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3q21.1CNV Type: Deletion-Duplication


Largest CNV size: 69628 bp

Statistics Box:
Number of Reports: 8



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
Structural variation of chromosomes in autism spectrum disorder.
Duplication
Excess of rare, inherited truncating mutations in autism.
Duplication

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
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families.
Deletion
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Deletion
NA
Deletion
NA
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 egger_14_ASD_discovery_cases
 ASD probands from Austria (71 simplex, 2 multiplex) recruited from the catchment area of Styria using three recruitment sites (Institute of Human Genetics, Medical University of Graz, Club Libelle, Center for Autism, Styria, and Children's Hospital, University Hospital Graz).
 73
 Diagnosis of ASD made using ADOS and ADI-R according to DSM-IV or DSM-V categories
 N/A
 80.82% Male
 48946
 1
 0
 1
 girirajan_13a_ASD_discovery_cases
 1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
 2588
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 NA
 NA
 324000
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 4604
 0
 1
 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
 261000
 0
 1
 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
 
 
 69628
 0
 1
 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
 27098
 4
 0
 4
 stamouli_18_ASD/NDD_discovery_cases
  NA NA
 Affected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
 100 twin pairs
 Diagnoses based on DSM-5 criteria following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities an
 N/A
 N/A
 136854
 2
 0
 2
 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
 75514
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 egger_14_ASD_discovery_controls
 CNV data from POPGEN (n=1,123) and the Ottawa Heart Institute (n=1,234)
 2357
 Control
 N/A
 N/A
 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
 268963
 0
 2
 2
 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
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 25972
 3
 0
 3
 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
 75514
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 egger_14_ASD_discovery_cases
  68 European, 2 Asian, 1 African, 1 Turkish, 1 Egyptian
 Array SNP
  Affymetrix 6.0
 Birdsuite, iPattern, Affymetrix Genotyping Console
 
 None
 girirajan_13a_ASD_discovery_cases
  NA
 aCGH
  Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
 ADM-2
 Agilent Genomic Workbench
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 maini_18_ASD/DD/ID_discovery_cases
  Italian
 aCGH, array SNP
  Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
 
 
 None
 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
 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
 
 
 stamouli_18_ASD/NDD_discovery_cases
  Swedish
 Solid phase hybridization
  Illumina Infinium PsychArray-24 v1.1
 PennCNV, QuantiSNP, iPattern, iPsychCNV
 
 None
 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
  egger_14_ASD_discovery_controls
  European
  N/A
  N/A
 
 
 
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  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
 
 
  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
  egger_14_ASD_discovery_cases-caseA204
 N/A
 N/A
 ASD
 CNV: high stringency genic CNV call (2 or more algorithms), with no overlapping calls in 2,357 POPGEN and OHI controls, and <50% overlap in DGV.
 
 123705793
 123754738
  48946
 GRCh38
 Deletion
 No
  girirajan_13a_ASD_discovery_cases-AU0884301
 N/A
 N/A
 ASD
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 N/A
 122698463
 123028463
  330001
 GRCh38
 Duplication
 No
  krumm_15_ASD_discovery_cases-case12170.p1
 N/A
 Female
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 123735397
 123740001
  4605
 GRCh38
 Duplication
 Yes
  maini_18_ASD/DD/ID_discovery_cases-case_unknown150
  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)
 
 123259542
 123521533
  261992
 GRCh38
 Duplication
 No
  marshall_08_ASD_discovery_cases-NA0003-000
 NA
 M
 ASD
 NA
 NA
 123184836
 123254463
  69628
 GRCh38
 Duplication
 Yes
  sanders_11_ASD_discovery_cases-12115.p1
 12.1
 M
 Autism
 NA
 Full-scale IQ, 102; non-verbal IQ, 107; verbal IQ, 94
 123883550
 123910648
  27099
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12646.p1
 17.8
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 126; verbal IQ, 103
 123883550
 123905432
  21883
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13183.p1
 5.8
 M
 Autism
 NA
 Full-scale IQ, 60; non-verbal IQ, 69; verbal IQ, 56
 123733991
 123741666
  7676
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13296.p1
 5.9
 M
 Autism
 NA
 Full-scale IQ, 30; non-verbal IQ, 44; verbal IQ, 15
 123733991
 123741666
  7676
 GRCh38
 Deletion
 No
  stamouli_18_ASD/NDD_discovery_cases-family18_Twin_1
  NA NA
 N/A
 N/A
 ASD/NDD
 Case is from a monozygotic twin pair from the Concordant ASD/Concordant NDD diagnostic group
 
