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3q11.2CNV Type: Deletion-Duplication


Largest CNV size: 236686 bp

Statistics Box:
Number of Reports: 8



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
Structural variation of chromosomes in autism spectrum disorder.
Duplication
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
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
 692354
 0
 1
 1
 krumm_13_ASD_discovery_cases
 Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 81.265% Male
 147929
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 147929
 1
 0
 1
 marshall_08_ASD_discovery_cases
 Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
 427
 ASD
 
 
 83443
 0
 1
 1
 pinto_10_ASD_discovery_cases
 Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
 996
 ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
 
 
 236686
 0
 1
 1
 poultney_13_ASD_discovery_cases
 ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
 299
 Cases diagnosed with ASD
 N/A
 79.86% Male (before filtering)
 411463
 0
 2
 2
 sanders_11_ASD_discovery_cases
 Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
 1124
 ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
 Mean, 9.1 yrs.
 86.1% Male
 152018
 8
 2
 10
 yin_16_ASD_discovery_cases
 Discovery cohort of ASD cases recruited from the Department of Psychiatry of National Taiwan University Hospital (NTUH), Chang Gung Memorial Hospital (CGMH), Taoyuan, and Taoyuan Mental Hospital (TMH), Taiwan.
 335
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R. Cases' autistic behaviors assessed by Social Responsiveness Scale (SRS), and cognitive functions assessed by the Weschler Intelligence Scale for Children-Third Edition (WISC-III) and the Wisconsin Card Sorting Test (WCST).
 Mean, 9.39 4.04 yrs.
 89.3% Male
 298719
 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
 krumm_13_ASD_discovery_controls
 Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 46.47% Male
 0
 0
 0
 0
 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
 marshall_08_ASD_discovery_controls_1
 German PopGen project and entries from Database of Genomic Variants
 500
 Controls
 
 
 0
 0
 0
 0
 marshall_08_ASD_discovery_controls_2
 Non-disease controls from Ontario population
 1152
 Controls
 
 
 0
 0
 0
 0
 poultney_13_ASD_discovery_controls
 Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
 260
 Control
 N/A
 47.49% Male (before filtering)
 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.
 
 67482
 4
 3
 7
 yin_16_ASD_discovery_controls
 Individuals from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
 1093
 Controls
 Mean, 68.07 10.12 yrs.
 48.0% Male
 298719
 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
 krumm_13_ASD_discovery_cases
  N/A
 WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
 DNACopy, CGHCall
 CoNIFER
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 marshall_08_ASD_discovery_cases
  90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
 Array SNP, karotyping
  Affymetrix 500K
 dChip, CNAG, GEMCA
 
 qPCR, qmPCR
 pinto_10_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium 1M SNP microarray
 QuantiSNP, iPattern
 
 qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 sanders_11_ASD_discovery_cases
  White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
 Solid phase hybridization
  Illumina 1M v1, Illumina 1M v3
 PennCNV, QuantiSNP, GNOSIS
 
 
 yin_16_ASD_discovery_cases
  Han Chinese
 Array SNP
  Affymetrix 6.0
 
 Affymetrix Genotyping Console v.4.1
 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
 
  krumm_13_ASD_discovery_controls
  N/A
  WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
  DNACopy, CGHCall
  CoNIFER
  None
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  None
  marshall_08_ASD_discovery_controls_1
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  marshall_08_ASD_discovery_controls_2
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
 
  sanders_11_ASD_discovery_controls
 
  Solid phase hybridization
  Illumina 1M v1 or Illumina 1M v3
  PennCNV, QuantiSNP, GNOSIS
 
 
  yin_16_ASD_discovery_controls
  Han Chinese
  Array SNP
  Affymetrix 6.0
 
  Affymetrix Genotyping Console v.4.1
  None

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-ISCA00005195
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 95446191
 96138545
  692355
 GRCh38
 Duplication
 Yes
  krumm_13_ASD_discovery_cases-case13099.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 13099. SRS score of 86.
 Full-scale IQ (FSIQ) score of 92.
 97768107
 97916036
  147930
 GRCh38
 Deletion
 No (not tested)
  krumm_15_ASD_discovery_cases-case13099.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 97768107
 97916036
  147930
 GRCh38
 Deletion
 Yes
  marshall_08_ASD_discovery_cases-SK0023-003
 NA
 M
 ASD
 RL/EL moderate/severe delay, moderate speech unintelligibility and repetitive behavior, seizures
 IQ/LOF 82
 98199423
 98282866
  83444
 GRCh38
 Duplication
 Yes
  pinto_10_ASD_discovery_cases-case6203_4
 NA
 M
 Autism
 Language delay, normal physical exam, no epilepsy
 Severe MR
 94994003
 95230688
  236686
 Unknown
 Duplication
 Yes
  poultney_13_ASD_discovery_cases-case00HI1663A
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU056708; NDAR ID NDAR_INVAC801FDF)
 
 98087171
 98498633
  411463
 GRCh38
 Duplication
 No
  poultney_13_ASD_discovery_cases-case98HI0587A
 N/A
 M
 ASD
 ASD case from AGRE (AGRE ID AU020003; NDAR ID NDAR_INVRL878MR0)
 
