13q32.2-q32.3CNV Type: Deletion-Duplication
Largest CNV size: 15934566 bp
Statistics Box:
Number of Reports: 4
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
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
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
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
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 the Developmental Gene Anatomy Project at Harvard Medical School (DGAP), the Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP), the National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS), the Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database, 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
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
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
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
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
kaminsky_11_DD/ID/ASD_discovery_cases
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
nguyen_13_DD/ID/MCA/ASD_discovery_cases
N/A
aCGH
SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
FISH
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
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
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
nguyen_13_DD/ID/MCA/ASD_discovery_controls
N/A
N/A
N/A
N/A
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
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)
98609074
98709705
100632
GRCh38
Duplication
No
girirajan_13b_ASD_discovery_cases-16708109743
N/A
N/A
Autism
Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Caucasian
N/A
98421241
98791154
369914
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001747
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
97674476
99498445
1823970
GRCh38
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)
98498321
114319666
15821346
GRCh38
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)
98498875
114312465
15813591
GRCh38
Deletion
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case3205_3
Unknown
NUS1P4,CYCSP35,CALM2P4,RN7SL60P,SLC15A1
girirajan_13b_ASD_discovery_cases-16708109743
Unknown
Unknown
Unknown
FARP1-AS1,STK24-AS1,NUS1P4,CYCSP35,CALM2P4,RN7SL60P,FARP1,SLC15A1,STK24
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001747
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
RPL7AP61,FTLP8,RNF113B,RN7SKP8,MIR3170,FARP1-AS1,STK24-AS1,NUS1P4,CYCSP35,CALM2P4,RN7SL60P,DOCK9-AS1,RPL7L1P12,RNU6-83P,DOCK9-DT,RPS6P23,GAPDHP22,UBAC2-AS1,RN7SKP9,H2AFZP3,GPR18,MIR623,HMGB3P4,CCR12P,LINC01232,IPO5,GPR183,FARP1,SLC15A1,DOCK9,UBAC2,TM9SF2,STK24
nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC18255
FISH
Unknown
Unknown
Unknown
