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13q12.13CNV Type: Deletion


Largest CNV size: 22067 bp

Statistics Box:
Number of Reports: 6



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

Decipher

References

Major Reports

Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion

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
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
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
 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
 
 
 21191
 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
 22067
 4
 0
 4
 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
 324300
 1
 0
 1
 iourov_12_ASD/ID/EP_discovery_cases
 Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
 54
 Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
 Range, 3 mos.-11 yrs.
 NA
 3993
 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
 9767
 0
 1
 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
 53290
 0
 1
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 8400
 3
 0
 3
 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)
 9767
 0
 0
 0
 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
 0
 0
 0
 0
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 47776
 0
 1
 1

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 gai_11_ASD_replication_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3
 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 (n=334) or Illumina 1M v3 (n=840)
 PennCNV, QuantiSNP, & GNOSIS
 
 
 kaminsky_11_DD/ID/ASD_discovery_cases
  NA
 aCGH
  Agilent 44K or 105K
 
 Feature Extraction & DNA Analytics
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 iourov_12_ASD/ID/EP_discovery_cases
  Russian
 aCGH
  BACs aCGH
 
 
 None
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 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
  sanders_11_ASD_discovery_controls
 
  Solid phase hybridization
  Illumina 1M v1 or Illumina 1M v3
  PennCNV, QuantiSNP, & GNOSIS
 
 
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K or 105K
 
  Feature Extraction & DNA Analytics
 
  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
 
  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)

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  gai_11_ASD_replication_cases-AU0914301
 
 
 Autism
 
 
 25144328
 25165518
  21191
 
 Deletion
 No
  sanders_11_ASD_discovery_cases-11168.p1
 11
 M
 Autism
 NA
 Full-scale IQ, 96; non-verbal IQ, 106; verbal IQ, 119
 25490891
 25494950
  4059
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11919.p1
 4
 M
 ASD
 NA
 Full-scale IQ, 84; non-verbal IQ, 77; verbal IQ, 104
 25640798
 25649198
  8400
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-12670.p1
 10
 M
 ASD
 NA
 Full-scale IQ, 106; non-verbal IQ, 108; verbal IQ, 104
 25647538
 25661802
  14264
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-13045.p1
 11
 M
 Autism
 NA
 Full-scale IQ, 37; non-verbal IQ, 38; verbal IQ, 35
 25812040
 25834107
  22067
 hg18
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004343
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 25146721
 25471021
  324300
 NCBI36
 Deletion
 Yes
  iourov_12_ASD/ID/EP_discovery_cases-case49
 4 yrs. 10 mos.
 F
 Developmental delay/intellectual disability
 Facial dysmorphisms, clinodactyly, dentinogenesis imperfecta, enteroparesis. Karyotype: 9phqh, 17ps.
 Developmental delay/intellectual disability
 24807453
 24811446
  3993
 GRCh37/hg19
 Duplication
 No
  prasad_12_ASD_discovery_cases-case59800L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 25695049
 25704815
  9767
 
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case14164_2680
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 24431831
 24485121
  53290
 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
  sanders_11_ASD_discovery_controls-11178.s1
  5
  M
  Control (matched sibling)
  NA
  NA
  26655905
  26661223
  5318
  hg18
  Deletion
  No
  sanders_11_ASD_discovery_controls-11329.s1
  6
  M
  Control (matched sibling)
  NA
  NA
  24577445
  24579106
  1661
  hg18
  Deletion
  No
  sanders_11_ASD_discovery_controls-11919.s1
  6
  M
  Control (matched sibling)
  NA
  NA
  25640798
  25649198
  8400
  hg18
  Deletion
  No
  krumm_15_ASD_discovery_controls-control13792.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  26911703
  26959479
  47776
  hg19
  Duplication
  Yes

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gai_11_ASD_replication_cases-AU0914301
 
 
 Inherited
 
 
 ATP8A2 (intronic)
 
 sanders_11_ASD_discovery_cases-11168.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 ATP8A2
 
 sanders_11_ASD_discovery_cases-11919.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-12670.p1
 
 
 Maternal
 Simplex (trio)
 NA
 0 genes
 
 sanders_11_ASD_discovery_cases-13045.p1
 
 
 Maternal
 Simplex (trio)
 NA
 CDK8
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004343
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ATP8A2
 
 iourov_12_ASD/ID/EP_discovery_cases-case49
 
 
 Unknown
 Unknown
 Unknown
 SPATA13
 
 prasad_12_ASD_discovery_cases-case59800L
 
 
 Unknown
 Simplex
 Unknown
 0 genes
 
 engchuan_15_ASD_discovery_cases-case14164_2680
 
 
 Unknown
 
 
 TPTE2P1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11178.s1
 
 
  Maternal
  Simplex (quad)
  NA
  0 genes
 
sanders_11_ASD_discovery_controls-11329.s1
 
 
  Paternal
  Simplex (quad)
  NA
  0 genes
 
sanders_11_ASD_discovery_controls-11919.s1
 
 
  Maternal
  Simplex (quad)
  NA
  0 genes
 
krumm_15_ASD_discovery_controls-control13792.s1
  Omni2.5-4v1
 
  Maternal
 
 
  CDK8,Intron (2/12),Exon (3/13),Intron (3/12),Exon (4/13),Intron (4/12),Exon (5/13),Intron (5/12)
 

No Animal Model Data Available
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