21q22.2-q22.3CNV Type: Deletion
Largest CNV size: 6493264 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
Rare singleton deletion within this region was found in a case 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).
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
Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
The Role of mGluR Copy Number Variation in Genetic and Environmental Forms of Syndromic Autism Spectrum Disorder.
Deletion
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Deletion
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
6493264
1
0
1
kim_18_DD/ID_discovery_cases
Individuals who had visited Konyang University Hospital for evaluation of unexplained DD/ID in a one year period (September 2013-October 2014)
50
All cases presented with developmental delay/intellectual disability (DD/ID); 19 cases (38.0 %) presented with epilepsy, 9 cases (18.0%) presented with autism
Mean age, 5.4 5.9 yrs. (Range, 0.1-32 yrs.)
52.0% Male
816000
0
1
1
kushima_18_ASD_discovery_cases
Individuals predominantly recruited from the middle of Honshu Island (Japan)
1108
Cases were diagnosed with ASD according to DSM-5 criteria, with diagnostic and screening instruments (ADI-R, ADOS, ASQ, and SRS) used to evaluate ASD-related behaviors and symptoms in the majority of cases.
Median age, 19 years
78.0% Male
2587119
1
0
1
kushima_22_ASD_discovery_cases
Japanese ASD probands evaluated for copy number variation from an initial cohort of 1,236 probands before quality control.
1205
Cases diagnosed with autism spectrum disorder (ASD) according to DSM-5 criteria.
Median age, 19 yrs.
77.6% Male
2587120
1
0
1
wenger_16_ASD_discovery_cases
ASD cases with CNVs containing genes involved in the mGluR network from an initial cohort of 539 cases
62
ASD
N/A
N/A
6492846
1
0
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
kushima_18_ASD/SCZ_discovery_controls
Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
2095
Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
Median age, 37 years
52.0% Male
0
0
0
0
kushima_22_ASD/BPD/SCZ_discovery_controls
Psychiatrically normal control individuals selected from the general population evaluated for copy number variation from an initial cohort of 2,713 control individuals before quality control.
2671
Controls were psychiatrically normal and had no history of mental disorders based on responses to questionnaires or self-reporting.
Median age, 36 yrs.
47.8% 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, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
kim_18_DD/ID_discovery_cases
Korean
Array SNP
Affymetrix CytoScan 750K
Affymetrix ChAS
None
kushima_18_ASD_discovery_cases
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD_discovery_cases
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
wenger_16_ASD_discovery_cases
N/A
Solid phase hybridization
Illumina HumanHap 550 or Illumina Human610-Quad v1.0
PennCNV
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
kushima_18_ASD/SCZ_discovery_controls
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD/BPD/SCZ_discovery_controls
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
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-ISCA00004387
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
40127825
46670546
6542722
GRCh38
Deletion
Yes
kim_18_DD/ID_discovery_cases-case16
1 yr.
M
Developmental delay
Dysmorphic features, failure to thrive, atrophic dermatitis
Developmental delay
40519737
41336178
816442
GRCh38
Duplication
No
kushima_18_ASD_discovery_cases-caseASD0167
26 yrs.
M
ASD, ID, epilepsy/seizures
Epilepsy/seizures: positive for epileptic seizures/epilepsy. Family history: negative.
Intellectual disability (IQ < 70)
38981673
41568791
2587119
GRCh38
Deletion
N/A
kushima_22_ASD_discovery_cases-caseASD0167
NA
NA
ASD
