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13q14.3CNV Type: Deletion-Duplication


Largest CNV size: 66258 bp

Statistics Box:
Number of Reports: 9



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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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...
Duplication
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.
Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Deletion-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication

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
 
 
 183340
 1
 0
 1
 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
 60583
 7
 5
 12
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 66258
 1
 1
 2
 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
 540950
 0
 1
 1
 celestino-soper_11_ASD_discovery_cases
 ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
 99
 ASD
 
 87.88% Male
 322
 1
 0
 1
 o'roak_12_ASD_discovery_cases
 Autistic probands from the Simons Simplex Collection (SSC), from an initial cohort of 189 autism families
 122
 ASD/autism
 NA
 NA
 60583
 0
 1
 1
 iourov_12_ASD/ID/EP_discovery_cases
 Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
 54
 Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
 Range, 3 mos.-11 yrs.
 NA
 164989
 1
 0
 1
 engchuan_15_ASD_discovery_cases
 Samples from the Autism Genome Project (AGP)
 1892
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 N/A
 85.78% Male
 124790
 0
 2
 2
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 256748
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 69800
 0
 2
 2
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 66258
 0
 1
 1
 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
 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)
 774833
 0
 1
 1
 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
 1017325
 1
 2
 3
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 90556
 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
 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 (n=334) or Illumina 1M v3 (n=840)
 PennCNV, QuantiSNP, & GNOSIS
 
 
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 
 kaminsky_11_DD/ID/ASD_discovery_cases
  NA
 aCGH
  Agilent 44K or 105K
 
 Feature Extraction & DNA Analytics
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 celestino-soper_11_ASD_discovery_cases
 
 aCGH
  Agilent 1M
 ADM-2
 Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
 None
 o'roak_12_ASD_discovery_cases
  NA
 Exome capture
  Capture with NimbleGen EZ Exome V2.0, sequencing with Illumina GAIIx or HiSeq2000
 HMM
 mrsFAST aligner
 aCGH, Sanger sequencing
 iourov_12_ASD/ID/EP_discovery_cases
  Russian
 aCGH
  BACs aCGH
 
 
 None
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  sanders_11_ASD_discovery_controls
 
  Solid phase hybridization
  Illumina 1M v1 or Illumina 1M v3
  PennCNV, QuantiSNP, & GNOSIS
 
 
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K or 105K
 
  Feature Extraction & DNA Analytics
 
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  None
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  None
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)

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-AU025703
 
 
 Autism
 
 
 51066794
 51250133
  183340
 
 Deletion
 No
  sanders_11_ASD_discovery_cases-11083.p1
 8
 M
 Autism
 NA
 Full-scale IQ, 122; non-verbal IQ, 119; verbal IQ, 122
 49022622
 49083205
  60583
 hg18
 Duplication
 No
  sanders_11_ASD_discovery_cases-11276.p1
 7
 M
 Autism
 NA
 Full-scale IQ, 63; non-verbal IQ, 81; verbal IQ 59
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11446.p1
 8
 M
 Autism
 NA
 Full-scale IQ, 68; non-verbal IQ, 76; verbal IQ, 63
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11573.p1
 8
 M
 ASD
 NA
 Full-scale IQ, 68; non-verbal IQ, 85; verbal IQ, 51
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11592.p1
 10
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 109; verbal IQ, 122
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11625.p1
 11
 M
 Autism
 NA
 Full-scale IQ, 34; non-verbal IQ, 44; verbal IQ, 14
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-11780.p1
 4
 M
 Autism
 NA
 Full-scale IQ, 117; non-verbal IQ, 112; verbal IQ, 120
 49271585
 49271799
  214
 hg18
 Duplication
 No
  sanders_11_ASD_discovery_cases-12071.p1
 11
 F
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 102; verbal IQ, 112
 52065514
 52074190
  8676
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-12121.p1
 8
 M
 Autism
 NA
 Full-scale IQ, 130; non-verbal IQ, 134; verbal IQ, 110
 49271585
 49271799
  214
 hg18
 Deletion
 No
  sanders_11_ASD_discovery_cases-12430.p1
 9
 F
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 110; verbal IQ, 106
 49271585
 49271799
  214
 hg18
 Duplication
 No
  sanders_11_ASD_discovery_cases-12617.p1
 10
 F
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 112; verbal IQ, 106
 49271585
 49271799
  214
 hg18
 Duplication
 No
  sanders_11_ASD_discovery_cases-12742.p1
 4
 M
 ASD
 NA
 Full-scale IQ, 105; non-verbal IQ, 103; verbal IQ, 106
 49271585
 49271799
  214
 hg18
 Duplication
 No
  levy_11_ASD_discovery_cases-11083.p1
 NA
 M
 ASD
 NA
 NA
 49021857
 49088114
  66258
 hg18
 Duplication
 No
  levy_11_ASD_discovery_cases-11472.p1
 NA
 F
 ASD
 NA
 NA
 51811096
 51851390
  40295
 hg18
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002374
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 51189803
 51730753
  540950
 NCBI36
 Duplication
 Yes
  celestino-soper_11_ASD_discovery_cases-11455
 NA
 M
 ASD
 NA
 NA
 52158611
 52158933
  322
 hg19
 Deletion
 No
  o'roak_12_ASD_discovery_cases-case11083.p1
 NA
 M
 ASD/Autism
 Case also identified with de novo mutation. No additional clinical info available.
 High IQ. Non verbal IQ, 119
 49022622
 49083205
  60583
 hg18
 Duplication
 Yes
  iourov_12_ASD/ID/EP_discovery_cases-case39
 3 yrs.
 F
 Developmental delay/intellectual disability
 Hydrocephaly, seizures, facial dysmorphisms. Karyotype: 16qh-, 16qh-.
 Developmental delay/intellectual disability
 48903923
 49068912
  164989
 GRCh37/hg19
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case14135_2330
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 51046711
 51171501
  124790
 hg18
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case3128_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 49022622
 49083205
  60583
 hg18
 Duplication
 No
  krumm_15_ASD_discovery_cases-case13317.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 51287352
 51544100
  256748
 hg19
 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
  sanders_11_ASD_discovery_controls-11083.s1
  12
  F
  Control (matched sibling)
  NA
  NA
  49013405
  49083205
  69800
  hg18
  Duplication
  No
  sanders_11_ASD_discovery_controls-11298.s1
  13
  M
  Control (matched sibling)
  NA
  NA
  49022622
  49083205
  60583
  hg18
  Duplication
  No
  levy_11_ASD_discovery_controls-11083.s1
  NA
  F
  Control
  NA
  NA
  49021857
  49088114
  66258
  hg18
  Duplication
  No
  poultney_13_ASD_discovery_controls-control04C31069A
  N/A
  M
  Control
  NIMH Control (NIMH ID 68756)
 
