7p15.2CNV Type: Deletion-Duplication
Largest CNV size: 267528 bp
Statistics Box:
Number of Reports: 13
Number of Reports: 13
Summary Information
CNVs within this region were identified in cases with ASD (Prasad et al., 2012) and developmental delay (Kaminsky et al., 2011).
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
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion-Duplication
Copy number variation in Han Chinese individuals with autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion
Chromosomal Microarray Testing in 42 Korean Patients with Unexplained Developmental Delay, Intellectual Disability, Autism Spectrum Disorders, and ...
Deletion
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
akter_23_ASD/ADHD/DD/ID_discovery_cases
Bangladeshi NDD probands who underwent chromosomal microarray testing to identify CNVs from 2017 to 2020.
212
Individuals presented with autism spectrum disorder (ASD), ADHD, developmental delay (DD), intellectual disability (ID), and/or epilepsy/seizures, among other neurodevelopmental phenotypes; 95 individuals were diagnosed with ASD using DSM-V, ADOS, or ADOS-2.
NA
68.40% Male
50802
0
1
1
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
203
1
0
1
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
114583
1
0
1
gazzellone_14_ASD_discovery_cases
ASD-affected individuals referred to the Children Development and Behavior Research Center (CDRBC) at Harbin Medical University, China, between January 2007 and June 2011.
104
Diagnosis of ASD made using Autism Behavior Checklist (ABC) and Childhood Autism Rating Scale (CARS)
Mean age at enrollment, 4.31 1.80 yrs.
87.5% Male
40387
1
0
1
girirajan_13a_ASD_discovery_cases
1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
2588
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
NA
NA
417000
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
267528
1
1
2
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
3265
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
25631
0
1
1
lee_17_ASD/DD/ID/MCA_discovery_cases
Korean patients who had negative test results for metabolic disorders and other suspected disorders and did not present with any recognizable syndrome
42
Cases diagnosed with unexplained autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID), and/or multiple congenital anomalies (MCA)
Range, newborn-38 yrs.
69.05% Male
1096
1
0
1
pinto_14_ASD_discovery_cases
ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
1359
Cases classified according to ADOS and ADI-R
N/A
N/A
114584
1
1
2
poultney_13_ASD_discovery_cases
ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
299
Cases diagnosed with ASD
N/A
79.86% Male (before filtering)
10511
1
1
2
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
151756
2
3
5
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
102118
1
0
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
140706
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
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
0
0
0
0
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
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)
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)
151756
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
akter_23_ASD/ADHD/DD/ID_discovery_cases
Bangladesh
CMA
Illumina Global Screening Array-24 BeadChip
CNVPartition
Illumina Genomestudio
None
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
gazzellone_14_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix CytoScan HD
ChAS, iPattern, Nexus, Partek
None
girirajan_13a_ASD_discovery_cases
NA
aCGH
Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
ADM-2
Agilent Genomic Workbench
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
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
lee_17_ASD/DD/ID/MCA_discovery_cases
Korean
Array SNP
Affymetrix CytoScan 750K
Affymetrix ChAS v.3.2.0.1252
None
pinto_14_ASD_discovery_cases
Predominantly European
Solid phase hybridization
Illumina 1M (v.1 and v.3)
qPCR, MLPA, long-range PCR
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
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
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
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
akter_23_ASD/ADHD/DD/ID_discovery_cases-case102
3.08 yrs.
F
ADHD and developmental delay
ADHD, speech delay, behaviour problem, vomiting tendency, headache, hearing problem,low sensory integration. Growth parameters: height 0.89 m, weight 10 kg, head circumference 51 cm. Family history: no data on familial consanguinity.
26131310
26182111
50802
GRCh38
Duplication
No
brandler_18_ASD_discovery_cases-caseSSC06525
N/A
M
ASD
Case from SSC cohort
27379958
27380161
204
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case6346_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
26243036
26357619
114584
GRCh38
Deletion
No
gazzellone_14_ASD_discovery_cases-case537-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
27457770
27498157
40388
GRCh38
Deletion
No
girirajan_13a_ASD_discovery_cases-13716.p1
N/A
N/A
ASD
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
N/A
24903856
25323856
420001
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002558
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
27154807
27422335
267529
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004314
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
27107301
27314586
207286
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case11107.p1
N/A
M
ASD
ASD proband from SSC quad family 11107. SRS score of 90.
