3p26.1-p25.3CNV Type: Duplication
Largest CNV size: 161201 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
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.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Neurological and psychiatric phenotype of a multicenter cohort of patients with SETD5-related neurodevelopmental disorder
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
defalco_25_DD/ID_discovery_cases
Individuals with microdeletions affecting the SETD5 gene from an initial cohort of 28 previously unreported individuals with SETD5 variants who came from 9 European Centers for Genetics and Child or Adult Neurology (Italy, Germany, France).
2
Both individuals presented with developmental delay/intellectual disability (DD/ID); one individual also presented with seizures, while the other also presented with stereotypy.
Range, 2-9 yrs.
50% Male
1644238
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
2049512
1
2
3
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
107072
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
161201
0
1
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
472897
0
1
1
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
leppa_16_ASD_discovery_controls
Unaffected children from 1,464 families from the Autism Genetic Resource Exchange (AGRE)
572
Control
N/A
N/A
700000
0
1
1
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)
939803
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)
107072
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
defalco_25_DD/ID_discovery_cases
European
aCGH
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
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
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
leppa_16_ASD_discovery_controls
N/A
Solid phase hybridization
Illumina 550v1 and 550v3, Omni-1.0-B and -H, Omni 2.5
PennCNV, QuantiSNP, GNOSIS
GenomeStudio, CNVision
None
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
defalco_25_DD/ID_discovery_cases-case14
9 yrs.
F
Developmental delay, intellectual disability, and stereotypy
Developmental milestones: mild developmental delay/intellectual disability. Motor and musculoskeletal evaluation: left single palmar groove, fifth finger brachydactyly, clinodactyly, left 2-3 toe syndactyly, pectus excavatum. Behavioral/psychiatric evaluation: stereotypies. Brain imaging: large cisterna magna, pineal cyst formation, ectasia medulla. Dysmorphic features: micrognathia, hypertelorism, left eyelid ptosis, spaced teeth, epigastric cutaneous appendage.
Mild developmental delay/intellectual disability
7868348
9512585
1644238
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001848
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
8091665
8742586
650922
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002644
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
7975734
9038133
1062400
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003956
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
7400936
9450451
2049516
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case136064
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
8646703
8753774
107072
Unknown
Duplication
No
sanders_11_ASD_discovery_cases-11824.p1
8.9
M
Autism
NA
Full-scale IQ, 81; non-verbal IQ, 89; verbal IQ, 72
8542606
8703807
161202
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
engchuan_15_ASD_discovery_controls-controlHABC_900152_900152
N/A
N/A
Control
No previous psychiatric history
8239993
8712891
472899
GRCh38
Duplication
No
leppa_16_ASD_discovery_controls-AU1024302
N/A
F
Control
Unaffected sibling
7998313
8732314
734002
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C45305
N/A
F
Control
NIMH Control (NIMH ID 26586)
8501937
9441741
939805
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
defalco_25_DD/ID_discovery_cases-case14
De novo
CAV3,SSUH2,LMCD1,SETD5,RAD18,OR7E122P,LHFPL4,PGAM1P4,THUMPD3-AS1,OXTR,LMCD1-AS1,SRGAP3-AS3,SRGAP3-AS1,SRGAP3-AS4,SRGAP3-AS2,RNU4ATAC17P,SRGAP3,THUMPD3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001848
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
RNU4ATAC17P,OR7E122P,LMCD1,SSUH2,CAV3,LMCD1-AS1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002644
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RNU4ATAC17P,SRGAP3-AS1,OR7E122P,OXTR,LMCD1,SSUH2,CAV3,RAD18,SRGAP3,LMCD1-AS1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003956
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNU4ATAC17P,SRGAP3-AS1,SRGAP3-AS2,SRGAP3-AS3,PGAM1P4,GRM7-AS1,OR7E122P,OXTR,SRGAP3-AS4,THUMPD3-AS1,THUMPD3,LMCD1,SSUH2,CAV3,RAD18,SRGAP3,GRM7,SETD5,LMCD1-AS1
prasad_12_ASD_discovery_cases-case136064
Unknown
Unknown
Unknown
C3orf32,CAV3
sanders_11_ASD_discovery_cases-11824.p1
Paternal
Simplex (quad-proband unmatched)
Unknown
OR7E122P,LMCD1,SSUH2,LMCD1-AS1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900152_900152
Unknown
RNU4ATAC17P,OR7E122P,LMCD1,SSUH2,LMCD1-AS1
leppa_16_ASD_discovery_controls-AU1024302
Paternal
Multiplex
RNU4ATAC17P,OR7E122P,LMCD1,SSUH2,LMCD1-AS1
poultney_13_ASD_discovery_controls-control05C45305
Unknown
SRGAP3-AS1,SRGAP3-AS2,SRGAP3-AS3,PGAM1P4,OR7E122P,OXTR,SRGAP3-AS4,THUMPD3-AS1,THUMPD3,LMCD1,SSUH2,CAV3,RAD18,SRGAP3,SETD5,LMCD1-AS1
No Animal Model Data Available