4q13.1-q13.2CNV Type: Duplication
Largest CNV size: 39746 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
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
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
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
262823
0
1
1
quintela_17_DD/ID_discovery_cases
Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
573
All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
Range, 3 months-18 years
60.38% Male
3846405
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
39746
0
12
12
yuen_17_ASD_discovery_cases
ASD genomes (1745 ASD probands, 879 ASD-affected siblings, 1 ASD-affected father, and 1 ASD-affected grandfather) from AGRE (n=730), the AGRE; Autism Treatment Network cohort (n=192) ,the ASD: Genomes to Outcomes Study cohort (n=1421), the Baby Siblings Research Consortium (n=43), the Baby Siblings Research Consortium; The Autism Simplex Collection cohort (n=6), the Infant Sibling Study (n=62), th
2626
ASD diagnosis of research quality when meeting criteria on one (n=437) or both (n=1361) of the diagnostic measures ADI-R and ADOS; clinical diagnosis of ASD (n=819) when given by expert clinician according to DSM-IV or DSM-5
N/A
78.71% Male
3846000
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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)
262823
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.
39746
11
0
11
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
quintela_17_DD/ID_discovery_cases
North West Spain
Array SNP
Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
Affymetrix ChAS v.1.2.2
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
yuen_17_ASD_discovery_cases
N/A
WGS
Complete Genomics, Illumina HiSeq 2000, HiSeq X
aCGH (Agilent 1M), array SNP (Affymetrix 6.0, Affymetrix CytoScan HD), solid phase hybridization (Illumina 1M, Illumina OMNI 2.5M)
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
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
prasad_12_ASD_discovery_cases-case133399
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
66155007
66417829
262823
Unknown
Duplication
No
quintela_17_DD/ID_discovery_cases-caseID_191
9 yrs.
M
Developmental delay/intellectual disability
Patient originally reported in Quintela et al., 2015d (P1 in this report). CNV inherited from affected parent.
64870306
68716710
3846405
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11251.p1
7.3
M
Autism
NA
Full-scale IQ, 84; non-verbal IQ, 84; verbal IQ, 88
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11343.p1
8.3
M
ASD
NA
Full-scale IQ, 87; non-verbal IQ, 90; verbal IQ 87
65731139
65763257
32119
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11615.p1
12.6
M
Autism
NA
Full-scale IQ, 83; non-verbal IQ, 83; verbal IQ, 89
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11616.p1
10.3
M
Autism
NA
Full-scale IQ, 127; non-verbal IQ, 129; verbal IQ, 113
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11691.p1
14.7
M
Autism
NA
Full-scale IQ, 59; non-verbal IQ, 62; verbal IQ, 54
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11794.p1
8.3
M
Autism
NA
Full-scale IQ, 36; non-verbal IQ, 40; verbal IQ, 33
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11869.p1
10.1
M
Autism
NA
Full-scale IQ, 98; non-verbal IQ, 104; verbal IQ, 86
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12020.p1
17.3
M
Autism
NA
Full-scale IQ, 116; non-verbal IQ, 115; verbal IQ, 114
65731139
65763257
32119
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12492.p1
15.4
M
Autism
NA
Full-scale IQ, 26; non-verbal IQ, 30; verbal IQ, 19
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12671.p1
12.8
M
Autism
NA
Full-scale IQ, 101; non-verbal IQ, 98; verbal IQ, 108
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12735.p1
10.7
M
ASD
NA
Full-scale IQ, 55; non-verbal IQ, 53; verbal IQ, 59
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12784.p1
4.4
M
Autism
NA
Full-scale IQ, 99; non-verbal IQ, 106; verbal IQ, 87
65731139
65763257
32119
GRCh38
Duplication
No
yuen_17_ASD_discovery_cases-case2-1275-003
N/A
N/A
ASD
Case cohort: ASD: Genomes to Outcome Study. Clinical description: ADHD; Tourette's; lactose intolerant
64430282
68276282
3846001
GRCh38
Duplication
Yes
Controls
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
sanders_11_ASD_discovery_controls-11193.s1
4.8
F
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11251.s1
4.9
M
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11333.s1
6.9
M
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11450.s1
12.5
F
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11616.s1
6.8
M
Control (matched sibling)
NA
NA
65731139
65763257
32119
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11794.s1
4.3
F
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11954.s1
6.8
F
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12020.s1
13.8
M
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12690.s1
10.6
M
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12735.s1
9.1
M
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-13162.s1
6.7
F
Control (matched sibling)
NA
NA
65723511
65763257
39747
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
prasad_12_ASD_discovery_cases-case133399
Unknown
Unknown
Unknown
EPHA5,LOC100144602
quintela_17_DD/ID_discovery_cases-caseID_191
Maternal
Maternal
Multi-generational
Possibly segregated
RNU2-40P,MIR1269A,RPS23P3,RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,MT2P1,UGT2B29P,EPHA5-AS1,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,APOOP4,YTHDC1,TMPRSS11E,UGT2B15,EFL1P2,EPHA5,CENPC,UBA6,UBA6-AS1,UGT2B17,LINC02232
sanders_11_ASD_discovery_cases-11251.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11343.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11615.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11616.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11691.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11794.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11869.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12020.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12492.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12671.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12735.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12784.p1
Paternal
Simplex (quad-proband matched)
Not segregated
yuen_17_ASD_discovery_cases-case2-1275-003
Illumina OMNI 2.5M
Maternal
Simplex
Unknown
DPP3P1,MTCO3P27,MTCYBP16,MTND6P16,MTND5P13,MTND4LP31,MTND3P24,MTCO3P28,RNU2-40P,MIR1269A,RPS23P3,RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,EPHA5-AS1,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,EFL1P2,EPHA5,CENPC,UBA6,UBA6-AS1,LINC02232
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11193.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11251.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11333.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11450.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11616.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11794.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11954.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12020.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12690.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12735.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-13162.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available