 123778809
 123915662
  136854
 GRCh38
 Deletion
 No
  stamouli_18_ASD/NDD_discovery_cases-family18_Twin_2
  NA NA
 N/A
 N/A
 ASD/NDD
 Case is from a monozygotic twin pair from the Concordant ASD/Concordant NDD diagnostic group
 
 123778809
 123915662
  136854
 GRCh38
 Deletion
 No
  yin_16_ASD_discovery_cases-case121
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 123199350
 123274863
  75514
 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_15_ASD_discovery_controls-control12170.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  123735397
  123740001
  4605
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control13547.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  122692300
  122961263
  268964
  GRCh38
  Duplication
  Yes
  sanders_11_ASD_discovery_controls-12646.s1
  16.5
  M
  Control (matched sibling)
  NA
  NA
  123872725
  123898697
  25973
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12661.s1
  11.2
  F
  Control (matched sibling)
  NA
  NA
  123733991
  123741666
  7676
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13183.s1
  10.8
  F
  Control (matched sibling)
  NA
  NA
  123733991
  123744861
  10871
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 egger_14_ASD_discovery_cases-caseA204
 
 
 Unknown
 
 Unknown
 MYLK
 
 girirajan_13a_ASD_discovery_cases-AU0884301
 
 
 Unknown
 Multiplex
 Unknown
 LINC02035,HSPBAP1,SEMA5B,PARP14
 
 krumm_15_ASD_discovery_cases-case12170.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 MYLK
 
 maini_18_ASD/DD/ID_discovery_cases-case_unknown150
 
 
 Unknown
 Unknown
 Unknown
 HACD2,SEC22A,ADCY5
 
 marshall_08_ASD_discovery_cases-NA0003-000
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 PDIA5,SEC22A
 
 sanders_11_ASD_discovery_cases-12115.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 CCDC14,MYLK
 
 sanders_11_ASD_discovery_cases-12646.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 CCDC14,MYLK
 
 sanders_11_ASD_discovery_cases-13183.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 MYLK
 
 sanders_11_ASD_discovery_cases-13296.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 MYLK
 
 stamouli_18_ASD/NDD_discovery_cases-family18_Twin_1
 
 
 Maternal
 Multiplex
 Segregated (CNV present in both affected twins)
 CCDC14,MYLK
 
 stamouli_18_ASD/NDD_discovery_cases-family18_Twin_2
 
 
 Maternal
 Multiplex
 Segregated (CNV present in both affected twins)
 CCDC14,MYLK
 
 yin_16_ASD_discovery_cases-case121
 
 
 Unknown
 Unknown
 Unknown
 PDIA5,SEC22A
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_15_ASD_discovery_controls-control12170.s1
  Illumina 1MDuo
 
  Maternal
 
 
  MYLK
 
krumm_15_ASD_discovery_controls-control13547.s1
  1M-Duov3
 
  Paternal
 
 
  LINC02035,HSPBAP1,SEMA5B,PARP14
 
sanders_11_ASD_discovery_controls-12646.s1
 
 
  Unknown
  Simplex (quad)
  NA
  CCDC14,MYLK
 
sanders_11_ASD_discovery_controls-12661.s1
 
 
  Unknown
  Simplex (quad)
  NA
  MYLK
 
sanders_11_ASD_discovery_controls-13183.s1
 
 
  Unknown
  Simplex (quad)
  NA
  MYLK
 

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