 98132696
 98498633
  365938
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11041.p1
 13
 M
 Autism
 NA
 Full-scale IQ, 47; non-verbal IQ, 39; verbal IQ, 60
 95980302
 95994505
  14204
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11540.p1
 8.2
 M
 Autism
 NA
 Full-scale IQ, 59; non-verbal IQ, 67; verbal IQ, 55
 95980302
 95994505
  14204
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11625.p1
 11.6
 M
 Autism
 NA
 Full-scale IQ, 34; non-verbal IQ, 44; verbal IQ, 14
 94680561
 94689462
  8902
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11712.p1
 5.5
 M
 ASD
 NA
 Full-scale IQ, 79; non-verbal IQ, 94; verbal IQ, 60
 93786469
 93938487
  152019
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11910.p1
 5.8
 M
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 108; verbal IQ, 113
 96393335
 96452678
  59344
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11913.p1
 4.5
 F
 Autism
 NA
 Full-scale IQ, 102; non-verbal IQ, 99; verbal IQ, 105
 94680561
 94689462
  8902
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11979.p1
 7.5
 M
 ASD
 NA
 Full-scale IQ, 107; non-verbal IQ, 104; verbal IQ, 114
 94680561
 94689462
  8902
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12343.p1
 6.2
 F
 Autism
 NA
 Full-scale IQ, 30; non-verbal IQ, 42; verbal IQ, 18
 98215955
 98265712
  49758
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12960.p1
 6.6
 M
 Autism
 NA
 Full-scale IQ, 47; non-verbal IQ, 52; verbal IQ, 42
 98465103
 98493673
  28571
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13015.p1
 5.3
 M
 Autism
 NA
 Full-scale IQ, 78; non-verbal IQ, 80; verbal IQ, 81
 95980302
 95994505
  14204
 GRCh38
 Deletion
 No
  yin_16_ASD_discovery_cases-case118
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 94962568
 95261286
  298719
 GRCh38
 Deletion
 No

Controls

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  sanders_11_ASD_discovery_controls-11041.s1
  15.7
  M
  Control (matched sibling)
  NA
  NA
  95980302
  95994505
  14204
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11540.s1
  14.7
  F
  Control (matched sibling)
  NA
  NA
  95980302
  95994505
  14204
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11597.s1
  9
  M
  Control (matched sibling)
  NA
  NA
  95958848
  95994505
  35658
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12289.s1
  16.3
  M
  Control (matched sibling)
  NA
  NA
  94776175
  94843657
  67483
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12343.s1
  8
  F
  Control (matched sibling)
  NA
  NA
  98215955
  98265712
  49758
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12669.s1
  13.2
  M
  Control (matched sibling)
  NA
  NA
  95980302
  95994505
  14204
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13015.s1
  7.1
  F
  Control (matched sibling)
  NA
  NA
  95980302
  95994505
  14204
  GRCh38
  Deletion
  No

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-ISCA00005195
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 MTHFD2P1
 
 krumm_13_ASD_discovery_cases-case13099.p1
 
 
 Paternal
 Simplex
 Segregated
 ARL6,CRYBG3
 
 krumm_15_ASD_discovery_cases-case13099.p1
 1M-Duov3
 
 Paternal
 Simplex
 Segregated
 ARL6,CRYBG3
 
 marshall_08_ASD_discovery_cases-SK0023-003
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 OR5H3P,OR5H6,OR5H4P,OR5H7P
 
 pinto_10_ASD_discovery_cases-case6203_4
 qPCR
 
 maternal
 Simplex
 NA
 STX19 exonic, ARL13B exonic, PROS1 whole
 
 poultney_13_ASD_discovery_cases-case00HI1663A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 OR5AC2,OR5AC4P,POU5F1P7,OR5H1,OR5H15,OR5H5P,OR5H3P,OR5H6,OR5H2,OR5H8,OR5K4,OR5K3,UBFD1P1,OR5K2,OR5H14,OR5H4P,OR5H7P,OR5K1,CLDND1
 
 poultney_13_ASD_discovery_cases-case98HI0587A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 OR5H1,OR5H15,OR5H5P,OR5H3P,OR5H6,OR5H2,OR5H8,OR5K4,OR5K3,UBFD1P1,OR5K2,OR5H14,OR5H4P,OR5H7P,OR5K1,CLDND1
 
 sanders_11_ASD_discovery_cases-11041.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11540.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11625.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11712.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 RNU6-488P,PROS1
 
 sanders_11_ASD_discovery_cases-11910.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-11913.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11979.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 sanders_11_ASD_discovery_cases-12343.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 OR5H6,OR5H4P,OR5H7P
 
 sanders_11_ASD_discovery_cases-12960.p1
 
 
 Maternal
 Simplex (trio)
 NA
 OR5K1
 
 sanders_11_ASD_discovery_cases-13015.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 yin_16_ASD_discovery_cases-case118
 
 
 Unknown
 Unknown
 Unknown
 RPS18P6,LINC00879
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11041.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11540.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11597.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12289.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12343.s1
 
 
  Paternal
  Simplex (quad)
  NA
  OR5H6,OR5H4P,OR5H7P
 
sanders_11_ASD_discovery_controls-12669.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-13015.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 

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