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12q21.32CNV Type: Deletion-Duplication


Largest CNV size: 259857 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
Excess of rare, inherited truncating mutations in autism.
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-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
 55703
 2
 2
 4
 gai_11_ASD_replication_cases
 Replication case samples derived from AGRE sets 1-3
 593
 Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
 
 
 394755
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 10945
 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
 68371
 2
 0
 2
 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
 259857
 10
 1
 11
 yuan_23_ASD_discovery_cases
 ASD probands from 353 pedigrees (338 simplex trios, 15 multiplex families) recruited from the Department of Child and Adolescent Psychiatry, Shanghai Mental Health Center (Shanghai, China).
 369
 Cases diagnosed with ASD using DSM-IV.
 NA
 NA
 58706
 0
 1
 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
 453972
 0
 7
 7
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 6125
 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)
 68371
 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.
 
 98701
 11
 0
 11

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 gai_11_ASD_replication_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 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
 
 
 yuan_23_ASD_discovery_cases
  China
 WES
  Illumina HiSeq
 NA
 GATK v.4.2.0.0.
 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
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  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-case20151_1636001
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 87188670
 87234891
  46222
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case2299_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 87215109
 87270812
  55704
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4518_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 86582460
 86626600
  44141
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case4518_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 86981207
 87036432
  55226
 GRCh38
 Duplication
 No
  gai_11_ASD_replication_cases-AU062905
 
 
 Autism
 
 
 85475471
 85870225
  394755
 Unknown
 Deletion
 No
  krumm_15_ASD_discovery_cases-case13199.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 88083030
 88093975
  10946
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case134846
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 86286222
 86354592
  68371
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case78391
 NA
 F
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 85393137
 85406774
  13638
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11001.p1
 7.8
 M
 Autism
 NA
 Full-scale IQ, 124; non-verbal IQ, 123; verbal IQ, 113
 88106775
 88130475
  23701
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11002.p1
 7.7
 F
 Autism
 NA
 Full-scale IQ, 100; non-verbal IQ, 111; verbal IQ, 80
 86800666
 86855677
  55012
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11390.p1
 8.3
 F
 Autism
 NA
 Full-scale IQ, 66; non-verbal IQ, 77; verbal IQ, 57
 86285382
 86545240
  259859
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11733.p1
 5.5
 F
 Autism
 NA
 Full-scale IQ, 87; non-verbal IQ, 93; verbal IQ, 81
 88116665
 88130475
  13811
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12081.p1
 12.9
 M
 Autism
 NA
 Full-scale IQ, 88; non-verbal IQ, 87; verbal IQ, 92
 87469156
 87475573
  6418
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12201.p1
 13.3
 M
 Autism
 NA
 Full-scale IQ, 130; non-verbal IQ, 131; verbal IQ, 116
 87106240
 87151118
  44879
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12375.p1
 15.9
 M
 Autism
 NA
 Full-scale IQ, 94; non-verbal IQ, 93; verbal IQ, 85
 87469156
 87475573
  6418
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12695.p1
 12.3
 M
 Autism
 NA
 Full-scale IQ, 49; non-verbal IQ, 56; verbal IQ, 35
 87177815
 87188670
  10856
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12739.p1
 6.8
 M
 ASD
 NA
 Full-scale IQ, 98; non-verbal IQ, 112; verbal IQ, 77
 87740979
 87761241
  20263
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12829.p1
 11.4
 M
 Autism
 NA
 Full-scale IQ, 133; non-verbal IQ, 134; verbal IQ, 117
 86923242
 86994245
  71004
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13016.p1
 5.5
 M
 Aspergers
 NA
 Full-scale IQ, 98; non-verbal IQ, 102; verbal IQ, 93
 87503328
 87543172
  39845
 GRCh38
 Deletion
 No
  yuan_23_ASD_discovery_cases-qma00852d000
 NA
 NA
 ASD
 Case diagnosed with ASD according to DSM-IV criteria.
 
