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3q25.31CNV Type: Deletion-Duplication


Largest CNV size: 87537 bp

Statistics Box:
Number of Reports: 5



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-Duplication

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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 krumm_13_ASD_discovery_cases
 Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 81.265% Male
 12332
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 39089
 1
 9
 10
 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)
 39060
 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
 20676
 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
 87537
 1
 10
 11

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 krumm_13_ASD_discovery_controls
 Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 46.47% Male
 12332
 0
 1
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 12333
 0
 4
 4
 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)
 12332
 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)
 20676
 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.
 
 28566
 2
 4
 6

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 krumm_13_ASD_discovery_cases
  N/A
 WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
 DNACopy, CGHCall
 CoNIFER
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 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
  krumm_13_ASD_discovery_controls
  N/A
  WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
  DNACopy, CGHCall
  CoNIFER
  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
 
  None
  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
  krumm_13_ASD_discovery_cases-case13487.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 13487. SRS score of 56.
 Full-scale IQ (FSIQ) score of 96.
 155763516
 155775848
  12333
 GRCh38
 Duplication
 No (not tested)
  krumm_15_ASD_discovery_cases-case11257.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 155763517
 155775850
  12334
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case11498.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 155763517
 155775850
  12334
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case12007.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763517
 155775850
  12334
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case12494.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763517
 155775850
  12334
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case13072.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763517
 155802606
  39090
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case13576.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763516
 155775848
  12333
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case13655.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 155775701
 155802606
  26906
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case14123.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763516
 155775848
  12333
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case14231.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155767508
 155775848
  8341
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case14249.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 155763516
 155775848
  12333
 GRCh38
 Duplication
 Yes
  poultney_13_ASD_discovery_cases-case99HI0765
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU054805; NDAR ID NDAR_INVHV388WC3)
 
 155763517
 155802576
  39060
 GRCh38
 Duplication
 No
  prasad_12_ASD_discovery_cases-case85275L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 156552716
 156573391
  20676
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11113.p1
 15
 M
 Autism
 NA
 Full-scale IQ, 87; non-verbal IQ, 100; verbal IQ 86
 155352676
 155372196
  19521
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11257.p1
 5.5
 M
 Autism
 NA
 Full-scale IQ, 129; non-verbal IQ, 128; verbal IQ, 118
 155763308
 155801046
  37739
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11394.p1
 5.3
 M
 Autism
 NA
 Full-scale IQ, 76; non-verbal IQ, 74; verbal IQ 87
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11498.p1
 7.3
 M
 Autism
 NA
 Full-scale IQ, 113; non-verbal IQ, 102; verbal IQ, 110
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11634.p1
 5.7
 M
 Autism
 NA
 Full-scale IQ, 55; non-verbal IQ, 56; verbal IQ, 63
 156030905
 156118442
  87538
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12007.p1
 8.7
 F
 Autism
 NA
 Full-scale IQ, 64; non-verbal IQ, 54; verbal IQ, 83
 155763308
 155787808
  24501
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12232.p1
 7.7
 M
 Autism
 NA
 Full-scale IQ, 62; non-verbal IQ, 74; verbal IQ, 51
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12414.p1
 4.4
 M
 ASD
 NA
 Full-scale IQ, 116; non-verbal IQ, 129; verbal IQ, 90
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12434.p1
 5.3
 M
 Autism
 NA
 Full-scale IQ, 117; non-verbal IQ, 121; verbal IQ, 106
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12494.p1
 7.9
 M
 Autism
 NA
 Full-scale IQ, 59; non-verbal IQ, 67; verbal IQ, 56
 155763308
 155791874
  28567
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13072.p1
 15.5
 F
 Autism
 NA
 Full-scale IQ, 94; non-verbal IQ, 94; verbal IQ, 97
 155765530
 155791874
  26345
 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
  krumm_13_ASD_discovery_controls-control13922.s1
  N/A
  M
  Control
  Unaffected sibling from SSC quad family 13922. SRS score of 41.
 
