22q12.1-q12.2CNV Type: Deletion-Duplication
Largest CNV size: 3463521 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
Deletions within this region were found in four 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); a duplication within this region was also identified 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
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
digregorio_17_DD/ID_discovery_cases
Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
1015
Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
N/A
N/A
3000000
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
3463521
4
0
4
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
361914
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)
361914
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
digregorio_17_DD/ID_discovery_cases
Italian
aCGH
Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
ADM-2
Agilent CGH Analytics software ver. 4.0.81
qPCR
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
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
digregorio_17_DD/ID_discovery_cases-DECIPHER_300572
N/A
M
Developmental delay/intellectual disability
27851788
30827594
2975807
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002370
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
26221273
29477543
3256271
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004432
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
28441035
30276511
1835477
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004528
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
28278805
31742328
3463524
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004594
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
28856144
29506277
650134
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case102040
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
27731188
28093101
361914
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
digregorio_17_DD/ID_discovery_cases-DECIPHER_300572
qPCR
De novo
MIR3199-1,MIR3199-2,RN7SL757P,MIR5739,RN7SL162P,XBP1,ZNRF3-AS1,C22orf31,RNU6-810P,RNU6-1219P,RASL10A,SNORD125,RFPL4AP6,RPEP4,RNU6-331P,MIR6818,CNN2P1,LIF-AS1,OSM,CASTOR1,RNU6-564P,MTFP1,SDC4P,SIRPAP1,MIR3200,TTC28-AS1,HSCB,CCDC117,ZNRF3-IT1,RHBDD3,EWSR1,GAS2L1,RFPL1S,RFPL1,THOC5,NIPSNAP1,CABP7,UQCR10,ASCC2,LIF,TBC1D10A,SF3A1,CCDC157,SEC14L3,SEC14L4,GAL3ST1,PES1,TCN2,SLC35E4,DUSP18,PITPNB,CHEK2,ZNRF3,KREMEN1,EMID1,NEFH,NF2,ZMAT5,MTMR3,HORMAD2-AS1,HORMAD2,SEC14L6,OSBP2,TTC28,AP1B1,RNF215,SEC14L2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002370
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNA5SP495,MIR548J,HMGB1P10,ISCA2P1,RNU6-1066P,LINC01638,MIR3199-1,MIR3199-2,RN7SL757P,MIR5739,RN7SL162P,XBP1,ZNRF3-AS1,C22orf31,RNU6-810P,RNU6-1219P,RASL10A,SNORD125,RFPL4AP6,ASPHD2,SRRD,TFIP11,TPST2,CRYBA4,MIAT,LINC01422,LINC02554,TTC28-AS1,HSCB,CCDC117,ZNRF3-IT1,RHBDD3,EWSR1,GAS2L1,RFPL1S,RFPL1,HPS4,CRYBB1,MIATNB,MN1,PITPNB,CHEK2,ZNRF3,KREMEN1,EMID1,SEZ6L,TTC28,AP1B1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004432
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
MIR5739,RN7SL162P,XBP1,ZNRF3-AS1,C22orf31,RNU6-810P,RNU6-1219P,RASL10A,SNORD125,RFPL4AP6,RPEP4,RNU6-331P,MIR6818,CNN2P1,LIF-AS1,OSM,HSCB,CCDC117,ZNRF3-IT1,RHBDD3,EWSR1,GAS2L1,RFPL1S,RFPL1,THOC5,NIPSNAP1,CABP7,UQCR10,ASCC2,LIF,CHEK2,ZNRF3,KREMEN1,EMID1,NEFH,NF2,ZMAT5,MTMR3,HORMAD2-AS1,HORMAD2,TTC28,AP1B1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004528
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR5739,RN7SL162P,XBP1,ZNRF3-AS1,C22orf31,RNU6-810P,RNU6-1219P,RASL10A,SNORD125,RFPL4AP6,RPEP4,RNU6-331P,MIR6818,CNN2P1,LIF-AS1,OSM,CASTOR1,RNU6-564P,MTFP1,SDC4P,SIRPAP1,MIR3200,EIF4HP2,MORC2-AS1,TUG1,RN7SL633P,PLA2G3,MIR3928,RNF185-AS1,RNU6-1128P,PIK3IP1,RNA5SP496,LINC01521,RNU6-338P,RNU6-28P,H2AFZP6,MIR7109,HSCB,CCDC117,ZNRF3-IT1,RHBDD3,EWSR1,GAS2L1,RFPL1S,RFPL1,THOC5,NIPSNAP1,CABP7,UQCR10,ASCC2,LIF,TBC1D10A,SF3A1,CCDC157,SEC14L3,SEC14L4,GAL3ST1,PES1,TCN2,SLC35E4,DUSP18,SMTN,SELENOM,INPP5J,LIMK2,PISD,CHEK2,ZNRF3,KREMEN1,EMID1,NEFH,NF2,ZMAT5,MTMR3,HORMAD2-AS1,HORMAD2,SEC14L6,OSBP2,MORC2,RNF185,PIK3IP1-AS1,PATZ1,SFI1,PRR14L,TTC28,AP1B1,RNF215,SEC14L2,DRG1,EIF4ENIF1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004594
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
ZNRF3-AS1,C22orf31,RNU6-810P,RNU6-1219P,RASL10A,SNORD125,RFPL4AP6,ZNRF3-IT1,RHBDD3,EWSR1,GAS2L1,RFPL1S,RFPL1,THOC5,ZNRF3,KREMEN1,EMID1,NEFH,AP1B1
prasad_12_ASD_discovery_cases-case102040
Unknown
Unknown
Unknown
GAS2L1,ZNRF3,KREMEN1,EMID1,AP1B1,MIR3653,RHBDD3,C22orf31,EWSR1,SNORD125,RASL10A
Controls
No Control Data Available
No Animal Model Data Available