STK24-AS1,NUS1P4,CYCSP35,CALM2P4,RN7SL60P,DOCK9-AS1,RPL7L1P12,RNU6-83P,DOCK9-DT,RPS6P23,GAPDHP22,UBAC2-AS1,RN7SKP9,H2AFZP3,GPR18,MIR623,HMGB3P4,CCR12P,LINC01232,LINC01039,CFL1P8,MIR4306,CLYBL-AS2,CLYBL-AS1,ZIC5,ZIC2,LINC00554,NDUFA12P1,ASNSP3,RPL15P18,RPS26P47,COX5BP6,ARF4P3,RNU1-24P,HMGB3P7,MIR2681,LIPT1P1,RNY1P2,MIR4705,RPL39P29,FGF14-AS1,FGF14-AS2,LINC00555,METTL21C,TEX30,LINC01309,ATP6V1G1P7,RPL7P45,RNA5SP38,RPL35P9,ATP5MC1P5,PPIAP24,SNORD31B,MIR1267,RNA5SP39,HCFC2P1,MYO16-AS2,LINC01067,LINC00399,LINC00676,RN7SKP10,LINC00396,RN7SL783P,MIR8073,COL4A2-AS1,RPL21P107,LINC00567,LINC00346,ANKRD10-IT1,PARP1P1,ARHGEF7-AS2,ARHGEF7-AS1,LINC00354,SOX1,LINC00404,SOX1-OT,LINC01043,F10-AS1,MIR8075,LDHBP1,RNU1-16P,LINC00552,GAS6-DT,LINC00454,LINC00565,RASA3-IT1,MIR548AR,MIR4502,CLCP2,GPR183,LINC00449,PCCA-AS1,LINC00411,CCDC168,LINC00283,KDELC1,BIVM,BIVM-ERCC5,ERCC5,SLC10A2,DAOA-AS1,DAOA,LINC00343,LINC00460,EFNB2,LINC00551,LINC00443,FAM155A-IT1,LIG4,ABHD13,LINC00370,IRS2,COL4A2-AS2,RAB20,CARS2,ING1,LINC00431,LINC00368,ARHGEF7-IT1,TEX29,LINC02337,SPACA7,TUBGCP3,ATP11AUN,ATP11A-AS1,MCF2L-AS1,F10,KARSP2,PROZ,PCID2,LAMP1,GRTP1,GRTP1-AS1,ADPRHL1,DCUN1D2,DCUN1D2-AS,ATP4B,GRK1,GAS6-AS1,GAS6,C13orf46,CDC16,CHAMP1,SLC15A1,DOCK9,UBAC2,TM9SF2,PCCA,GGACT,NALCN-AS1,NALCN,FGF14-IT1,TPP2,METTL21EP,ARGLU1,FAM155A,TNFSF13B,MYO16-AS1,COL4A1,COL4A2,NAXD,ANKRD10,LINC01044,ATP11A,MCF2L,F7,TMCO3,TFDP1,TMEM255B,LINC00452,RASA3,CFAP97D2,STK24,CLYBL,ITGBL1,FGF14,ARHGEF7,LINC01070,CUL4A,UPF3A,TMTC4,MYO16
nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC40227
FISH
De novo
Unknown
Possibly segregated
STK24-AS1,NUS1P4,CYCSP35,CALM2P4,RN7SL60P,DOCK9-AS1,RPL7L1P12,RNU6-83P,DOCK9-DT,RPS6P23,GAPDHP22,UBAC2-AS1,RN7SKP9,H2AFZP3,GPR18,MIR623,HMGB3P4,CCR12P,LINC01232,LINC01039,CFL1P8,MIR4306,CLYBL-AS2,CLYBL-AS1,ZIC5,ZIC2,LINC00554,NDUFA12P1,ASNSP3,RPL15P18,RPS26P47,COX5BP6,ARF4P3,RNU1-24P,HMGB3P7,MIR2681,LIPT1P1,RNY1P2,MIR4705,RPL39P29,FGF14-AS1,FGF14-AS2,LINC00555,METTL21C,TEX30,LINC01309,ATP6V1G1P7,RPL7P45,RNA5SP38,RPL35P9,ATP5MC1P5,PPIAP24,SNORD31B,MIR1267,RNA5SP39,HCFC2P1,MYO16-AS2,LINC01067,LINC00399,LINC00676,RN7SKP10,LINC00396,RN7SL783P,MIR8073,COL4A2-AS1,RPL21P107,LINC00567,LINC00346,ANKRD10-IT1,PARP1P1,ARHGEF7-AS2,ARHGEF7-AS1,LINC00354,SOX1,LINC00404,SOX1-OT,LINC01043,F10-AS1,MIR8075,LDHBP1,RNU1-16P,LINC00552,GAS6-DT,LINC00454,LINC00565,RASA3-IT1,MIR548AR,MIR4502,CLCP2,GPR183,LINC00449,PCCA-AS1,LINC00411,CCDC168,LINC00283,KDELC1,BIVM,BIVM-ERCC5,ERCC5,SLC10A2,DAOA-AS1,DAOA,LINC00343,LINC00460,EFNB2,LINC00551,LINC00443,FAM155A-IT1,LIG4,ABHD13,LINC00370,IRS2,COL4A2-AS2,RAB20,CARS2,ING1,LINC00431,LINC00368,ARHGEF7-IT1,TEX29,LINC02337,SPACA7,TUBGCP3,ATP11AUN,ATP11A-AS1,MCF2L-AS1,F10,KARSP2,PROZ,PCID2,LAMP1,GRTP1,GRTP1-AS1,ADPRHL1,DCUN1D2,DCUN1D2-AS,ATP4B,GRK1,GAS6-AS1,GAS6,C13orf46,CDC16,SLC15A1,DOCK9,UBAC2,TM9SF2,PCCA,GGACT,NALCN-AS1,NALCN,FGF14-IT1,TPP2,METTL21EP,ARGLU1,FAM155A,TNFSF13B,MYO16-AS1,COL4A1,COL4A2,NAXD,ANKRD10,LINC01044,ATP11A,MCF2L,F7,TMCO3,TFDP1,TMEM255B,LINC00452,RASA3,CFAP97D2,STK24,CLYBL,ITGBL1,FGF14,ARHGEF7,LINC01070,CUL4A,UPF3A,TMTC4,MYO16
Controls
No Control Data Available
No Animal Model Data Available