  155763516
  155775848
  12333
  GRCh38
  Duplication
  No (not tested)
  krumm_15_ASD_discovery_controls-control12007.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  155763517
  155775850
  12334
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control12494.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  155763517
  155775850
  12334
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control13922.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  155763516
  155775848
  12333
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control14123.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  155763516
  155775848
  12333
  GRCh38
  Duplication
  Yes
  poultney_13_ASD_discovery_controls-control04C27774A
  N/A
  F
  Control
  NIMH Control (NIMH ID 62995)
 
  155763517
  155775848
  12332
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11909.s1
  5.7
  M
  Control (matched sibling)
  NA
  NA
  156660082
  156674402
  14321
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11909.s1
  5.7
  M
  Control (matched sibling)
  NA
  NA
  156717618
  156732802
  15185
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12007.s1
  10.9
  M
  Control (matched sibling)
  NA
  NA
  155763308
  155787808
  24501
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12434.s1
  8.8
  F
  Control (matched sibling)
  NA
  NA
  155763308
  155791874
  28567
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12494.s1
  11
  F
  Control (matched sibling)
  NA
  NA
  155763308
  155791874
  28567
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12682.s1
  8.1
  M
  Control (matched sibling)
  NA
  NA
  155763308
  155791874
  28567
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 krumm_13_ASD_discovery_cases-case13487.p1
 
 
 Paternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case11257.p1
 Illumina 1M
 
 Maternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case11498.p1
 Illumina 1M
 
 Paternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case12007.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 C3orf33
 
 krumm_15_ASD_discovery_cases-case12494.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 C3orf33
 
 krumm_15_ASD_discovery_cases-case13072.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case13576.p1
 1M-Duov3
 
 Paternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case13655.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case14123.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 C3orf33
 
 krumm_15_ASD_discovery_cases-case14231.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Segregated
 C3orf33
 
 krumm_15_ASD_discovery_cases-case14249.p1
 Omni2.5-4v1
 
 Maternal
 Simplex
 Segregated
 C3orf33
 
 poultney_13_ASD_discovery_cases-case99HI0765
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 C3orf33
 
 prasad_12_ASD_discovery_cases-case85275L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11113.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-11257.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 C3orf33
 
 sanders_11_ASD_discovery_cases-11394.p1
 
 
 Paternal
 Simplex (trio)
 NA
 C3orf33
 
 sanders_11_ASD_discovery_cases-11498.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 C3orf33
 
 sanders_11_ASD_discovery_cases-11634.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 ALG1L15P,MRE11P1,VN2R1P,KCNAB1
 
 sanders_11_ASD_discovery_cases-12007.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 C3orf33
 
 sanders_11_ASD_discovery_cases-12232.p1
 
 
 Paternal
 Simplex (trio)
 NA
 C3orf33
 
 sanders_11_ASD_discovery_cases-12414.p1
 
 
 Maternal
 Simplex (trio)
 NA
 C3orf33
 
 sanders_11_ASD_discovery_cases-12434.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 C3orf33
 
 sanders_11_ASD_discovery_cases-12494.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 C3orf33
 
 sanders_11_ASD_discovery_cases-13072.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 C3orf33
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control13922.s1
 
 
  Paternal
  Simplex
 
  C3orf33
 
krumm_15_ASD_discovery_controls-control12007.s1
  Illumina 1MDuo
 
  Maternal
 
 
  C3orf33
 
krumm_15_ASD_discovery_controls-control12494.s1
  Illumina 1MDuo
 
  Paternal
 
 
  C3orf33
 
krumm_15_ASD_discovery_controls-control13922.s1
  Omni2.5-4v1
 
  Paternal
 
 
  C3orf33
 
krumm_15_ASD_discovery_controls-control14123.s1
  Omni2.5-4v1
 
  Maternal
 
 
  C3orf33
 
poultney_13_ASD_discovery_controls-control04C27774A
 
 
  Unknown
 
 
  C3orf33
 
sanders_11_ASD_discovery_controls-11909.s1
 
 
  Unknown
  Simplex (quad)
  NA
  TIPARP-AS1,TIPARP
 
sanders_11_ASD_discovery_controls-11909.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12007.s1
 
 
  Maternal
  Simplex (quad)
  NA
  C3orf33
 
sanders_11_ASD_discovery_controls-12434.s1
 
 
  Maternal
  Simplex (quad)
  NA
  C3orf33
 
sanders_11_ASD_discovery_controls-12494.s1
 
 
  Paternal
  Simplex (quad)
  NA
  C3orf33
 
sanders_11_ASD_discovery_controls-12682.s1
 
 
  Paternal
  Simplex (quad)
  NA
  C3orf33
 

No Animal Model Data Available
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