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13q32.2-q32.3CNV Type: Deletion-Duplication


Largest CNV size: 15934566 bp

Statistics Box:
Number of Reports: 4



Summary Information

CNVs within this region were identified in cases from two recent reports (Kaminsky et al., 2011; Nguyen et al., 2013).

Additional Locus Information

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USCS Symbol             NCBI Symbol

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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...
Duplication
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Global increases in both common and rare copy number load associated with autism.
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
 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
 1823969
 0
 1
 1
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
 Patients from five databases: The Developmental Gene Anatomy Project at Harvard Medical School (DGAP, n=200); The Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP, n=120); The National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS, n=45); Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database (n=45,744); and DECIPHER
 57365
 Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD
 N/A
 N/A
 15934566
 2
 0
 2
 girirajan_13b_ASD_discovery_cases
 Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)
 243
 Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol
 N/A
 N/A
 369913
 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
 100631
 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
 nguyen_13_DD/ID/MCA/ASD_discovery_controls
 Control data from the Database of Genomic Variants (DGV, n=12,145) and a published dataset of 8,329 individuals from Moriarty et al., 1998.
 20474
 Control
 N/A
 N/A
 N/A
 N/A
 N/A
 N/A
 girirajan_13b_ASD_discovery_controls
 Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)
 223
 Control
 N/A
 N/A
 0
 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

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
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
  N/A
 aCGH (n=45,744 from Signature Genomic Labs)
  SignatureChip BACs aCGH or SignatureChip Oligo whole-genome microarray (n=45,744)
 
 
 FISH
 girirajan_13b_ASD_discovery_cases
  133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American
 aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
 DNA Copy Number v1.6
 
 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
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K or 105K
 
  Feature Extraction & DNA Analytics
 
  nguyen_13_DD/ID/MCA/ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
  N/A
  girirajan_13b_ASD_discovery_controls
  116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American
  aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
  DNA Copy Number v1.6
 
 
  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
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001747
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 97124731
 98948700
  1823969
 NCBI36
 Duplication
 Yes
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC18255
 N/A
 M
 DD/ID/MCA
 Database: Signature. Indication for study: 46,XY,del(13)(q31q3?2.3)
 
 99150575
 115085141
  15934566
 hg19
 Deletion
 Yes
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC40227
 N/A
 F
 DD/ID/MCA
 Database: Signature. Indication for study: Possible Trisomy 13 with 2 abnormal cell lines, mosaic r(13)
 
 99151129
 115077940
  15926811
 hg19
 Deletion
 Yes
  girirajan_13b_ASD_discovery_cases-16708109743
 N/A
 N/A
 Autism
 Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Caucasian
 N/A
 97871496
 98241409
  369913
 Build36/hg18
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case3205_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 98059329
 98159960
  100631
 hg18
 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-ISCA00001747
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 IPO5,FARP1,RNF113B,STK24,SLC15A1,DOCK9,UBAC2,GPR18,GPR183
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC18255
 FISH
 
 Unknown
 Unknown
 Unknown
 STK24,SLC15A1,DOCK9,UBAC2,GPR18,GPR183,TM9SF2,CLYBL,ZIC5,ZIC2,PCCA,GGACT,TMTC4,NALCN,ITGBL1,FGF14,TPP2,METTL21C,CCDC168,TEX30,KDELC1,BIVM,BIVM-ERCC5,ERCC5,SLC10A2,DAOA,EFNB2,ARGLU1,FAM155A,LIG4,ABHD13,TNFSF13B,MYO16,IRS2,COL4A1,COL4A2,RAB20,CARKD,CARS2,ING1,ANKRD10,ARHGEF7,TEX29,SOX1,SPACA7,TUBGCP3,C13orf35,ATP11A,MCF2L,F7,F10,PROZ,PCID2,CUL4A,LAMP1,GRTP1,ADPRHL1,DCUN1D2,TMCO3,TFDP1,ATP4B,GRK1,TMEM255B,GAS6,RASA3,CDC16,UPF3A,CHAMP1
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC40227
 FISH
 
 De novo
 Unknown
 Possibly segregated
 STK24,SLC15A1,DOCK9,UBAC2,GPR18,GPR183,TM9SF2,CLYBL,ZIC5,ZIC2,PCCA,GGACT,TMTC4,NALCN,ITGBL1,FGF14,TPP2,METTL21C,CCDC168,TEX30,KDELC1,BIVM,BIVM-ERCC5,ERCC5,SLC10A2,DAOA,EFNB2,ARGLU1,FAM155A,LIG4,ABHD13,TNFSF13B,MYO16,IRS2,COL4A1,COL4A2,RAB20,CARKD,CARS2,ING1,ANKRD10,ARHGEF7,TEX29,SOX1,SPACA7,TUBGCP3,C13orf35,ATP11A,MCF2L,F7,F10,PROZ,PCID2,CUL4A,LAMP1,GRTP1,ADPRHL1,DCUN1D2,TMCO3,TFDP1,ATP4B,GRK1,TMEM255B,GAS6,RASA3,CDC16,UPF3A
 
 girirajan_13b_ASD_discovery_cases-16708109743
 
 
 Unknown
 Unknown
 Unknown
 FARP1,STK24,SLC15A1
 
 engchuan_15_ASD_discovery_cases-case3205_3
 
 
 Unknown
 
 
 SLC15A1
 

Controls

No Control Data Available
No Animal Model Data Available
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