6p12.3CNV Type: Deletion-Duplication
Largest CNV size: 109319 bp
Statistics Box:
Number of Reports: 10
Number of Reports: 10
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability.
Deletion
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
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_cases
Samples from the Autism Genome Project (AGP)
1892
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
N/A
85.78% Male
109318
0
1
1
iourov_12_ASD/ID/EP_discovery_cases
Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
54
Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
Range, 3 mos.-11 yrs.
NA
177179
0
1
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
507533
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
4153
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
235545
2
1
3
pinto_10_ASD_discovery_cases
Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
996
ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
109319
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
123609
0
3
3
qiao_12_ASD/ID_discovery_cases
Cohort recruited through Autism Spectrum Interdisciplinary Research (ASPIRE) program of the University of Britisn Columbia Provincial Medical Genetics Program in Vancouver, Canada (ASD-CARC)
52
ASD and/or ID (intellectual disability)
NA
NA
205000
1
0
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
581309
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
16803
1
2
3
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
156067
0
3
3
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
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
96164
1
1
2
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
235545
2
2
4
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
186469
1
0
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)
425677
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)
123609
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.
194900
1
0
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
iourov_12_ASD/ID/EP_discovery_cases
Russian
aCGH
BACs aCGH
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
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)
pinto_10_ASD_discovery_cases
European
Solid phase hybridization
Illumina Infinium 1M SNP microarray
QuantiSNP, iPattern
qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
qiao_12_ASD/ID_discovery_cases
Canadian
Array SNP
Affymetrix 2.7M
Affymetrix ChAS v.1.1
QMPSF
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
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
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
Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
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
engchuan_15_ASD_discovery_cases-case5453_4
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
48633987
48743404
109418
GRCh38
Duplication
No
iourov_12_ASD/ID/EP_discovery_cases-case54
5 yrs. 10 mos.
F
Developmental delay/intellectual disability and autism
Autism, Rett syndrome-like phenotype. Karyotype: 1phqh.
Developmental delay/intellectual disability
133465134
133642313
177180
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005220
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
45507351
46014903
507553
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case11229.p1
N/A
M
ASD
ASD proband from SSC quad family 11229. SRS score of 73.
Full-scale IQ (FSIQ) score of 63.
51883092
51887245
4154
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case11229.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
51883092
51887245
4154
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case12281.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
51632564
51868109
235546
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13805.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
46799105
46809537
10433
GRCh38
Deletion
Yes
pinto_10_ASD_discovery_cases-case5453_4
NA
M
Autism
Lowfunctioning autism, language delay, no epilepsy, no dysmorphic features
Unable to complete IQ measure
48633987
48743404
109418
GRCh38
Duplication
Yes
prasad_12_ASD_discovery_cases-case125391
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
45429183
45496931
67749
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case126173
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
49473679
49533777
60099
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case83989
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
48702794
48826402
123609
Unknown
Duplication
No
qiao_12_ASD_discovery_cases-case07-203A
NA
NA
ASD and/or ID
NA
NA
48459554
48664816
205000
Unknown
Deletion
Yes
quintela_17_DD/ID_discovery_cases-caseID_265
9 yrs.
F
Intellectual disability
Dysmorphic facial features
Intellectual disability
50490464
51071772
581309
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11450.p1
5.8
M
ASD
NA
Full-scale IQ, 78; non-verbal IQ, 79; verbal IQ, 82
49461993
49478796
16804
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11512.p1
5.7
M
Autism
NA
Full-scale IQ, 33; non-verbal IQ, 43; verbal IQ, 22
50172958
50184610
11653
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12628.p1
11.2
M
Autism
NA
Full-scale IQ, 118; non-verbal IQ, 102; verbal IQ, 120
49165157
49169327
4171
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
engchuan_15_ASD_discovery_controls-control110036017135_
N/A
N/A
Control
No previous psychiatric history
45983090
46099754
116665
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB481737_1007875851
N/A
N/A
Control
No previous psychiatric history
48446137
48602204
156068
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB911786_1007854079
N/A
N/A
Control
No previous psychiatric history
45979730
46099754
120025
GRCh38
Duplication
No
krumm_13_ASD_discovery_controls-control11013.s1
N/A
M
Control
Unaffected sibling from SSC quad family 11013. SRS score of 47.
