2q12.2-q12.3CNV Type: Duplication
Largest CNV size: 1637793 bp
Statistics Box:
Number of Reports: 11
Number of Reports: 11
Summary Information
Summary statement in development
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
Rare deletions at the neurexin 3 locus in autism spectrum disorder.
Deletion
Phenotypic heterogeneity of genomic disorders and rare copy-number variants.
Deletion
Genome-wide copy number variation analysis in a Chinese autism spectrum disorder cohort.
Duplication
Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion
Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder.
Duplication
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
gai_11_ASD_replication_cases
Replication case samples derived from AGRE sets 1-3
593
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
1637793
0
1
1
girirajan_12_ASD/DD/ID_discovery_cases
Samples from affected children submitted to Signature Genomic Laboratories from 2008-2010.
32587
Developmental delay with or without congenital malformations
1473997
1
0
1
guo_17_ASD_discovery_cases
ASD subjects (with 343 trios) screened for rare, large (>1 Mb) CNVs
546
Diagnosis of ASD based on DSM-IV-TR criteria
Mean, 5.065 years
N/A
1544210
0
1
1
guo_18_ASD/DD/ID_discovery_cases
Patients from 180 families (153 simplex, 27 multiplex) with at least one proband diagnosed with ASD who had been been clinically evaluated at the Seattle Children's Autism Center from SAGE collection
213
Patients were ascertained based on the presence of a diagnosis of ASD, intellectual disability (ID) or developmental delay (DD). ASD diagnoses were confirmed by meeting cutoff criteria on the Autism Diagnostic Observation Schedule and DSM-5 criteria; cognitive abilities were assessed using age-appropriate cognitive batteries, including DAS-2, Wechsler tests (WPPSI-IV, WISC-V, WASI-2), and Mullen.
N/A
N/A
1644199
0
2
2
hnoonual_17_ASD_discovery_cases
Cohort of 114 Thai ASD probands (68 retrospective ASD cases with the use of chromosomal microarray/CMA as a second line test; 46 prospective ASD and developmental delay cases with the use of CMA as the first-tier test)
114
68 cases with non-syndromic ASD (61 of which also presented with intellectual disability) were diagnosed with ASD based on meeting DSM-IV criteria for ASD, whereas an additional 46 prospective ASD and DD cases were given a clinical diagnosis of ASD based on DSM-5 criteria.
Range, 1-18 years (at time of recruitment)
79.82% Male
1000000
0
1
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
2252019
3
1
4
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
1358869
0
1
1
kushima_18_SCZ_discovery_cases
Individuals predominantly recruited from the middle of Honshu Island (Japan)
2458
Cases were diagnosed with schizophrenia (SCZ) according to DSM-5 criteria.
Median age, 44 years
55.0% Male
1394456
1
0
1
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
1474000
1
0
1
quintela_17_DD/ID_discovery_cases
Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
573
All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
Range, 3 months-18 years
60.38% Male
1587494
1
0
1
vaags_11_ASD_replication_cases_2
Replication cohort consisting of patients referred to the Mayo Clinic
1796
Autism or pervasive developmental disorder (PDD)
NA
NA
1654579
1
0
1
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
1298069
0
1
1
girirajan_12_ASD/DD/ID_discovery_controls
Persons found to have no overt neurological disorders during screening for other studies
8329
Control
1473997
NA
NA
NA
guo_17_ASD_discovery_controls
Control subjects screened for rare, large (>1 Mb) CNVs
988
No history of ASD or any other psychiatric diseases; no family history of psychiatric, neurological or autoimmune diseases
Mean, 34.3 years
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
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
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
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
232123
0
1
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
None
girirajan_12_ASD/DD/ID_discovery_cases
aCGH
BACs aCGH, SignatureChipOS
FISH, aCGH, or confirmation by inheritance
guo_17_ASD_discovery_cases
Chinese Han
Solid phase hybridization
Illumina 370K or 660K BeadChip
PennCNV
qPCR
guo_18_ASD/DD/ID_discovery_cases
N/A
WGS
Illumina HiSeq X Ten
dCGH, Genome STRiP, LUMPY, WHAMG, CNVnator, DELLY
aCGH, Sanger sequencing
hnoonual_17_ASD_discovery_cases
Thai
Solid phase hybridization
Illumina Infinium CytoSNP-850K v1.1 BeadChip
BlueFuse Multi v4.3, GenomeStudio Data Analysis v.2011.1
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
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
kushima_18_SCZ_discovery_cases
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
quintela_17_DD/ID_discovery_cases
North West Spain
Array SNP
Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
Affymetrix ChAS v.1.2.2
None
vaags_11_ASD_replication_cases_2
NA
aCGH
Agilent 44K & 244K
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_12_ASD/DD/ID_discovery_controls
aCGH
BACs ACGH (SignatureChipoWG) or oligoarray (SignatureChipOS)
guo_17_ASD_discovery_controls
Chinese Han
Solid phase hybridization
Illumina 610K BeadChip
PennCNV
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
kushima_18_ASD/SCZ_discovery_controls
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
gai_11_ASD_replication_cases-AU013903
Autism
106270907
107908699
1637793
Unknown
Duplication
No
girirajan_12_ASD/DD/ID_discovery_cases-case37514
11 yrs.
M
Intellectual disability and ASD
Global developmental delays. Behavioral problems: ASD, anxiety, ADHD, trichotillomania, Tourette syndrome. Normal tone. Nondysmorphic. Growth parameters: weight 10th-25th %ile, height 10th %ile, OFC +0.4 SD. Family history: not specified.