 88053403
 88112108
  58706
 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-controlHABC_900482_900482
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86582460
  87036432
  453973
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901110_901110
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86582460
  86626600
  44141
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901110_901110
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86977784
  87036432
  58649
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86582460
  86626600
  44141
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86977784
  87036432
  58649
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902641_902641
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86582460
  86626600
  44141
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902641_902641
  N/A
  N/A
  Control
  No previous psychiatric history
 
  86977784
  87026862
  49079
  GRCh38
  Duplication
  No
  krumm_15_ASD_discovery_controls-control11954.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  87980293
  87986418
  6126
  GRCh38
  Duplication
  Yes
  sanders_11_ASD_discovery_controls-11551.s1
  12.8
  F
  Control (matched sibling)
  NA
  NA
  86762936
  86861637
  98702
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12201.s1
  12.1
  M
  Control (matched sibling)
  NA
  NA
  87106240
  87151118
  44879
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12334.s1
  4.2
  M
  Control (matched sibling)
  NA
  NA
  87469156
  87475573
  6418
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12377.s1
  20.6
  F
  Control (matched sibling)
  NA
  NA
  87622858
  87679147
  56290
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12403.s1
  9.7
  F
  Control (matched sibling)
  NA
  NA
  87584726
  87638355
  53630
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12701.s1
  10.4
  M
  Control (matched sibling)
  NA
  NA
  86923242
  87003741
  80500
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12829.s1
  14.1
  M
  Control (matched sibling)
  NA
  NA
  86923242
  87003741
  80500
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12924.s1
  7.9
  F
  Control (matched sibling)
  NA
  NA
  87740979
  87750186
  9208
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13016.s1
  9.5
  F
  Control (matched sibling)
  NA
  NA
  87503328
  87543172
  39845
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13166.s1
  5.6
  M
  Control (matched sibling)
  NA
  NA
  87594046
  87638355
  44310
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13301.s1
  12.3
  M
  Control (matched sibling)
  NA
  NA
  87469156
  87475573
  6418
  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-case20151_1636001
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case2299_1
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case4518_1
 
 
 Unknown
 
 
 MGAT4C
 
 engchuan_15_ASD_discovery_cases-case4518_1
 
 
 Unknown
 
 
 
 
 gai_11_ASD_replication_cases-AU062905
 
 
 Inherited
 
 
 MGAT4C
 
 krumm_15_ASD_discovery_cases-case13199.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 CEP290
 
 prasad_12_ASD_discovery_cases-case134846
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-case78391
 
 
 Unknown
 Unknown
 Unknown
 MGAT4C
 
 sanders_11_ASD_discovery_cases-11001.p1
 
 
 Unknown
 Simplex (trio)
 NA
 CEP290
 
 sanders_11_ASD_discovery_cases-11002.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 MGAT4C
 
 sanders_11_ASD_discovery_cases-11390.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 MGAT4C
 
 sanders_11_ASD_discovery_cases-11733.p1
 
 
 Unknown
 Simplex (trio)
 NA
 CEP290
 
 sanders_11_ASD_discovery_cases-12081.p1
 
 
 Unknown
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12201.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12375.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12695.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12739.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 CYCSP30
 
 sanders_11_ASD_discovery_cases-12829.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-13016.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 yuan_23_ASD_discovery_cases-qma00852d000
 
 
 De novo
 
 
 CEP290
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900482_900482
 
 
  Unknown
 
 
  MGAT4C
 
engchuan_15_ASD_discovery_controls-controlHABC_901110_901110
 
 
  Unknown
 
 
  MGAT4C
 
engchuan_15_ASD_discovery_controls-controlHABC_901110_901110
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
 
 
  Unknown
 
 
  MGAT4C
 
engchuan_15_ASD_discovery_controls-controlHABC_901174_901174
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlHABC_902641_902641
 
 
  Unknown
 
 
  MGAT4C
 
engchuan_15_ASD_discovery_controls-controlHABC_902641_902641
 
 
  Unknown
 
 
 
 
krumm_15_ASD_discovery_controls-control11954.s1
  Illumina 1MDuo
 
  Paternal
 
 
  C12orf50
 
sanders_11_ASD_discovery_controls-11551.s1
 
 
  Unknown
  Simplex (quad)
  NA
  MGAT4C
 
sanders_11_ASD_discovery_controls-12201.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12334.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12377.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12403.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12701.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12829.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12924.s1
 
 
  Maternal
  Simplex (quad)
  NA
  CYCSP30
 
sanders_11_ASD_discovery_controls-13016.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-13166.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-13301.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 

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