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3q12.1CNV Type: Deletion-Duplication


Largest CNV size: 300000 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

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References

Major Reports

Title
Author, Year
Report Class
CNV Type
Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
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
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
 christian_08_ASD_discovery_cases
 Subset of unrelated AGRE subjects (362 from multiplex families, 35 from simplex families)
 397
 ASD
 
 58.4% Male
 300000
 0
 1
 1
 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
 
 
 190186
 1
 0
 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
 503217
 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
 35969
 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
 13336
 5
 0
 5
 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
 69098
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 christian_08_ASD_discovery_controls
 Control subjects from NIMH Genetics Initiative Control sample set, characterized for Axis I disorders
 372
 Controls
 
 
 300000
 0
 0
 0
 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
 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)
 35969
 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.
 
 17250
 2
 0
 2
 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
 69098
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 christian_08_ASD_discovery_cases
  235 White/Not Hispanic, 28 White/Hispanic, 9 Asians, 4 Blacks, 14 Mixed/Not Hispanic, 7 Mixed/Hispanic, 98 Unknown
 aCGH
  RPCI 19K BAC microarray
 
 
 FISH, microsatellite, qPCR
 gai_11_ASD_replication_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 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
 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
 
 
 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
  christian_08_ASD_discovery_controls
  262 Caucasians, 100 African-Americans
  aCGH
  RPCI 19K BAC microarray
 
 
 
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  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
  christian_08_ASD_discovery_cases-AU021503
 NA
 M
 ASD
 NA
 NA
 100484823
 100768441
  283619
 GRCh38
 Duplication
 Yes
  gai_11_ASD_replication_cases-AU052103
 
 
 Autism
 
 
 101217279
 101407464
  190186
 Unknown
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004625
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 99118476
 99621693
  503218
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case140054L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 100249973
 100285941
  35969
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11359.p1
 5.5
 M
 ASD
 NA
 Full-scale IQ, 88; non-verbal IQ, 96; verbal IQ, 81
 99215668
 99229004
  13337
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11455.p1
 7.6
 M
 ASD
 NA
 Full-scale IQ, 68; non-verbal IQ, 73; verbal IQ, 69
 100067050
 100071620
  4571
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12052.p1
 7.4
 M
 Autism
 NA
 Full-scale IQ, 85; non-verbal IQ, 100; verbal IQ, 64
 98686461
 98692205
  5745
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12656.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 40; non-verbal IQ, 46; verbal IQ, 29
 99333303
 99334991
  1689
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13382.p1
 4.3
 M
 Autism
 NA
 Full-scale IQ, 76; non-verbal IQ, 74; verbal IQ, 83
 99332309
 99334991
  2683
 GRCh38
 Deletion
 No
  yin_16_ASD_discovery_cases-case119
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 99970524
 100039621
  69098
 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
  sanders_11_ASD_discovery_controls-11981.s1
  8.6
  F
  Control (matched sibling)
  NA
  NA
  99278465
  99288426
  9962
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12041.s1
  4.3
  M
  Control (matched sibling)
  NA
  NA
  99200164
  99217414
  17251
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 christian_08_ASD_discovery_cases-AU021503
 FISH, microsatellite, qPCR
 
 inherited
 Multiplex
 NA
 GMFBP1,TFG,TMEM45A,ABI3BP,ADGRG7
 
 gai_11_ASD_replication_cases-AU052103
 
 
 Inherited
 
 
 C3orf26, FILIP1L, TMEM30C
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004625
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ACTG1P13
 
 prasad_12_ASD_discovery_cases-case140054L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11359.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 ACTG1P13
 
 sanders_11_ASD_discovery_cases-11455.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 CMSS1,FILIP1L
 
 sanders_11_ASD_discovery_cases-12052.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-12656.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-13382.p1
 
 
 Paternal
 Simplex (trio)
 NA
 
 
 yin_16_ASD_discovery_cases-case119
 
 
 Unknown
 Unknown
 Unknown
 CMSS1,FILIP1L
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11981.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12041.s1
 
 
  Unknown
  Simplex (quad)
  NA
  ACTG1P13
 

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