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4q28.2CNV Type: Deletion-Duplication


Largest CNV size: 155570 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type

No Major Reports

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
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder.
Duplication
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
 brandler_18_ASD_replication_cases
 Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
 1979
 Cases diagnosed with ASD
 N/A
 N/A
 356
 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
 153477
 1
 1
 2
 hnoonual_17_ASD_discovery_cases
 Cohort of 114 Thai ASD probands (68 retrospective ASD cases with the use of chromosomal microarray/CMA as a second line test; 46 prospective ASD and developmental delay cases with the use of CMA as the first-tier test)
 114
 68 cases with non-syndromic ASD (61 of which also presented with intellectual disability) were diagnosed with ASD based on meeting DSM-IV criteria for ASD, whereas an additional 46 prospective ASD and DD cases were given a clinical diagnosis of ASD based on DSM-5 criteria.
 Range, 1-18 years (at time of recruitment)
 79.82% Male
 1260000
 0
 1
 1
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 155570
 0
 1
 1
 sajan_13_ACC/CBLH/PMG_discovery_cases
 Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
 487
 Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
 N/A
 N/A
 153430
 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
 153477
 3
 1
 4

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
 149728
 3
 1
 4
 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
 153430
 0
 2
 2
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 59139
 1
 0
 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
 155570
 0
 1
 1
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 153477
 3
 1
 4

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 brandler_18_ASD_replication_cases
  N/A
 WGS
  Illumina HiSeq X10
 ForestSV, Lumpy, Manta, Mobster, SV2
 
 None
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 hnoonual_17_ASD_discovery_cases
  Thai
 Solid phase hybridization
  Illumina Infinium CytoSNP-850K v1.1 BeadChip
 
 BlueFuse Multi v4.3, GenomeStudio Data Analysis v.2011.1
 None
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 
 sajan_13_ACC/CBLH/PMG_discovery_cases
  81.31% Caucasian
 Solid phase hybridization
  Illumina InfiniumII HumanHap610
 PennCNV
 
 None (not tested or failure to confirm by qPCR)
 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
  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
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  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
  brandler_18_ASD_replication_cases-case3-0209-000
 N/A
 M
 ASD
 Case from MSSNG cohort
 
 128811418
 128811773
  356
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case20068_1324001
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 128853220
 129006697
  153478
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case6340_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 130062450
 130131794
  69345
 GRCh38
 Deletion
 No
  hnoonual_17_ASD_discovery_cases-caseTM35-3
 N/A
 F
 ASD
 No additional clinical features
 
 127980247
 129242409
  1262163
 GRCh38
 Duplication
 No
  levy_11_ASD_discovery_cases-11977.p1
 NA
 M
 ASD
 NA
 NA
 128852435
 129008004
  155570
 GRCh38
 Duplication
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR00-120
 N/A
 N/A
 CBLH-PMG
 Diagnosis of cerebellar hypoplasia (CBLH) and polymicrogyria (PMG).
 
 128853220
 129006649
  153430
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11059.p1
 6.6
 M
 Autism
 NA
 Full-scale IQ, 111; non-verbal IQ, 103; verbal IQ, 119
 130027717
 130094957
  67241
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11393.p1
 8.2
 M
 Autism
 NA
 Full-scale IQ, 28; non-verbal IQ, 37; verbal IQ, 17
 130053048
 130068334
  15287
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11464.p1
 4.5
 M
 Autism
 NA
 Full-scale IQ, 92; non-verbal IQ, 103; verbal IQ, 78
 129791418
 129793613
  2196
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11977.p1
 10.2
 M
 ASD
 NA
 Full-scale IQ, 74; non-verbal IQ, 74; verbal IQ, 80
 128853220
 129006697
  153478
 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
  engchuan_15_ASD_discovery_controls-controlB679348_1007851283
  N/A
  N/A
  Control
  No previous psychiatric history
 
  128856921
  129006649
  149729
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900443_900443
  N/A
  N/A
  Control
  No previous psychiatric history
 
  130041108
  130082450
  41343
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900547_900547
  N/A
  N/A
  Control
  No previous psychiatric history
 
  130041108
  130082450
  41343
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901236_901236
  N/A
  N/A
  Control
  No previous psychiatric history
 
  130061900
  130139904
  78005
  GRCh38
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split1764
  N/A
  N/A
  Control
  Control 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
 
  129774375
  129927804
  153430
  Unknown
  Duplication
  No
  kanduri_15_ASD_discovery_controls-control_split216
  N/A
  N/A
  Control
  Control 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
 
  129774375
  129927804
  153430
  Unknown
  Duplication
  No
  krumm_15_ASD_discovery_controls-control14155.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  127930682
  127989821
  59140
  GRCh38
  Deletion
  Yes
  levy_11_ASD_discovery_controls-11977.s1
  NA
  F
  Control
  NA
  NA
  128852435
  129008004
  155570
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11059.s1
  9.3
  F
  Control (matched sibling)
  NA
  NA
  129974373
  130094957
  120585
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11393.s1
  9.1
  M
  Control (matched sibling)
  NA
  NA
  130053048
  130068334
  15287
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11977.s1
  13.3
  F
  Control (matched sibling)
  NA
  NA
  128853220
  129006697
  153478
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12015.s1
  9
  F
  Control (matched sibling)
  NA
  NA
  129597231
  129659873
  62643
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 brandler_18_ASD_replication_cases-case3-0209-000
 No validation step reported
 
 De novo
 
 
 JADE1
 
 engchuan_15_ASD_discovery_cases-case20068_1324001
 
 
 Unknown
 
 
 JADE1,SCLT1
 
 engchuan_15_ASD_discovery_cases-case6340_3
 
 
 Unknown
 
 
 
 
 hnoonual_17_ASD_discovery_cases-caseTM35-3
 
 
 Paternal
 
 
 JADRR,ABHD18,FOSL1P1,PGRMC2,ZSWIM5P3,LARP1B,JADE1,C4orf33,SCLT1
 
 levy_11_ASD_discovery_cases-11977.p1
 
 
 Maternal
 Simplex
 Not segregated
 JADE1,SCLT1
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR00-120
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 JADE1,SCLT1
 
 sanders_11_ASD_discovery_cases-11059.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11393.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11464.p1
 
 
 Paternal
 Simplex (trio)
 NA
 LINC02465
 
 sanders_11_ASD_discovery_cases-11977.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 JADE1,SCLT1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB679348_1007851283
 
 
  Unknown
 
 
  JADE1,SCLT1
 
engchuan_15_ASD_discovery_controls-controlHABC_900443_900443
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_900547_900547
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_901236_901236
 
 
  Unknown
 
 
 
 
kanduri_15_ASD_discovery_controls-control_split1764
 
 
  Unknown
 
 
  JADE1,SCLT1
 
kanduri_15_ASD_discovery_controls-control_split216
 
 
  Unknown
 
 
  JADE1,SCLT1
 
krumm_15_ASD_discovery_controls-control14155.s1
  Omni2.5-4v1
 
  Maternal
 
 
  ABHD18,MFSD8
 
levy_11_ASD_discovery_controls-11977.s1
 
 
  Maternal
  Simplex
  NA
  JADE1,SCLT1
 
sanders_11_ASD_discovery_controls-11059.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11393.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11977.s1
 
 
  Maternal
  Simplex (quad)
  NA
  JADE1,SCLT1
 
sanders_11_ASD_discovery_controls-12015.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 

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