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3q13.12CNV Type: Deletion-Duplication


Largest CNV size: 574043 bp

Statistics Box:
Number of Reports: 5



Summary Information

Summary statement in development

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type

No Major Reports

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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Copy number variation in Han Chinese individuals with autism spectrum disorder.
Deletion
NA
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 gai_11_ASD_discovery_cases
 Discovery case samples derived from AGRE set 4 (most recent patient recruitment)
 631
 Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
 
 
 45827
 1
 0
 1
 gazzellone_14_ASD_discovery_cases
 ASD-affected individuals referred to the Children Development and Behavior Research Center (CDRBC) at Harbin Medical University, China, between January 2007 and June 2011.
 104
 Diagnosis of ASD made using Autism Behavior Checklist (ABC) and Childhood Autism Rating Scale (CARS)
 Mean age at enrollment, 4.31 1.80 yrs.
 87.5% Male
 31924
 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
 605000
 0
 1
 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
 15786
 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
 574043
 1
 1
 2

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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)
 15786
 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.
 
 591441
 1
 1
 2

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 gai_11_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 None
 gazzellone_14_ASD_discovery_cases
  Han Chinese
 Array SNP
  Affymetrix CytoScan HD
 ChAS, iPattern, Nexus, Partek
 
 None
 maini_18_ASD/DD/ID_discovery_cases
  Italian
 aCGH, array SNP
  Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
 
 
 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
  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
  gai_11_ASD_discovery_cases-AU1274302
 
 
 Autism
 
 
 107883845
 107929671
  45827
 Unknown
 Deletion
 No
  gazzellone_14_ASD_discovery_cases-case632-3
 N/A
 F
 ASD
 ASD; no other clinical information provided
 N/A
 107119058
 107150982
  31925
 GRCh38
 Deletion
 No
  maini_18_ASD/DD/ID_discovery_cases-case_unknown148
  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), CNV reported as 3q13.2 in original report
 
 107055769
 107660820
  605052
 GRCh38
 Duplication
 No
  prasad_12_ASD_discovery_cases-case74431
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 108117408
 108133193
  15786
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11092.p1
 13.1
 M
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 125; verbal IQ, 108
 107203900
 107232115
  28216
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13128.p1
 11
 F
 Autism
 NA
 Full-scale IQ, 98; non-verbal IQ, 104; verbal IQ, 88
 106894454
 107468497
  574044
 GRCh38
 Duplication
 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-11092.s1
  10.5
  F
  Control (matched sibling)
  NA
  NA
  107203900
  107232115
  28216
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13128.s1
  8.8
  M
  Control (matched sibling)
  NA
  NA
  106877056
  107468497
  591442
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gai_11_ASD_discovery_cases-AU1274302
 
 
 Inherited
 
 
 0 genes
 
 gazzellone_14_ASD_discovery_cases-case632-3
 
 
 Unknown
 Unknown
 Unknown
 LINC00882
 
 maini_18_ASD/DD/ID_discovery_cases-case_unknown148
 
 
 Maternal
 Unknown
 Unknown
 CCDC54,DUBR,LINC01990,BBX,LINC00882
 
 prasad_12_ASD_discovery_cases-case74431
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11092.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 LINC00882
 
 sanders_11_ASD_discovery_cases-13128.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 MTND4P16,MTND4LP3,MTND3P6,MTCO3P35,MTATP6P22,MTND5P16,MTND6P6,MTCO1P35,MTND1P16,MTND2P14,RNU6-1308P,CCDC54,DUBR,LINC01990,LINC00882
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11092.s1
 
 
  Maternal
  Simplex (quad)
  NA
  LINC00882
 
sanders_11_ASD_discovery_controls-13128.s1
 
 
  Paternal
  Simplex (quad)
  NA
  MTND4P16,MTND4LP3,MTND3P6,MTCO3P35,MTATP6P22,MTND5P16,MTND6P6,MTCO1P35,MTND1P16,MTND2P14,RNU6-1308P,CCDC54,DUBR,LINC01990,LINC00882
 

No Animal Model Data Available
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