9q34.13CNV Type: Deletion-Duplication
Largest CNV size: 165499 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
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization.
Deletion
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
50
1
0
1
celestino-soper_11_ASD_discovery_cases
ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
99
ASD
87.88% Male
271
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
569418
0
2
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
94700
0
1
1
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
165499
0
2
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
21464
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
145141
5
2
7
sandoval_talamantes_23_ASD_discovery_cases
ASD patients recruited from 2016 to 2019 among patients from the genetic or neuropediatric clinics of La Paz University Hospital (Madrid, Spain).
212
All cases met DSM-5 diagnostic criteria for ASD.
Mean age, 10.73 +/- 6.42 yrs. (median age, 10 yrs.)
87.73% Male
20389
0
1
1
yatsenko_12_ASD/DD/ID_discovery_cases
Unrelated children with variable phenotypes found to have a gain in DNA copy number in the subtelomeric 9q34 region revealed by aCGH, FISH, or chromosome analysis performed at Baylor College of Medicine and elsewhere.
20
Phenotypes include one or more of the following: ASD, DD, ID, dysmorphic features, multiple congenital anomalies (MCA)
Range, 1 yr.-16 yrs.
60.0% Male
253838
1
0
1
yin_16_ASD_discovery_cases
Discovery cohort of ASD cases recruited from the Department of Psychiatry of National Taiwan University Hospital (NTUH), Chang Gung Memorial Hospital (CGMH), Taoyuan, and Taoyuan Mental Hospital (TMH), Taiwan.
335
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R. Cases' autistic behaviors assessed by Social Responsiveness Scale (SRS), and cognitive functions assessed by the Weschler Intelligence Scale for Children-Third Edition (WISC-III) and the Wisconsin Card Sorting Test (WCST).
Mean, 9.39 4.04 yrs.
89.3% Male
55265
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
152224
1
3
4
itsara_10_ASD_discovery_controls_1
Unaffected siblings of ASD probands from multiplex (n=368) and simplex (n=59) families from AGRE collection
427
Controls: Unaffected or Not Met
31182
1
0
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_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
65208
0
1
1
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
92628
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)
6201
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)
21464
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.
45542
3
1
4
yin_16_ASD_discovery_controls
Individuals from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
1093
Controls
Mean, 68.07 10.12 yrs.
48.0% Male
55265
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
celestino-soper_11_ASD_discovery_cases
aCGH
Agilent 1M
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
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_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
levy_11_ASD_discovery_cases
aCGH
NimbleGen HD2
HMM
aCGH (Agilent 244K)
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
qPCR
sandoval_talamantes_23_ASD_discovery_cases
Spain
aCGH
KaryoArray v.3.0
NA
Agilent CytoGenomics
None
yatsenko_12_ASD/DD/ID_discovery_cases
NA
aCGH, FISH
Custom 9q34 oligonucleotide array (Agilent)
PCR
yin_16_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
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
itsara_10_ASD_discovery_controls_1
Solid phase hybridization
Illumina HumanHap550v1 and v3 SNP array
HMM
Illumina GenomeStudio
aCGH (custom NimbleGen 12 X 135)
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
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
yin_16_ASD_discovery_controls
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
None
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
brandler_18_ASD_discovery_cases-caseSSC05143
N/A
M
ASD
Case from SSC cohort
131204448
131204498
51
GRCh38
Deletion
Yes
celestino-soper_11_ASD_discovery_cases-11303
NA
M
ASD
NA
NA
132379015
132379286
272
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001666
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
131261516
131741175
479660
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004085
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
131702422
132271840
569419
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12378.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
131484947
131579647
94701
GRCh38
Duplication
Yes
levy_11_ASD_discovery_cases-12370.p1
NA
M
ASD
NA
NA
131900442
132065940
165499
GRCh38
Duplication
Yes
levy_11_ASD_discovery_cases-12378.p1
NA
F
ASD
NA
NA
131486024
131578651
92628
GRCh38
Duplication
No
prasad_12_ASD_discovery_cases-case155486L
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
133715256
133736719
21464
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11129.p1
4.7
F
Autism
NA
Full-scale IQ, 81; non-verbal IQ, 79; verbal IQ 91
132716637
132716696
60
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11917.p1
8
M
Autism
NA
Full-scale IQ, 98; non-verbal IQ, 115; verbal IQ, 71
131440617
131530211
89595
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12287.p1
7.9
M
Autism
NA
Full-scale IQ, 43; non-verbal IQ, 55; verbal IQ, 28
131507286
131523454
16169
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12370.p1
8.2
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 127; verbal IQ, 123
131914458
132059599
145142
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-12378.p1
6.2
F
Autism
NA
Full-scale IQ, 82; non-verbal IQ, 84; verbal IQ, 81
131535631
131578589
42959
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12518.p1
5.8
M
ASD
NA
Full-scale IQ, 88; non-verbal IQ, 95; verbal IQ, 83
131507286
131523454
16169
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13183.p1
5.8
M
Autism
NA
Full-scale IQ, 60; non-verbal IQ, 69; verbal IQ, 56
131507286
131523454
16169
GRCh38
Deletion
No
sandoval_talamantes_23_ASD_discovery_cases-caseAUT95
NA
NA
ASD and intellectual disability
Case met DSM-5 diagnostic criteria for ASD. Case also presented with intellectual disability.