Diagnosis of ASD according to DSM-5 criteria.
38981672
41568791
2587120
GRCh38
Deletion
Yes
wenger_16_ASD_discovery_cases-case19
N/A
N/A
ASD
Prior clinical diagnosis of genetic syndrome: Deletion of 6.53 Mb region within 21q22.2q22.3; Mosaic deletion of 1.06 Mb region within 21q22.2
40220217
46665077
6444861
GRCh38
Deletion
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-ISCA00004387
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR4760,DSCAM-AS1,YRDCP3,LINC00323,MIR3197,PLAC4,BACE2-IT1,LINC00112,MIR6814,ZNF295-AS1,RNA5SP492,TFF3,TFF2,TFF1,RNU6-1149P,ERVH48-1,MIR5692B,MRPL51P2,FRGCA,LINC00322,LINC01679,RPL31P1,MIR6070,CSTB,TMEM97P1,MYL6P1,RNU6-859P,RNU6-1150P,H2AFZP1,LINC01678,LRRC3-DT,LRRC3,MTCYBP21,MTND6P21,MTND5P1,LINC02575,TSPEAR-AS2,KRTAP10-1,KRTAP10-2,KRTAP10-3,KRTAP10-5,KRTAP10-6,KRTAP10-7,KRTAP10-8,KRTAP10-9,KRTAP10-10,KRTAP10-11,KRTAP12-4,KRTAP12-3,KRTAP12-2,IMMTP1,KRTAP12-1,KRTAP12-6P,KRTAP10-12,KRTAP10-13P,LINC01424,LINC01547,LINC00165,PICSAR,LINC00205,LINC00316,MTCO1P3,COL18A1-AS2,COL18A1-AS1,MIR6815,PSMA6P3,FTCD-AS1,YBEY,RPL18AP2,RNU6-396P,S100B,DSTNP1,DSCAM-IT1,BACE2,FAM3B,MX2,MX1,TMPRSS2,LINC00479,RIPK4,ZBTB21,UMODL1-AS1,TMPRSS3,UBASH3A,RSPH1,SLC37A1,LINC01671,LINC01668,NDUFV3,CBS,U2AF1,CRYAA,SIK1,LINC00319,LINC00313,RRP1B,PDXK,RRP1,AATBC,PWP2,ICOSLG,DNMT3L,AIRE,CFAP410,TRPM2-AS,TSPEAR-AS1,KRTAP10-4,UBE2G2,SUMO3,PTTG1IP,ITGB2,ITGB2-AS1,LINC00163,SSR4P1,LINC00334,POFUT2,LINC00315,SLC19A1,LINC01694,COL6A1,COL6A2,SPATC1L,LSS,MCM3AP-AS1,C21orf58,DIP2A-IT1,DSCAM,LINC00111,PRDM15,UMODL1,ABCG1,PDE9A,WDR4,HSF2BP,AGPAT3,GATD3A,PFKL,TRPM2,TSPEAR,FAM207A,COL18A1,PCBP3,MCM3AP,PCNT,DIP2A,PRMT2,PKNOX1,TRAPPC10,ADARB1,FTCD,C2CD2
kim_18_DD/ID_discovery_cases-case16
Paternal
YRDCP3,LINC00323,MIR3197,PLAC4,BACE2-IT1,DSCAM-IT1,BACE2,FAM3B,DSCAM
kushima_18_ASD_discovery_cases-caseASD0167
While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
Unknown
Simplex
Unknown
RPL23AP12,PCBP2P1,PSMG1,TIMM9P2,BRWD1-IT1,METTL21AP1,BRWD1-AS2,HMGN1,RNF6P1,MIR6508,MYL6P2,RPS26P4,MIR4760,DSCAM-AS1,YRDCP3,LINC00323,MIR3197,PLAC4,BACE2-IT1,WRB,LCA5L,B3GALT5-AS1,IGSF5,PCP4,DSCAM-IT1,BACE2,FAM3B,MX2,MX1,TMPRSS2,BRWD1,BRWD1-AS1,WRB-SH3BGR,SH3BGR,B3GALT5,DSCAM
kushima_22_ASD_discovery_cases-caseASD0167
qRT-PCR
Unknown
DSCAM,BRWD1,FAM3B,B3GALT5-AS1,IGSF5,LCA5L,PLAC4,HMGN1,BACE2-IT1,LINC00323,RPL23AP12,RPS26P4,JCADP1,MX1,MX2,RNF6P1,METTL21AP1,MIR3197,MYL6P2,DSCAM-AS1,MIR4760,TIMM9P2,YRDCP3,BRWD1-AS1,DSCAM-IT1,PCBP2P1,PCP4,MIR6508,BRWD1-AS2,TMPRSS2,SH3BGR,BRWD1-IT1,GET1-SH3BGR,GET1,PSMG1,B3GALT5,BACE2
wenger_16_ASD_discovery_cases-case19
Unknown
DSCAM-AS1,YRDCP3,LINC00323,MIR3197,PLAC4,BACE2-IT1,LINC00112,MIR6814,ZNF295-AS1,RNA5SP492,TFF3,TFF2,TFF1,RNU6-1149P,ERVH48-1,MIR5692B,MRPL51P2,FRGCA,LINC00322,LINC01679,RPL31P1,MIR6070,CSTB,TMEM97P1,MYL6P1,RNU6-859P,RNU6-1150P,H2AFZP1,LINC01678,LRRC3-DT,LRRC3,MTCYBP21,MTND6P21,MTND5P1,LINC02575,TSPEAR-AS2,KRTAP10-1,KRTAP10-2,KRTAP10-3,KRTAP10-5,KRTAP10-6,KRTAP10-7,KRTAP10-8,KRTAP10-9,KRTAP10-10,KRTAP10-11,KRTAP12-4,KRTAP12-3,KRTAP12-2,IMMTP1,KRTAP12-1,KRTAP12-6P,KRTAP10-12,KRTAP10-13P,LINC01424,LINC01547,LINC00165,PICSAR,LINC00205,LINC00316,MTCO1P3,COL18A1-AS2,COL18A1-AS1,MIR6815,PSMA6P3,FTCD-AS1,YBEY,RPL18AP2,RNU6-396P,S100B,DSTNP1,DSCAM-IT1,BACE2,FAM3B,MX2,MX1,TMPRSS2,LINC00479,RIPK4,ZBTB21,UMODL1-AS1,TMPRSS3,UBASH3A,RSPH1,SLC37A1,LINC01671,LINC01668,NDUFV3,CBS,U2AF1,CRYAA,SIK1,LINC00319,LINC00313,RRP1B,PDXK,RRP1,AATBC,PWP2,ICOSLG,DNMT3L,AIRE,CFAP410,TRPM2-AS,TSPEAR-AS1,KRTAP10-4,UBE2G2,SUMO3,PTTG1IP,ITGB2,ITGB2-AS1,LINC00163,SSR4P1,LINC00334,POFUT2,LINC00315,SLC19A1,LINC01694,COL6A1,COL6A2,SPATC1L,LSS,MCM3AP-AS1,C21orf58,DIP2A-IT1,DSCAM,LINC00111,PRDM15,UMODL1,ABCG1,PDE9A,WDR4,HSF2BP,AGPAT3,GATD3A,PFKL,TRPM2,TSPEAR,FAM207A,COL18A1,PCBP3,MCM3AP,PCNT,DIP2A,PRMT2,PKNOX1,TRAPPC10,ADARB1,FTCD,C2CD2
Controls
No Control Data Available
No Animal Model Data Available