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3q27.1CNV Type: Deletion


Largest CNV size: 11468 bp

Statistics Box:
Number of Reports: 7



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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Deletion
The landscape of copy number variations in Finnish families with autism spectrum disorders.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 1490
 1
 0
 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
 456662
 1
 1
 2
 kanduri_15_ASD_discovery_cases
 Autistic cases from an initial sample of 83 Finnish families comprising 257 family members following quality control
 80
 Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patients screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and Asperger's Syndrome Diagnostic Interview.
 N/A
 N/A
 164696
 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
 184332
 2
 0
 2
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 39242
 1
 0
 1
 prasad_12_ASD_discovery_cases
 Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
 676
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
 NA
 82.84% Male
 32372
 1
 3
 4
 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
 11468
 2
 0
 2

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
 kanduri_15_ASD_discovery_controls
 Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
 269
 Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 N/A
 N/A
 0
 0
 0
 0
 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
 2372
 1
 0
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 31311
 0
 1
 1
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 73966
 0
 2
 2
 nord_11_ASD_discovery_controls
 Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
 123
 Controls (no history of psychiatric symptoms by self-report)
 30 yrs.
 
 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)
 216540
 0
 1
 1
 prasad_12_ASD_discovery_controls
 PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
 5139
 Control
 NA
 NA (PDx controls 50.2% male)
 32372
 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.
 
 39384
 2
 1
 3

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 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
 kanduri_15_ASD_discovery_cases
  Finnish
 Solid phase hybridization
  Illumina Human OmniExpress-12v1.0 BeadChip
 QuantiSNP, PennCNV
 Illumina BeadStudio
 None
 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
 nord_11_ASD_discovery_cases
  29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
 aCGH
  NimbleGen HD2
 Sliding-window algorithm, ~10 kb minumum size threshold
 
 None
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 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
 
 

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
 
  kanduri_15_ASD_discovery_controls
  Finnish
  Solid phase hybridization
  Illumina Infinium HD Human610-Quad BeadChip
  QuantiSNP, PennCNV
  Illumina BeadStudio
  None
  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
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  nord_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  Sliding-window algorithm, ~10 kb minumum size threshold
 
  None
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  None
  prasad_12_ASD_discovery_controls
  NA
  aCGH
  Agilent 1M
  ADM-2, DNAcopy (R Bioconductor)
  DNA Analytics v4.0.85 (Agilent), DNAcopy
 
  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
  celestino-soper_11_ASD_discovery_cases-11197
 NA
 M
 ASD
 NA
 NA
 184287854
 184289344
  1491
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002138
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 184200139
 184656801
  456663
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004427
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 184239109
 184391437
  152329
 GRCh38
 Deletion
 Yes
  kanduri_15_ASD_discovery_cases-case1970
 N/A
 N/A
 ASD
 Diagnosis of ASD based on DSM-IV, 4th edition, or ICD-10 criteria; patient screened based on Childhood Autism Rating Scale (CARS), Asperger Syndrome Screening Questionnaire, and/or Asperger's Syndrome Diagnostic Interview.
 
 183881775
 184046470
  164696
 Unknown
 Duplication
 No
  krumm_13_ASD_discovery_cases-case11075.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 11075. SRS score of 67.
 Full-scale IQ (FSIQ) score of 39.
 184387050
 184571382
  184333
 GRCh38
 Deletion
 No (not tested)
  krumm_13_ASD_discovery_cases-case11788.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 11788. SRS score of 84.
 Full-scale IQ (FSIQ) score of 84.
 184104786
 184105969
  1184
 GRCh38
 Deletion
 No (not tested)
  nord_11_ASD_discovery_cases-207-1
 
 
 ASD
 
 
 184497339
 184536580
  39242
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case133142
 NA
 F
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 185696902
 185729273
  32372
 Unknown
 Deletion
 No
  prasad_12_ASD_discovery_cases-case165216L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 185220547
 185231471
  10925
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case165447L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 185216329
 185232994
  16666
 Unknown
 Duplication
 No
  prasad_12_ASD_discovery_cases-case69812
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 185220547
 185231471
  10925
 Unknown
 Duplication
 No
  sanders_11_ASD_discovery_cases-12456.p1
 14.3
 F
 Autism
 NA
 Full-scale IQ, 40; non-verbal IQ, 45; verbal IQ, 30
 183475370
 183476938
  1569
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13195.p1
 8.3
 M
 Autism
 NA
 Full-scale IQ, 76; non-verbal IQ, 88; verbal IQ, 63
 183266103
 183277571
  11469
 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
  krumm_13_ASD_discovery_controls-control11075.s1
  N/A
  M
  Control
  Unaffected sibling from SSC quad family 11075. SRS score of 36.
 
