4q31.21CNV Type: Deletion-Duplication
Largest CNV size: 109670 bp
Statistics Box:
Number of Reports: 9
Number of Reports: 9
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
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
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion-Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
The landscape of copy number variations in Finnish families with autism spectrum disorders.
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
72564
2
1
3
glessner_09_ASD_discovery_cases
Autism Case-Control (ACC) case cohort: 54% from simplex families, 46% from multiplex families
859
859 autism (ADI). 708 autism, 124 ASD, 27 not autism (based on ADOS)
Range, 2-21
81.8% Male
7177
0
3
3
glessner_09_ASD_replication_cases
Autism Genetic Resource Exchange (AGRE) case cohort: 5% from simplex families, 95% from multiplex families
1336
1202 autism, 134 ASD (AGRE status). 775 autism, 171 ASD, 76 not ASD or autism (based on ADOS)
Mean, 9.2 5.3
78.7% Male
7177
0
7
7
kanduri_15_ASD_discovery_cases
Autistic cases from an initial sample of 83 Finnish families comprising 257 family members following quality control
80
Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patients screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and Asperger's Syndrome Diagnostic Interview.
N/A
N/A
68507
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
35699
0
1
1
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
63928
0
1
1
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
190000
2
2
4
nord_11_ASD_discovery_cases
Youth with ASD (as part of mother-father-child trios)
41
ASD
85.4% Male
13770
1
0
1
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)
13167
2
1
3
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
109670
4
5
9
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_controls
Unaffected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (112 individuals from 311 families) and the Simons Simplex 1 (SSC1) cohort (518 controls from simplex quad families)
630
Control
N/A
N/A
62769
1
0
1
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
151526
1
0
1
kanduri_15_ASD_discovery_controls
Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
269
Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
N/A
N/A
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
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
0
0
0
0
nord_11_ASD_discovery_controls
Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
123
Controls (no history of psychiatric symptoms by self-report)
30 yrs.
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)
91783
1
2
3
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
29650
2
1
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
glessner_09_ASD_discovery_cases
European
Solid phase hybridization
HumanHap550 BeadChip
PennCNV
qPCR, MLPA, array SNP
glessner_09_ASD_replication_cases
European
Solid phase hybridization
HumanHap550 BeadChip
PennCNV
qPCR, MLPA, array SNP
kanduri_15_ASD_discovery_cases
Finnish
Solid phase hybridization
Illumina Human OmniExpress-12v1.0 BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
None
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
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
nord_11_ASD_discovery_cases
29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
brandler_18_ASD_discovery_controls
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
glessner_09_ASD_discovery_controls
Caucasian
Solid phase hybridization
HumanHap550 BeadChip
PennCNV
glessner_09_ASD_replication_controls
Caucasian
Solid phase hybridization
HumanHap550 BeadChip
PennCNV
kanduri_15_ASD_discovery_controls
Finnish
Solid phase hybridization
Illumina Infinium HD Human610-Quad BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
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-case14393_5020
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
143759801
143794203
34403
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4423_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
143594735
143657779
63045
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case6175_6
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
141314339
141386903
72565
GRCh38
Duplication
No
glessner_09_ASD_discovery_cases-10444_59477
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_discovery_cases-AU56003
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_discovery_cases-B200903
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_replication_cases-AU054504
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_replication_cases-AU054505
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
Yes
glessner_09_ASD_replication_cases-AU068609
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
Yes
glessner_09_ASD_replication_cases-AU077704
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
Yes
glessner_09_ASD_replication_cases-AU1547302
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_replication_cases-AU1764301
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_replication_cases-AU1764302
NA
ASD
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
kanduri_15_ASD_discovery_cases-case2964
N/A
N/A
ASD
Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patient screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and/or Asperger's Syndrome Diagnostic Interview.
144825754
144894260
68507
Unknown
Duplication
No
krumm_15_ASD_discovery_cases-case11052.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
143433490
143469189
35700
GRCh38
Duplication
Yes
levy_11_ASD_discovery_cases-11052.p1
NA
M
ASD
NA
NA
143431293
143495220
63928
GRCh38
Duplication
No
maini_18_ASD/DD/ID_discovery_cases-case_unknown164
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB), CNV reported as 4q31.21-q31.22 in original report
144045897
144112189
66293
GRCh38
Deletion
No
maini_18_ASD/DD/ID_discovery_cases-case_unknown165
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
143921435
144112189
190755
GRCh38
Tetrasomy
No
maini_18_ASD/DD/ID_discovery_cases-case_unknown166
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
144045897
144112189
66293
GRCh38
Deletion
No
nord_11_ASD_discovery_cases-277-1
ASD
142258561
142272330
13770
Unknown
Deletion
No
poultney_13_ASD_discovery_cases-case03HI2512A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0531302; NDAR ID NDAR_INVJF187BNY)
