovery_cases-DECIPHER263441
N/A
M
Autism and ID
Intellectual disability; Iris coloboma; Autism
181666686
182783186
1116501
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002186
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
181710887
181748657
37771
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004129
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
181504586
182287821
783236
GRCh38
Deletion
Yes
marshall_08_ASD_discovery_cases-NA0090-000
NA
M
ASD
NA
NA
182637216
182739579
102364
GRCh38
Duplication
Yes
pfundt_16_NDD_discovery_cases-case46
N/A
N/A
NDD
Disease cohort: neurodevelopmental disorder. Description: DNAJC19 duplication
180986997
180989519
2523
GRCh38
Duplication
No
pfundt_16_nonNDD_discovery_cases-case49
N/A
N/A
Non-NDD
Disease cohort: complex phenotype. Description: DNAJC19 duplication
180985925
180989519
3595
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case76222
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
181381774
181402389
20616
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-12743.p1
10.1
M
Autism
NA
Full-scale IQ, 116; non-verbal IQ, 114; verbal IQ, 108
181018465
181040391
21927
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
levy_11_ASD_discovery_controls-11961.s1
NA
M
Control
NA
NA
181490088
181607895
117808
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12851.s1
5.8
M
Control (matched sibling)
NA
NA
182647000
182664474
17475
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case13DG0963
Unknown
Unknown
Unknown
DNAJC19,RNU6-4P,FAUP2,RPL7AP25,SOX2,FXR1,SOX2-OT
ben-david_11_ASD_discovery_cases-proband13
MLPA
Maternal
Unknown
Unknown
GNB4
Monoallelic expression of AUTS2
fitzgerald_14_ASD/DD/ID_discovery_cases-DECIPHER263441
Paternal
De novo
Father
Not segregated
SOX2,RN7SL703P,RNA5SP150,RN7SKP265,EIF4EP3,RPL7L1P8,LINC01206,LINC01995,LINC02031,SOX2-OT,LINC01994
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002186
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SOX2,SOX2-OT
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004129
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPL7AP25,SOX2,RN7SL703P,RNA5SP150,RN7SKP265,LINC01206,SOX2-OT
marshall_08_ASD_discovery_cases-NA0090-000
qPCR, qmPCR
Unknown
NA
NA
LINC02031
pfundt_16_NDD_discovery_cases-case46
DNAJC19
pfundt_16_nonNDD_discovery_cases-case49
DNAJC19
prasad_12_ASD_discovery_cases-case76222
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-12743.p1
Maternal
Simplex (quad-proband matched)
Segregated
SOX2-OT
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
levy_11_ASD_discovery_controls-11961.s1
De novo
Simplex
NA
RPL7AP25,SOX2-OT
sanders_11_ASD_discovery_controls-12851.s1
Maternal
Simplex (quad)
NA
LINC02031
No Animal Model Data Available