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2q12.2-q12.3CNV Type: Duplication


Largest CNV size: 1637793 bp

Statistics Box:
Number of Reports: 11



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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            Decipher Symbol

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
Excess of rare, inherited truncating mutations in autism.
Duplication
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
NA
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
 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
  NA NA
 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
  NA NA
 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
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