Intellectual disability
131503431
131523819
20389
GRCh38
Duplication
No
yatsenko_12_ASD/DD/ID_discovery_cases-caseP50
6 yrs.
F
Intellectual disability
Speech delay
ID
131117000
131370838
253839
GRCh38
Deletion
Yes
yin_16_ASD_discovery_cases-case375
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
132297025
132352289
55265
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-control110036017630_
N/A
N/A
Control
No previous psychiatric history
131255157
131350185
95029
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB264221_1007841409
N/A
N/A
Control
No previous psychiatric history
132316086
132416968
100883
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900488_900488
N/A
N/A
Control
No previous psychiatric history
130968474
131016460
47987
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_901104_901104
N/A
N/A
Control
No previous psychiatric history
132715611
132867835
152225
GRCh38
Duplication
No
itsara_10_ASD_discovery_controls_1-HI2663
NA
NA
Unaffected
NA
NA
132198490
132229672
31183
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control14037.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
132863664
132928872
65209
GRCh38
Duplication
Yes
levy_11_ASD_discovery_controls-12378.s1
NA
M
Control
NA
NA
131486024
131578651
92628
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C45035
N/A
M
Control
NIMH Control (NIMH ID 17924)
131504217
131510417
6201
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11818.s1
14.3
F
Control (matched sibling)
NA
NA
131507286
131523454
16169
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12378.s1
4.4
M
Control (matched sibling)
NA
NA
131533047
131578589
45543
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12518.s1
4.7
F
Control (matched sibling)
NA
NA
131507286
131523454
16169
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12892.s1
15.4
F
Control (matched sibling)
NA
NA
131507286
131523454
16169
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC05143
PCR
Paternal
NUP214
celestino-soper_11_ASD_discovery_cases-11303
Unknown
Simplex
NA
TTF1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001666
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
SNORD62A,SNORD62B,RN7SL328P,FAM78A,POMT1,UCK1,PRRT1B,PLPP7,PRRC2B,RAPGEF1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004085
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RN7SL328P,EIF4A1P3,NTNG2,SETX,RAPGEF1,MED27
krumm_15_ASD_discovery_cases-case12378.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
SNORD62A,SNORD62B,POMT1,UCK1,PRRT1B,PRRC2B,RAPGEF1
levy_11_ASD_discovery_cases-12370.p1
aCGH (Agilent 244K)
De novo
Simplex
Segregated
MED27
levy_11_ASD_discovery_cases-12378.p1
Paternal
Simplex
Not segregated
SNORD62B,POMT1,UCK1,PRRT1B,PRRC2B,RAPGEF1
prasad_12_ASD_discovery_cases-case155486L
Unknown
Unknown
Unknown
MED27
sanders_11_ASD_discovery_cases-11129.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11917.p1
Unknown
Simplex (quad-proband matched)
Not segregated
SNORD62A,SNORD62B,POMT1,UCK1,PRRC2B
sanders_11_ASD_discovery_cases-12287.p1
Maternal
Simplex (trio)
NA
POMT1
sanders_11_ASD_discovery_cases-12370.p1
qPCR
De Novo
Simplex (quad-proband matched)
Segregated
MED27
sanders_11_ASD_discovery_cases-12378.p1
Paternal
Simplex (quad-proband matched)
Not segregated
PRRT1B,RAPGEF1
sanders_11_ASD_discovery_cases-12518.p1
Unknown
Simplex (quad-proband matched)
Not segregated
POMT1
sanders_11_ASD_discovery_cases-13183.p1
Unknown
Simplex (quad-proband matched)
Not segregated
POMT1
sandoval_talamantes_23_ASD_discovery_cases-caseAUT95
Unknown
UCK1,POMT1
yatsenko_12_ASD/DD/ID_discovery_cases-caseP50
PCR
De novo
RNU6-881P,AIF1L,FAM78A,NUP214,PLPP7
yin_16_ASD_discovery_cases-case375
Unknown
Unknown
Unknown
SETX
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036017630_
Unknown
FAM78A,PLPP7
engchuan_15_ASD_discovery_controls-controlB264221_1007841409
Unknown
SETX,TTF1,CFAP77
engchuan_15_ASD_discovery_controls-controlHABC_900488_900488
Unknown
LAMC3
engchuan_15_ASD_discovery_controls-controlHABC_901104_901104
Unknown
AK8
itsara_10_ASD_discovery_controls_1-HI2663
aCGH (custom NimbleGen 12 X 135)
De novo
Multiplex
NTNG2
krumm_15_ASD_discovery_controls-control14037.s1
Omni2.5-4v1
Maternal
SPACA9,AK8,TSC1
levy_11_ASD_discovery_controls-12378.s1
Paternal
Simplex
NA
SNORD62B,POMT1,UCK1,PRRT1B,PRRC2B,RAPGEF1
poultney_13_ASD_discovery_controls-control05C45035
Unknown
POMT1
sanders_11_ASD_discovery_controls-11818.s1
Unknown
Simplex (quad)
NA
POMT1
sanders_11_ASD_discovery_controls-12378.s1
Paternal
Simplex (quad)
NA
PRRT1B,RAPGEF1
sanders_11_ASD_discovery_controls-12518.s1
Unknown
Simplex (quad)
NA
POMT1
sanders_11_ASD_discovery_controls-12892.s1
Unknown
Simplex (quad)
NA
POMT1
No Animal Model Data Available