Mild ID and global developmental delays
106312800
107786797
1473998
GRCh38
Deletion
Yes
guo_17_ASD_discovery_cases-caseM16053
N/A
N/A
ASD
Diagnosis of ASD based on DSM-IV-TR criteria; no other clinical information available
106262145
107806354
1544210
GRCh38
Duplication
Yes
guo_18_ASD/DD/ID_discovery_cases-caseBK-246-03
N/A
M
ASD and learning disabilities
Plagiocephaly, GI problems
Learning disabilities; FSIQ 100, NVIQ 94, VIQ 106
106270001
107914000
1644000
GRCh38
Duplication
Yes
guo_18_ASD/DD/ID_discovery_cases-caseBK-246-05
N/A
M
ASD and intellectual disability
Epilepsy, hypotonia
Intellectual disability (FSIQ 19, NVIQ 20, VIQ 17)
106269401
107913600
1644200
GRCh38
Duplication
Yes
hnoonual_17_ASD_discovery_cases-caseRA15
N/A
M
ASD and intellectual disability
No additional clinical features
Intellectual disability
106020971
107026026
1005056
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001976
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
106260759
107904531
1643773
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004028
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
106261594
107786796
1525203
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004732
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
105828398
108080417
2252020
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004948
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
106261594
107786796
1525203
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case14250.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
106468216
107827085
1358870
GRCh38
Duplication
Yes
kushima_18_SCZ_discovery_cases-caseSCZ0208
47 yrs.
F
Schizophrenia
Behavioral/psychiatric evaluation: onset of schizophrenia at 30 years of age (core symptoms include persecutory delusions, visual and auditory hallucinations). Family history: positive for schizophrenia (SCZ).
IQ > 70
106445028
107839483
1394456
GRCh38
Deletion
N/A
maini_18_ASD/DD/ID_discovery_cases-case_unknown133
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
106312601
107786937
1474337
GRCh38
Deletion
No
quintela_17_DD/ID_discovery_cases-caseID_409
12 yrs.
M
Intellectual disability
Additional clinical information N/A
Mild intellectual disability
106236807
107824300
1587494
GRCh38
Deletion
No
vaags_11_ASD_replication_cases_2-probandF4-003
3 yrs. 6 mos.
M
Autism
Diagnosis of autism based on clinical diagnosis, C-TRF (Caregiver-Teacher Report Form), and DSM-Oriented Scales for Boys (>97th %ile). Aggression, anger, anxiety, temper tantrums, social avoidance, sucking and biting of hands and fingers, sleep-onset disorder, upper-body hypotonia, thumb-flexion difficulty, oppositional defiance, previous head banging, and prior speech delay
Leiter-R IQ: incomplete (test attempted but proband failed to complete)
106261594
107916172
1654579
GRCh38
Deletion
Yes
Controls
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_controls-controlHABC_901266_901266
N/A
N/A
Control
No previous psychiatric history
106587654
107885723
1298070
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-13070.s1
11.6
M
Control (matched sibling)
NA
NA
106554145
106786268
232124
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
gai_11_ASD_replication_cases-AU013903
Inherited
PLGLA, RGPD3, ST6GAL2, ST6GAL2, LOC729121, RGPD4
girirajan_12_ASD/DD/ID_discovery_cases-case37514
FISH, aCGH, or confirmation by inheritance
Unknown
Unknown
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
guo_17_ASD_discovery_cases-caseM16053
qPCR
Paternal
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
guo_18_ASD/DD/ID_discovery_cases-caseBK-246-03
aCGH, Sanger sequencing
Paternal
Multiplex
Incomplete segregation
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
guo_18_ASD/DD/ID_discovery_cases-caseBK-246-05
aCGH, Sanger sequencing
Paternal
Multiplex
Incomplete segregation
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
hnoonual_17_ASD_discovery_cases-caseRA15
Maternal
RPL22P10,PLGLA,EEF1A1P12,PPP1R2P5,C2orf40,CD8B2,UXS1,RGPD3,ST6GAL2,ST6GAL2-IT1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001976
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004028
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004732
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
RPL22P10,PLGLA,EEF1A1P12,PPP1R2P5,RPL22P8,C2orf40,CD8B2,LINC01886,GACAT1,RGPD4-AS1,LINC01593,NCK2,UXS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4,SLC5A7
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004948
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
krumm_15_ASD_discovery_cases-case14250.p1
Omni2.5-4v1
Maternal
Simplex
Segregated
EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
kushima_18_SCZ_discovery_cases-caseSCZ0208
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
Not simplex
EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
maini_18_ASD/DD/ID_discovery_cases-case_unknown133
Maternal
Unknown
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
quintela_17_DD/ID_discovery_cases-caseID_409
Unknown
Unknown
RPL22P10,PLGLA,EEF1A1P12,PPP1R2P5,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885
vaags_11_ASD_replication_cases_2-probandF4-003
FISH
Maternal
Simplex
Unknown
PLGLA,EEF1A1P12,PPP1R2P5,RPL22P8,CD8B2,LINC01886,GACAT1,RGPD4-AS1,RGPD3,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_901266_901266
Unknown
EEF1A1P12,PPP1R2P5,LINC01886,GACAT1,RGPD4-AS1,ST6GAL2,ST6GAL2-IT1,LINC01789,LINC01885,RGPD4
sanders_11_ASD_discovery_controls-13070.s1
Maternal
Simplex (quad)
NA
EEF1A1P12
No Animal Model Data Available