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13q12.11-q12.12CNV Type: Deletion-Duplication


Largest CNV size: 5047112 bp

Statistics Box:
Number of Reports: 2



Summary Information

CNVs within this region were found in seven cases from a study of 15,749 individuals from the International Standards for Cytogenomic Arrays (ISCA) consortium with unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome (Kaminsky et al., 2011), as well as in an ASD case (Prasad et al., 2012).

Additional Locus Information

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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-Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 5047112
 2
 5
 7
 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
 383829
 0
 1
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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)
 383829
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  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
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003776
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 19309535
 24356647
  5047112
 NCBI36
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004814
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 19309535
 22376894
  3067359
 NCBI36
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002409
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 22144927
 22961637
  816710
 NCBI36
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002451
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 22413514
 23758280
  1344766
 NCBI36
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004073
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 22464762
 23808884
  1344122
 NCBI36
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003920
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 22464962
 23808743
  1343781
 NCBI36
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004088
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 22464962
 23808743
  1343781
 NCBI36
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case69180
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 22140179
 22524007
  383829
 
 Duplication
 No

Controls

No Control Data Available

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003776
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ZMYM5,ZMYM2,GJA3,GJB2,GJB6,CRYL1,IFT88,IL17D,N6AMT2,XPO4,LATS2,SAP18,SKA3,MRP63,ZDHHC20,EFHA1,FGF9,SGCG,SACS,TNFRSF19,MIPEP,C1QTNF9B-AS1,C1QTNF9B,SPATA13,C1QTNF9,PARP4,ATP12A,RNF17,CENPJ
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004814
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ZMYM5,ZMYM2,GJA3,GJB2,GJB6,CRYL1,IFT88,IL17D,N6AMT2,XPO4,LATS2,SAP18,SKA3,MRP63,ZDHHC20,EFHA1,FGF9
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002409
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 SGCG,SACS
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002451
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 SGCG,SACS,TNFRSF19,MIPEP,C1QTNF9B-AS1,C1QTNF9B,SPATA13
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004073
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 SGCG,SACS,TNFRSF19,MIPEP,C1QTNF9B-AS1,C1QTNF9B,SPATA13,C1QTNF9
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003920
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 SGCG,SACS,TNFRSF19,MIPEP,C1QTNF9B-AS1,C1QTNF9B,SPATA13,C1QTNF9
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004088
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 SGCG,SACS,TNFRSF19,MIPEP,C1QTNF9B-AS1,C1QTNF9B,SPATA13,C1QTNF9
 
 prasad_12_ASD_discovery_cases-case69180
 
 
 Unknown
 Multiplex
 Unknown
 BASP1P1
 

Controls

No Control Data Available
No Animal Model Data Available
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