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3q13.2CNV Type: Deletion-Duplication


Largest CNV size: 139186 bp

Statistics Box:
Number of Reports: 4



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
Excess of rare, inherited truncating mutations in autism.
Deletion

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
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 5001
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 44857
 1
 0
 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
 21399
 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
 139186
 12
 1
 13

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 10195
 1
 0
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 44857
 1
 0
 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)
 11732
 1
 0
 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)
 21399
 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.
 
 12525
 8
 0
 8

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 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
 
 

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  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)
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  qPCR
  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
  celestino-soper_11_ASD_discovery_cases-11418
 NA
 M
 ASD
 NA
 NA
 113659384
 113664385
  5002
 GRCh38
 Deletion
 No
  krumm_15_ASD_discovery_cases-case14343.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 112974790
 113019647
  44858
 GRCh38
 Deletion
 Yes
  prasad_12_ASD_discovery_cases-case110408
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 113499766
 113521164
  21399
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11604.p1
 17.2
 F
 Autism
 NA
 Full-scale IQ, 18; non-verbal IQ, 23; verbal IQ 13
 111743113
 111750527
  7415
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11773.p1
 13.1
 M
 Autism
 NA
 Full-scale IQ, 43; non-verbal IQ, 50; verbal IQ, 28
 113536296
 113536968
  673
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11800.p1
 13.3
 M
 Autism
 NA
 Full-scale IQ, 34; non-verbal IQ, 34; verbal IQ, 35
 113536296
 113536968
  673
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11941.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 85; non-verbal IQ, 87; verbal IQ, 86
 113536296
 113536968
  673
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12074.p1
 6.3
 F
 Autism
 NA
 Full-scale IQ, 75; non-verbal IQ, 82; verbal IQ, 79
 112383718
 112394487
  10770
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12086.p1
 14.5
 M
 Autism
 NA
 Full-scale IQ, 118; non-verbal IQ, 108; verbal IQ, 131
 111743113
 111762099
  18987
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12437.p1
 10.1
 M
 Autism
 NA
 Full-scale IQ, 75; non-verbal IQ, 78; verbal IQ, 72
 112383718
 112394487
  10770
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12534.p1
 7
 F
 Autism
 NA
 Full-scale IQ, 81; non-verbal IQ, 83; verbal IQ, 84
 113536296
 113536968
  673
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12631.p1
 17.2
 M
 Autism
 NA
 Full-scale IQ, 80; non-verbal IQ, 87; verbal IQ, 76
 112383718
 112395969
  12252
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12794.p1
 8.3
 M
 Autism
 NA
 Full-scale IQ, 96; non-verbal IQ, 96; verbal IQ, 97
 113326368
 113465554
  139187
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12809.p1
 5.6
 M
 ASD
 NA
 Full-scale IQ, 86; non-verbal IQ, 88; verbal IQ, 88
 112383718
 112395969
  12252
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12961.p1
 4.4
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 125; verbal IQ, 93
 112384293
 112394487
  10195
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13065.p1
 5.6
 M
 Autism
 NA
 Full-scale IQ, 91; non-verbal IQ, 101; verbal IQ, 81
 113536296
 113536968
  673
 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
  kanduri_15_ASD_discovery_controls-control_split286
  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
 
  112103140
  112113334
  10195
  Unknown
  Deletion
  No
  krumm_15_ASD_discovery_controls-control14343.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  112974790
  113019647
  44858
  GRCh38
  Deletion
  Yes
  poultney_13_ASD_discovery_controls-control05C45305
  N/A
  F
  Control
  NIMH Control (NIMH ID 26586)
 
  111638077
  111649808
  11732
  GRCh38
  Deletion
  Yes
  sanders_11_ASD_discovery_controls-11665.s1
  12.9
  M
  Control (matched sibling)
  NA
  NA
  113524443
  113536968
  12526
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11809.s1
  8.4
  F
  Control (matched sibling)
  NA
  NA
  113536296
  113536968
  673
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11941.s1
  8.7
  F
  Control (matched sibling)
  NA
  NA
  113536296
  113536968
  673
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12345.s1
  12.9
  F
  Control (matched sibling)
  NA
  NA
  112383718
  112395969
  12252
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12437.s1
  14.1
  M
  Control (matched sibling)
  NA
  NA
  112383718
  112394487
  10770
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12517.s1
  11.7
  M
  Control (matched sibling)
  NA
  NA
  113536296
  113546147
  9852
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12631.s1
  18.8
  M
  Control (matched sibling)
  NA
  NA
  112383718
  112395969
  12252
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12780.s1
  5.9
  M
  Control (matched sibling)
  NA
  NA
  112383718
  112394487
  10770
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 celestino-soper_11_ASD_discovery_cases-11418
 
 
 Unknown
 Simplex
 NA
 USF3
 
 krumm_15_ASD_discovery_cases-case14343.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 CD200R1,GTPBP8,NEPRO
 
 prasad_12_ASD_discovery_cases-case110408
 
 
 Unknown
 Multiplex
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11604.p1
 
 
 Maternal
 Simplex (trio)
 NA
 PLCXD2,PHLDB2
 
 sanders_11_ASD_discovery_cases-11773.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 SIDT1
 
 sanders_11_ASD_discovery_cases-11800.p1
 
 
 Unknown
 Simplex (quad-proband unmatched)
 Unknown
 SIDT1
 
 sanders_11_ASD_discovery_cases-11941.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 SIDT1
 
 sanders_11_ASD_discovery_cases-12074.p1
 
 
 Paternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12086.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 PLCXD2,PHLDB2
 
 sanders_11_ASD_discovery_cases-12437.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12534.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 SIDT1
 
 sanders_11_ASD_discovery_cases-12631.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12794.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 MIR8076,CFAP44-AS1,CFAP44,SPICE1
 
 sanders_11_ASD_discovery_cases-12809.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12961.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-13065.p1
 
 
 Unknown
 Simplex (trio)
 NA
 SIDT1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kanduri_15_ASD_discovery_controls-control_split286
 
 
  Unknown
 
 
  Intergenic CNV: nearest genes, CD200(dist=21482),BTLA(dist=69479)
 
krumm_15_ASD_discovery_controls-control14343.s1
  Omni2.5-4v1
 
  Maternal
 
 
  CD200R1,GTPBP8,NEPRO
 
poultney_13_ASD_discovery_controls-control05C45305
  qPCR
 
  Unknown
 
 
  CD96
 
sanders_11_ASD_discovery_controls-11665.s1
 
 
  Unknown
  Simplex (quad)
  NA
  SIDT1
 
sanders_11_ASD_discovery_controls-11809.s1
 
 
  Unknown
  Simplex (quad)
  NA
  SIDT1
 
sanders_11_ASD_discovery_controls-11941.s1
 
 
  Unknown
  Simplex (quad)
  NA
  SIDT1
 
sanders_11_ASD_discovery_controls-12345.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12437.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12517.s1
 
 
  Paternal
  Simplex (quad)
  NA
  SIDT1
 
sanders_11_ASD_discovery_controls-12631.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12780.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 

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