  52539006
  53313838
  774833
  hg19
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900457_900457
  N/A
  N/A
  Control
  No previous psychiatric history
 
  49416729
  50434054
  1017325
  hg18
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900208_900208
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52017705
  52187095
  169390
  hg18
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB983717_1007842477
  N/A
  N/A
  Control
  No previous psychiatric history
 
  51632859
  52081863
  449004
  hg18
  Duplication
  No
  krumm_15_ASD_discovery_controls-control13589.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  52158823
  52249379
  90556
  hg19
  Duplication
  Yes

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gai_11_ASD_replication_cases-AU025703
 
 
 Inherited
 
 
 WDFY2, DHRS12
 
 sanders_11_ASD_discovery_cases-11083.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 RCBTB1
 
 sanders_11_ASD_discovery_cases-11276.p1
 
 
 Both parents
 Simplex (quad-proband unmatched)
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11446.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-11573.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-11592.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-11625.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-11780.p1
 
 
 Maternal
 Simplex (trio)
 NA
 0 genes
 
 sanders_11_ASD_discovery_cases-12071.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-12121.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-12430.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-12617.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 0 genes
 
 sanders_11_ASD_discovery_cases-12742.p1
 
 
 Both parents
 Simplex (trio)
 NA
 0 genes
 
 levy_11_ASD_discovery_cases-11083.p1
 
 
 Paternal
 Simplex
 Not segregated
 RCBTB1
 
 levy_11_ASD_discovery_cases-11472.p1
 
 
 Paternal
 Simplex
 Segregated
 THSD1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002374
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 WDFY2,DHRS12,CCDC70,ATP7B,ALG11,UTP14C,NEK5,NEK3
 
 celestino-soper_11_ASD_discovery_cases-11455
 
 
 Unknown
 Simplex
 NA
 WDFY2
 
 o'roak_12_ASD_discovery_cases-case11083.p1
 aCGH, Sanger sequencing
 
 Paternal
 Simplex (quad)
 Unknown
 RCBTB1
 
 iourov_12_ASD/ID/EP_discovery_cases-case39
 
 
 Unknown
 Unknown
 Unknown
 RB1,LPAR6,RCBTB2
 
 engchuan_15_ASD_discovery_cases-case14135_2330
 
 
 Unknown
 
 
 WDFY2
 
 engchuan_15_ASD_discovery_cases-case3128_3
 
 
 Unknown
 
 
 RCBTB1
 
 krumm_15_ASD_discovery_cases-case13317.p1
 1M-Duov3
 
 Maternal
 Simplex
 Segregated
 DLEU7,RNASEH2B,Intron (1/1),Exon (1/2),Exon (2/2),Exon (1/10),Intron (1/9),Intron (2/9),Intron (3/9),Intron (4/9),Intron (5/9),Exon (6/10),Intron (6/9),Intron (7/9),Intron (8/9),Intron (9/9),Exon (1/11),Intron (1/10),Intron (2/10),Intron (3/10),Intron (4/10),Intron (5/10),Exon (6/11),Intron (6/10),Intron (7/10),Intron (8/10),Intron (9/10),Exon (10/11),Intron (10/10),Exon (11/11)
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11083.s1
 
 
  Paternal
  Simplex (quad)
  NA
  RCBTB1
 
sanders_11_ASD_discovery_controls-11298.s1
 
 
  Maternal
  Simplex (quad)
  NA
  RCBTB1
 
levy_11_ASD_discovery_controls-11083.s1
 
 
  Paternal
  Simplex
  NA
  RCBTB1
 
poultney_13_ASD_discovery_controls-control04C31069A
 
 
  Unknown
 
 
  ATP7B,ALG11,UTP14C,NEK5,NEK3,THSD1,VPS36,CKAP2,HNRNPA1L2,SUGT1,LECT1
 
engchuan_15_ASD_discovery_controls-controlHABC_900457_900457
 
 
  Unknown
 
 
  DLEU1;DLEU2;DLEU7;KCNRG;MIR15A;MIR16-1;MIR3613;RNASEH2B;ST13P4;TRIM13
 
engchuan_15_ASD_discovery_controls-controlHABC_900208_900208
 
 
  Unknown
 
 
  HNRNPA1L2;LECT1;SUGT1;TPTE2P3
 
engchuan_15_ASD_discovery_controls-controlB983717_1007842477
 
 
  Unknown
 
 
  CKAP2;THSD1;THSD1P1;TPTE2P2;TPTE2P3;VPS36
 
krumm_15_ASD_discovery_controls-control13589.s1
  1M-Duov3
 
  Maternal
 
 
  WDFY2,Intron (1/11),Intron (2/11)
 

No Animal Model Data Available
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