  184387050
  184389422
  2373
  GRCh38
  Deletion
  No (not tested)
  krumm_15_ASD_discovery_controls-control12187.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  184290792
  184322103
  31312
  GRCh38
  Duplication
  Yes
  levy_11_ASD_discovery_controls-11961.s1
  NA
  M
  Control
  NA
  NA
  183417519
  183491484
  73966
  GRCh38
  Duplication
  No
  levy_11_ASD_discovery_controls-12187.s1
  NA
  F
  Control
  NA
  NA
  184291724
  184321260
  29537
  GRCh38
  Duplication
  No
  poultney_13_ASD_discovery_controls-control04C28760A
  N/A
  M
  Control
  NIMH Control (NIMH ID 97777)
 
  184136610
  184353149
  216540
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11196.s1
  10
  M
  Control (matched sibling)
  NA
  NA
  183338810
  183378194
  39385
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12187.s1
  10.2
  F
  Control (matched sibling)
  NA
  NA
  184291798
  184322956
  31159
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12456.s1
  12
  M
  Control (matched sibling)
  NA
  NA
  183475370
  183476718
  1349
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 celestino-soper_11_ASD_discovery_cases-11197
 
 
 Unknown
 Simplex
 NA
 EEF1AKMT4-ECE2,ECE2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002138
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 MIR1224,ALG3,CAMK2N2,SNORD66,POLR2H,THPO,LINC01839,VWA5B2,EEF1AKMT4,PSMD2,EIF4G1,FAM131A,CLCN2,CHRD,EPHB3,EEF1AKMT4-ECE2,ECE2,LINC02054,LINC01840
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004427
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 MIR1224,ALG3,CAMK2N2,SNORD66,POLR2H,THPO,VWA5B2,EEF1AKMT4,PSMD2,EIF4G1,FAM131A,CLCN2,CHRD,EEF1AKMT4-ECE2,ECE2
 
 kanduri_15_ASD_discovery_cases-case1970
 
 
 Paternal
 Unknown
 Unknown
 ABCF3,ALG3,AP2M1,CAMK2N2,DVL3,ECE2,EIF4G1,PSMD2,VWA5B2
 
 krumm_13_ASD_discovery_cases-case11075.p1
 
 
 Maternal
 Simplex
 Not segregated
 LINC01839,CHRD,EPHB3,LINC02054,LINC01840
 
 krumm_13_ASD_discovery_cases-case11788.p1
 
 
 Maternal
 Simplex
 Segregated
 HTR3E-AS1,HTR3E
 
 nord_11_ASD_discovery_cases-207-1
 
 
 Paternal
 
 
 MCF2L2
 
 prasad_12_ASD_discovery_cases-case133142
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-case165216L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 prasad_12_ASD_discovery_cases-case165447L
 
 
 Unknown
 Unknown
 Unknown
 ABCC5,HTR3D
 
 prasad_12_ASD_discovery_cases-case69812
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-12456.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-13195.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 B3GNT5,MCF2L2
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control11075.s1
 
 
  Maternal
  Simplex
 
  CHRD
 
krumm_15_ASD_discovery_controls-control12187.s1
  Illumina 1MDuo
 
  Paternal
 
 
  PSMD2,EIF4G1,EEF1AKMT4-ECE2,ECE2
 
levy_11_ASD_discovery_controls-11961.s1
 
 
  De novo
  Simplex
  NA
  SNORA63D,LINC00888,MCF2L2,KLHL6
 
levy_11_ASD_discovery_controls-12187.s1
 
 
  Paternal
  Simplex
  NA
  PSMD2,EIF4G1,EEF1AKMT4-ECE2,ECE2
 
poultney_13_ASD_discovery_controls-control04C28760A
 
 
  Unknown
 
 
  AP2M1,MIR1224,ALG3,CAMK2N2,SNORD66,EIF2B5,ABCF3,VWA5B2,EEF1AKMT4,PSMD2,EIF4G1,FAM131A,CLCN2,DVL3,EEF1AKMT4-ECE2,ECE2
 
sanders_11_ASD_discovery_controls-11196.s1
 
 
  Unknown
  Simplex (quad)
  NA
  MCF2L2
 
sanders_11_ASD_discovery_controls-12187.s1
 
 
  Paternal
  Simplex (quad)
  NA
  PSMD2,EIF4G1,EEF1AKMT4-ECE2,ECE2
 
sanders_11_ASD_discovery_controls-12456.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 

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