144646674
144659840
13167
GRCh38
Deletion
No
poultney_13_ASD_discovery_cases-case04HI2865A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0953301; NDAR ID NDAR_INVTX007WT8)
144111392
144118754
7363
GRCh38
Deletion
No
poultney_13_ASD_discovery_cases-case99HI1140A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU062604; NDAR ID NDAR_INVBJ302UPL)
144111392
144118754
7363
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11052.p1
5.5
M
Autism
NA
Full-scale IQ, 93; non-verbal IQ, 97; verbal IQ, 90
143432093
143494692
62600
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11409.p1
4.1
M
Autism
NA
Full-scale IQ, 96; non-verbal IQ, 101; verbal IQ 90
142874194
142879208
5015
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11475.p1
7.8
M
Autism
NA
Full-scale IQ, 94; non-verbal IQ, 86; verbal IQ, 110
142874194
142879208
5015
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11550.p1
8.1
M
Autism
NA
Full-scale IQ, 99; non-verbal IQ, 99; verbal IQ, 99
141059086
141110014
50929
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11568.p1
13.5
F
Autism
NA
Full-scale IQ, 51; non-verbal IQ, 72; verbal IQ, 28
142874194
142879208
5015
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12250.p1
10.8
F
Aspergers
NA
Full-scale IQ, 85; non-verbal IQ, 78; verbal IQ, 103
143706799
143720238
13440
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12484.p1
9.4
M
Autism
NA
Full-scale IQ, 98; non-verbal IQ, 107; verbal IQ, 83
143432093
143494692
62600
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12722.p1
11.6
M
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 73; verbal IQ, 77
142053689
142073191
19503
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13327.p1
12.6
M
Aspergers
NA
Full-scale IQ, 103; non-verbal IQ, 95; verbal IQ, 118
143713976
143823646
109671
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
brandler_18_ASD_discovery_controls-controlSSC09456
N/A
F
Control
Control from SSC_phase1 cohort
142310752
142373521
62770
GRCh38
Deletion
Yes
engchuan_15_ASD_discovery_controls-controlHABC_902847_902847
N/A
N/A
Control
No previous psychiatric history
142936324
143087850
151527
GRCh38
Deletion
No
glessner_09_ASD_replication_controls-repcontrol50
NA
Control
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
glessner_09_ASD_replication_controls-repcontrol51
NA
Control
NA
NA
143706799
143713976
7178
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C32540A
N/A
M
Control
NIMH Control (NIMH ID 54799)
144111392
144118754
7363
GRCh38
Deletion
No
poultney_13_ASD_discovery_controls-control05C43611
N/A
F
Control
NIMH Control (NIMH ID 49957)
144111392
144118754
7363
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C44280
N/A
M
Control
NIMH Control (NIMH ID 81186)
142082029
142173811
91783
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11474.s1
19
M
Control (matched sibling)
NA
NA
142282898
142300982
18085
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11630.s1
8.3
M
Control (matched sibling)
NA
NA
140789160
140818810
29651
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12250.s1
6
F
Control (matched sibling)
NA
NA
143706799
143720238
13440
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case14393_5020
Unknown
engchuan_15_ASD_discovery_cases-case4423_1
Unknown
FREM3
engchuan_15_ASD_discovery_cases-case6175_6
Unknown
LINC02432
glessner_09_ASD_discovery_cases-10444_59477
Unknown
Unknown
NA
glessner_09_ASD_discovery_cases-AU56003
Unknown
Unknown
NA
glessner_09_ASD_discovery_cases-B200903
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU054504
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU054505
qPCR
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU068609
qPCR
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU077704
qPCR
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU1547302
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU1764301
Unknown
Unknown
NA
glessner_09_ASD_replication_cases-AU1764302
Unknown
Unknown
NA
kanduri_15_ASD_discovery_cases-case2964
Paternal
Unknown
Unknown
GYPE
krumm_15_ASD_discovery_cases-case11052.p1
Illumina 1M
Maternal
Simplex
Segregated
GAB1
levy_11_ASD_discovery_cases-11052.p1
Maternal
Simplex
Segregated
GAB1
maini_18_ASD/DD/ID_discovery_cases-case_unknown164
Maternal
Unknown
Unknown
GYPA
maini_18_ASD/DD/ID_discovery_cases-case_unknown165
Both parents
Unknown
Unknown
GYPB,GYPA
maini_18_ASD/DD/ID_discovery_cases-case_unknown166
Paternal
Unknown
Unknown
GYPA
nord_11_ASD_discovery_cases-277-1
Maternal
RNF150
poultney_13_ASD_discovery_cases-case03HI2512A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
HHIP-AS1,HHIP
poultney_13_ASD_discovery_cases-case04HI2865A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
GYPA
poultney_13_ASD_discovery_cases-case99HI1140A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
GYPA
sanders_11_ASD_discovery_cases-11052.p1
Maternal
Simplex (quad-proband matched)
Segregated
GAB1
sanders_11_ASD_discovery_cases-11409.p1
Maternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-11475.p1
Maternal
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-11550.p1
Paternal
Simplex (quad-proband matched)
Segregated
RNF150
sanders_11_ASD_discovery_cases-11568.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12250.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12484.p1
Maternal
Simplex (quad-proband unmatched)
Unknown
GAB1
sanders_11_ASD_discovery_cases-12722.p1
Maternal
Simplex (quad-proband matched)
Not segregated
INPP4B
sanders_11_ASD_discovery_cases-13327.p1
Maternal
Simplex (quad-proband matched)
Not segregated
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC09456
PCR or SNP data validation
Paternal
LSM3P4,INPP4B
engchuan_15_ASD_discovery_controls-controlHABC_902847_902847
Unknown
glessner_09_ASD_replication_controls-repcontrol50
Unknown
Unknown
NA
glessner_09_ASD_replication_controls-repcontrol51
Unknown
Unknown
NA
poultney_13_ASD_discovery_controls-control04C32540A
Unknown
GYPA
poultney_13_ASD_discovery_controls-control05C43611
Unknown
GYPA
poultney_13_ASD_discovery_controls-control05C44280
Unknown
INPP4B
sanders_11_ASD_discovery_controls-11474.s1
Unknown
Simplex (quad)
NA
RPL5P13,INPP4B
sanders_11_ASD_discovery_controls-11630.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12250.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available