Full-scale IQ (FSIQ) score of 30.
26197314
26200579
3266
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_cases-case13160.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
26346404
26372035
25632
GRCh38
Duplication
Yes
lee_17_ASD/DD/ID/MCA_discovery_cases-case33
4 yrs.
M
Developmental delay
Developmental delay, iron-deficiency anemia
27183972
27185068
1097
GRCh38
Deletion
No
pinto_14_ASD_discovery_cases2-case6346_3
N/A
M
ASD
Clinical profile: N/A.
Cognitive profile: N/A.
26243036
26357619
114584
GRCh38
Deletion
Yes
pinto_14_ASD_discovery_cases2-case9809_202
N/A
M
ASD
Autism (based on ADI-R and ADOS), no language delay, verbal, seizures
mild ID (WPPSI-III: VIQ 67, PIQ 65, FSIQ 66)
25034792
25089169
54378
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case01HI2165A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU084503; NDAR ID NDAR_INVEM293ETW)
26192514
26197463
4950
GRCh38
Deletion
No
poultney_13_ASD_discovery_cases-case99HI0868A
N/A
F
ASD
ASD case from AGRE (AGRE ID AU002003; NDAR ID NDAR_INVXV984GE7)
26192514
26203024
10511
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case125855
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
26180912
26202927
22016
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case128963
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
25098652
25119028
20377
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case142468
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
25277098
25288457
11360
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case62249L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
26826305
26839440
13136
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case83548L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
26020603
26172358
151756
Unknown
Duplication
No
quintela_17_DD/ID_discovery_cases-caseID_10
3 yrs.
F
Developmental delay
Language delay, macrocephaly
Global developmental delay
27601411
27703528
102118
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-controlHABC_900942_900942
N/A
N/A
Control
No previous psychiatric history
25609182
25749888
140707
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
akter_23_ASD/ADHD/DD/ID_discovery_cases-case102
Unknown
HNRNPA2B1,NFE2L3
brandler_18_ASD_discovery_cases-caseSSC06525
Not available
Unknown
engchuan_15_ASD_discovery_cases-case6346_3
Unknown
SNX10
gazzellone_14_ASD_discovery_cases-case537-3
Unknown
Unknown
Unknown
EIF4HP1,PSMC1P2
girirajan_13a_ASD_discovery_cases-13716.p1
Unknown
Simplex
Unknown
SNRPCP19,CYCS,NPVF,TSEN15P3,OSBPL3,C7orf31
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002558
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
HOXA7,HOXA10-AS,MIR196B,HOXA10,HOXA11,HOXA11-AS,HOTTIP,RPL35P4,HNRNPA1P73,HOXA9,HOXA13,EVX1-AS,EVX1,HOXA-AS3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004314
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
HOXA4,HOXA5,HOXA7,HOXA10-AS,MIR196B,HOXA10,HOXA11,HOXA11-AS,HOTTIP,RPL35P4,HOXA6,HOXA9,HOXA13,EVX1-AS,EVX1,HOXA3,HOXA-AS2,HOXA-AS3
krumm_13_ASD_discovery_cases-case11107.p1
Maternal
Simplex
Segregated
HNRNPA2B1
krumm_15_ASD_discovery_cases-case13160.p1
1M-Duov3
Maternal
Simplex
Segregated
SNX10
lee_17_ASD/DD/ID/MCA_discovery_cases-case33
Unknown
HOXA11,HOXA11-AS
pinto_14_ASD_discovery_cases2-case6346_3
qPCR
Maternal
Simplex
(not tested)
SNX10
pinto_14_ASD_discovery_cases2-case9809_202
qPCR
Maternal
Simplex
(not tested)
poultney_13_ASD_discovery_cases-case01HI2165A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
HNRNPA2B1
poultney_13_ASD_discovery_cases-case99HI0868A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
CBX3,HNRNPA2B1
prasad_12_ASD_discovery_cases-case125855
Unknown
Unknown
Unknown
NFE2L3,HNRNPA2B1
prasad_12_ASD_discovery_cases-case128963
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case142468
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case62249L
Unknown
Unknown
Unknown
SKAP2
prasad_12_ASD_discovery_cases-case83548L
Unknown
Unknown
Unknown
NFE2L3
quintela_17_DD/ID_discovery_cases-caseID_10
Unknown
Unknown
HIBADH
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900942_900942
Unknown
No Animal Model Data Available