HELP     Sign In

13q12.3CNV Type: Deletion-Duplication


Largest CNV size: 31345 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

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
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 31345
 2
 1
 3
 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
 275
 0
 1
 1
 prasad_12_ASD_discovery_cases
 Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children in Toronto, Ontario; McMaster University, Hamilton, Ontario; Memorial University of Newfoundland, St. John's, Newfoundland); the majority of these cases had been previously genotyped by SNP arrays with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were exclu
 676
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
 NA
 82.84% Male
 9725
 1
 0
 1
 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)
 132191
 0
 1
 1
 al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
 Retrospective chart review of patients (n=584) with a neurocognitive phenotype (mainly referred from pediatric neurology clinics) seen by a single clinical geneticist from September 2007 to July 2013
 584
 Inclusion criteria: presence of a neurocognitive phenotype (i.e., syndromic and non-syndromic cases of developmental delay, autism, intellectual disability, and epilepsy) with a normal karyotype
 N/A
 N/A
 2314000
 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
 160197
 0
 1
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 nord_11_ASD_discovery_controls
 Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
 123
 Controls (no history of psychiatric symptoms by self-report)
 ? 30 yrs.
 
 104061
 1
 0
 1
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 3874
 3
 0
 3
 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)
 9725
 0
 0
 0
 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)
 132191
 0
 1
 1
 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
 81192
 0
 1
 1

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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 (n=334) or Illumina 1M v3 (n=840)
 PennCNV, QuantiSNP, & GNOSIS
 
 
 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
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
  Saudi Arabia
 Array SNP
  Affymetrix 6.0, Cyto-V2, or CytoScan HD
 HMM
 Affymetrix GeneChip Command Console (version 1.2); Chromosome Analysis Suite version Cyto 2.0.0.195
 None
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  nord_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  Sliding-window algorithm, ~10 kb minumum size threshold
 
  None
  sanders_11_ASD_discovery_controls
 
  Solid phase hybridization
  Illumina 1M v1 or Illumina 1M v3
  PennCNV, QuantiSNP, & GNOSIS
 
 
  prasad_12_ASD_discovery_controls
  NA
  aCGH (PDx controls)
  Agilent 1M (PDx controls)
  PDx controls: ADM-2, DNAcopy (R Bioconductor)
  PDx controls: DNA Analytics v4.0.85 (Agilent), DNAcopy
 
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  None
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  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
  sanders_11_ASD_discovery_cases-12072.p1
 15
 F
 Autism
 NA
 Full-scale IQ, 139; non-verbal IQ, 116; verbal IQ, 167
 28977484
 28989819
  12335
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-12454.p1
 5
 M
 Autism
 NA
 Full-scale IQ, 72; non-verbal IQ, 82; verbal IQ, 62
 29994630
 30025975
  31345
 hg18
 Duplication
 No
  sanders_11_ASD_discovery_cases-12524.p1
 6
 F
 Autism
 NA
 Full-scale IQ, 146; non-verbal IQ, 130; verbal IQ, 166
 30324211
 30324436
  225
 hg18
 Deletion
 No
  celestino-soper_11_ASD_discovery_cases-11345
 NA
 M
 ASD
 NA
 NA
 31712504
 31712779
  275
 hg19
 Duplication
 No
  prasad_12_ASD_discovery_cases-case47607
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 28867917
 28877641
  9725
 
 Deletion
 No
  poultney_13_ASD_discovery_cases-case05HI4737A
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU1482302; NDAR ID NDAR_INVEE937MZQ)
 
 31728768
 31860958
  132191
 hg19
 Duplication
 No
  al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case08DG00254
 N/A
 N/A
 Intellectual disability, epilepsy, and ADHD
 Intellectual disability and speech delay, epilepsy, ADHD, microbrachycephaly, obesity, hypogonadism, exaggerated reflexes, in-toe gait. Non-consanguineous parents. Father has learning difficulties and psychological problems.
 Intellectual disability
 29226273
 31540272
  2314000
 GRCh37/hg19
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case2285_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30624653
 30784850
  160197
 hg18
 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
  nord_11_ASD_discovery_controls-04C27213
 
 
  Control
 
 
  28590261
  28694321
  104061
 
  Deletion
 
  sanders_11_ASD_discovery_controls-11446.s1
  11
  F
  Control (matched sibling)
  NA
  NA
  30324211
  30325259
  1048
  hg18
  Deletion
  No
  sanders_11_ASD_discovery_controls-12647.s1
  9
  M
  Control (matched sibling)
  NA
  NA
  30324211
  30324436
  225
  hg18
  Deletion
  No
  sanders_11_ASD_discovery_controls-12821.s1
  9
  F
  Control (matched sibling)
  NA
  NA
  31022602
  31026476
  3874
  hg18
  Deletion
  No
  poultney_13_ASD_discovery_controls-control05C40631
  N/A
  F
  Control
  NIMH Control (NIMH ID 80004)
 
  31728768
  31860958
  132191
  hg19
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB958271_1007843897
  N/A
  N/A
  Control
  No previous psychiatric history
 
  28689137
  28770329
  81192
  hg18
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 sanders_11_ASD_discovery_cases-12072.p1
 
 
 Unknown
 Simplex (quad-proband unmatched)
 Unknown
 KIAA0774, SLC7A1
 
 sanders_11_ASD_discovery_cases-12454.p1
 
 
 Paternal
 Simplex (trio)
 NA
 0 genes
 
 sanders_11_ASD_discovery_cases-12524.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 0 genes
 
 celestino-soper_11_ASD_discovery_cases-11345
 
 
 Unknown
 Simplex
 NA
 HSPH1
 
 prasad_12_ASD_discovery_cases-case47607
 
 
 Unknown
 Unknown
 Unknown
 MTUS2
 
 poultney_13_ASD_discovery_cases-case05HI4737A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 HSPH1,B3GALTL
 
 al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case08DG00254
 
 Paternal
 Paternal
 Multi-generational
 Possibly segregated
 POMP,SLC46A3,MTUS2,SLC7A1,UBL3,KATNAL1,HMGB1,USPL1,ALOX5AP,MEDAG,TEX26
 
 engchuan_15_ASD_discovery_cases-case2285_1
 
 
 Unknown
 
 
 B3GALTL;HSPH1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
nord_11_ASD_discovery_controls-04C27213
 
 
 
 
 
  MTUS2
 
sanders_11_ASD_discovery_controls-11446.s1
 
 
  Maternal
  Simplex (quad)
  NA
  0 genes
 
sanders_11_ASD_discovery_controls-12647.s1
 
 
  Maternal
  Simplex (quad)
  NA
  0 genes
 
sanders_11_ASD_discovery_controls-12821.s1
 
 
  Unknown
  Simplex (quad)
  NA
  0 genes
 
poultney_13_ASD_discovery_controls-control05C40631
 
 
  Unknown
 
 
  HSPH1,B3GALTL
 
engchuan_15_ASD_discovery_controls-controlB958271_1007843897
 
 
  Unknown
 
 
  MTUS2
 

No Animal Model Data Available
HELP