49459081
49472858
13778
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_controls-control11220.s1
N/A
F
Control
Unaffected sibling from SSC quad family 11220. SRS score of 41.
47503279
47599443
96165
GRCh38
Deletion
No (not tested)
krumm_15_ASD_discovery_controls-control11220.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
47503279
47599443
96165
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control12281.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
51632564
51868109
235546
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control13805.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
46799105
46809537
10433
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control14495.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
49456079
49472858
16780
GRCh38
Duplication
Yes
levy_11_ASD_discovery_controls-11220.s1
NA
F
Control
NA
NA
47414053
47600521
186469
GRCh38
Deletion
No
poultney_13_ASD_discovery_controls-control04C36033A
N/A
M
Control
NIMH Control (NIMH ID 14132)
49470175
49472185
2011
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C42425A
N/A
F
Control
NIMH Control (NIMH ID 39669)
49431726
49857402
425677
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11220.s1
13.6
F
Control (matched sibling)
NA
NA
47414428
47609328
194901
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case5453_4
Unknown
iourov_12_ASD/ID/EP_discovery_cases-case54
Unknown
Unknown
Unknown
HSPE1P21,EYA4,TARID
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005220
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RUNX2-AS1,RUNX2,CLIC5
krumm_13_ASD_discovery_cases-case11229.p1
aCGH (Agilent SurePrint G3 4x180K)
Paternal
Simplex
Segregated
PKHD1
krumm_15_ASD_discovery_cases-case11229.p1
Illumina 1M
Paternal
Simplex
Segregated
PKHD1
krumm_15_ASD_discovery_cases-case12281.p1
Illumina 1MDuo
Paternal
Simplex
Not segregated (CNV in unaffected sibling)
PKHD1
krumm_15_ASD_discovery_cases-case13805.p1
Omni2.5-4v1
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
MEP1A
pinto_10_ASD_discovery_cases-case5453_4
Agilent1M
paternal
Simplex
NA
prasad_12_ASD_discovery_cases-case125391
Unknown
Unknown
Unknown
RUNX2,SUPT3H
prasad_12_ASD_discovery_cases-case126173
Unknown
Unknown
Unknown
MUT
prasad_12_ASD_discovery_cases-case83989
Unknown
Unknown
Unknown
0 genes
qiao_12_ASD_discovery_cases-case07-203A
QMPSF
Maternal
Unknown
Unknown
0 genes
quintela_17_DD/ID_discovery_cases-caseID_265
Unknown
Unknown
RPS17P5,FTH1P5,TFAP2B,TFAP2D
sanders_11_ASD_discovery_cases-11450.p1
Paternal
Simplex (quad-proband matched)
Segregated
CENPQ
sanders_11_ASD_discovery_cases-11512.p1
Maternal
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12628.p1
Paternal
Simplex (quad-proband matched)
Not segregated
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036017135_
Unknown
RNU6-754P,CLIC5
engchuan_15_ASD_discovery_controls-controlB481737_1007875851
Unknown
engchuan_15_ASD_discovery_controls-controlB911786_1007854079
Unknown
RNU6-754P,CLIC5
krumm_13_ASD_discovery_controls-control11013.s1
aCGH (Agilent SurePrint G3 4x180K)
Maternal
Simplex
CENPQ
krumm_13_ASD_discovery_controls-control11220.s1
Paternal
Simplex
CD2AP
krumm_15_ASD_discovery_controls-control11220.s1
Illumina 1M
Paternal
CD2AP
krumm_15_ASD_discovery_controls-control12281.s1
Illumina 1MDuo
Paternal
PKHD1
krumm_15_ASD_discovery_controls-control13805.s1
Omni2.5-4v1
Maternal
MEP1A
krumm_15_ASD_discovery_controls-control14495.s1
Omni2.5-4v1
Maternal
CENPQ
levy_11_ASD_discovery_controls-11220.s1
Paternal
Simplex
NA
CD2AP
poultney_13_ASD_discovery_controls-control04C36033A
Unknown
CENPQ
poultney_13_ASD_discovery_controls-control05C42425A
Unknown
PGK2,CENPQ,GLYATL3,C6orf141,CYP2AC1P,RHAG,CRISP2,CRISP3,CRISP1
sanders_11_ASD_discovery_controls-11220.s1
Paternal
Simplex (quad)
NA
CD2AP
No Animal Model Data Available