13q12.11-q12.12CNV Type: Deletion-Duplication
Largest CNV size: 5047112 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
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
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
monteiro_19_ASD_discovery_cases
Patients from an aCGH database from the Department of Genetics of the Faculty of Medicine, University of Porto, Portugal, over a 5-year-period (2012-2017).
253
Diagnosis of ASD confirmed by ADOS and ADI-R and based on DSM-IV-TR
N/A
76.68% Male
911000
1
0
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
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, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
monteiro_19_ASD_discovery_cases
Portuguese
aCGH
Agilent SurePrint G3 4x180K
Agilent Cytogenomics
None
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, Agilent 105K
Feature Extraction, DNA Analytics
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
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-ISCA00002409
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
22672788
23489498
816711
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002451
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
22941375
24286142
1344768
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003776
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
19837395
24884509
5047115
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003920
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
22992823
24336605
1343783
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004073
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
22992623
24336746
1344124
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004088
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
22992823
24336605
1343783
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004814
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
19837395
22904755
3067361
GRCh38
Duplication
Yes
monteiro_19_ASD_discovery_cases_case26
N/A
M
ASD
Diagnosis of ASD confirmed by ADOS and ADI-R and based on DSM-IV-TR. Developmental milestones: normal (no developmental delay). Dysmorphic features: none reported.
Normal (no intellectual disability)
22421671
23332878
911208
GRCh38
Deletion
No
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
Unknown
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-ISCA00002409
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
FTH1P7,DDX39AP1,RPL7AP73,IPMKP1,RFESDP1,BASP1P1,NUS1P2,RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00621,HMGA1P6,LINC00327,SGCG,SACS
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002451
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00352,MTCO3P2,PCOTH,C1QTNF9B,ANKRD20A19P,IPO7P2,MIR2276,SPATA13-AS1,HMGA1P6,LINC00327,SGCG,SACS,TNFRSF19,MIPEP,SPATA13
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003776
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
PPIAP28,LINC00556,GJB2,GJB6,MIR4499,SLC35E1P1,RNU2-7P,RANP8,PPIAP27,RPSAP54,LATS2-AS1,RNU4-9P,RPS12P23,IPPKP1,SAP18,MRPL57,LINC01046,GRK6P1,GAPDHP52,RNA5SP25,ZDHHC20-IT1,HIST1H2BPS3,FNTAP2,RNU6-59P,RPS7P10,LINC00424,NME1P1,MTND3P1,FTH1P7,DDX39AP1,RPL7AP73,IPMKP1,RFESDP1,BASP1P1,NUS1P2,RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00352,MTCO3P2,PCOTH,C1QTNF9B,ANKRD20A19P,IPO7P2,MIR2276,SPATA13-AS1,C1QTNF9-AS1,NUS1P3,LINC00566,CYCSP33,PSPC1P2,RNY1P7,RPL26P34,IRX1P1,ANKRD20A10P,ZMYM5,KRR1P1,LINC01072,GJA3,EEF1AKMT1,CNOT4P1,HNRNPA1P30,LATS2,SKA3,ESRRAP2,MIPEPP3,LINC00539,ZDHHC20,FGF9,RN7SL766P,LINC00621,HMGA1P6,LINC00327,C1QTNF9,ATP12A,ZMYM2,CRYL1,IFT88,IL17D,XPO4,MICU2,LINC00540,SGCG,SACS,TNFRSF19,MIPEP,SPATA13,TPTE2P6,PARP4,RNF17,CENPJ
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003920
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00352,MTCO3P2,PCOTH,C1QTNF9B,ANKRD20A19P,IPO7P2,MIR2276,SPATA13-AS1,C1QTNF9-AS1,NUS1P3,LINC00566,HMGA1P6,LINC00327,C1QTNF9,SGCG,SACS,TNFRSF19,MIPEP,SPATA13
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004073
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00352,MTCO3P2,PCOTH,C1QTNF9B,ANKRD20A19P,IPO7P2,MIR2276,SPATA13-AS1,C1QTNF9-AS1,NUS1P3,LINC00566,HMGA1P6,LINC00327,C1QTNF9,SGCG,SACS,TNFRSF19,MIPEP,SPATA13
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004088
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,RPLP1P13,SACS-AS1,LINC00352,MTCO3P2,PCOTH,C1QTNF9B,ANKRD20A19P,IPO7P2,MIR2276,SPATA13-AS1,C1QTNF9-AS1,NUS1P3,LINC00566,HMGA1P6,LINC00327,C1QTNF9,SGCG,SACS,TNFRSF19,MIPEP,SPATA13
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004814
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
PPIAP28,LINC00556,GJB2,GJB6,MIR4499,SLC35E1P1,RNU2-7P,RANP8,PPIAP27,RPSAP54,LATS2-AS1,RNU4-9P,RPS12P23,IPPKP1,SAP18,MRPL57,LINC01046,GRK6P1,GAPDHP52,RNA5SP25,ZDHHC20-IT1,HIST1H2BPS3,FNTAP2,RNU6-59P,RPS7P10,LINC00424,NME1P1,MTND3P1,FTH1P7,DDX39AP1,RPL7AP73,IPMKP1,RFESDP1,BASP1P1,ZMYM5,KRR1P1,LINC01072,GJA3,EEF1AKMT1,CNOT4P1,HNRNPA1P30,LATS2,SKA3,ESRRAP2,MIPEPP3,LINC00539,ZDHHC20,FGF9,RN7SL766P,LINC00621,ZMYM2,CRYL1,IFT88,IL17D,XPO4,MICU2,LINC00540
monteiro_19_ASD_discovery_cases_case26
Maternal
FTH1P7,DDX39AP1,RPL7AP73,IPMKP1,RFESDP1,BASP1P1,NUS1P2,RNY3P4,LINC00362,RNU6-58P,TATDN2P3,SDAD1P4,LINC00621,HMGA1P6,SGCG,SACS
prasad_12_ASD_discovery_cases-case69180
Unknown
Multiplex
Unknown
BASP1P1
Controls
No Control Data Available
No Animal Model Data Available