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3p21.1CNV Type: Deletion


Largest CNV size: 90755 bp

Statistics Box:
Number of Reports: 7



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
NA
Duplication
Paternally inherited cis-regulatory structural variants are associated with 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
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Duplication
Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-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
 brandler_18_ASD_discovery_cases
 Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
 880
 REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
 N/A
 N/A
 1100
 1
 0
 1
 digregorio_17_DD/ID_discovery_cases
  NA NA
 Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
 1015
 Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
 N/A
 N/A
 1100000
 0
 1
 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
 287033
 3
 1
 4
 girirajan_11_ASD_discovery_cases
 ASD cases with sporadic autism from the Simons Simplex Collection (SSC)
 336
 Diagnosis of ASD based on meeting criteria on ADOS, ADI-R, and expert clinical judgment. 246 cases with no intellectual disability, 90 cases with intellectual disability. Exclusion criteria: significant hearing, vision, or motor problems; significant birth complications; a diagnosis of ASD-related disorders, such as Fragile X; or having a relative (up to 3rd degree) with ASD or sibling showing ASD-related symptoms.
 
 
 470979
 0
 1
 1
 leblond_12_ASD_replication_cases
 Dataset featuring ASD patients from the Autism Genome Project carrying de novo SHANK2 deletions previously identified by Pinto et al. 2010. CNV validation information taken from Pinto report.
 2
 1 patient diagnosed with autism, 1 patient diagnosed with PDD-NOS.
 NA
 100% Male
 26745
 2
 0
 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
 90755
 5
 0
 5
 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
 84725
 2
 0
 2

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 142051
 5
 1
 6
 girirajan_11_ASD_discovery_controls
 Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
 337
 Control. Individuals screened specifically for eight mental health disorders.
 
 
 470979
 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.
 
 100631
 2
 1
 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
 84725
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 brandler_18_ASD_discovery_cases
  N/A
 WGS
  Illumina HiSeq X10 or HiSeq 2500
 ForestSV, Lumpy, Manta, Mobster, SV2
 
 PCR, array SNP
 digregorio_17_DD/ID_discovery_cases
  Italian
 aCGH
  Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
 ADM-2
 Agilent CGH Analytics software ver. 4.0.81
 qPCR
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 girirajan_11_ASD_discovery_cases
 
 aCGH
  Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
 HMM
 
 None
 leblond_12_ASD_replication_cases
  1 Canadian, 1 French
 Solid phase hybridization
  Illumina 1M SNP array
 QuantiSNP, PennCNV
 
 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
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  None
  girirajan_11_ASD_discovery_controls
 
  aCGH
  Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
  HMM
 
 
  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
  brandler_18_ASD_discovery_cases-caseMT_26.3
 N/A
 M
 PDD-NOS
 Case from REACH cohort
 
 53489686
 53490786
  1101
 GRCh38
 Deletion
 Yes
  digregorio_17_DD/ID_discovery_cases-DECIPHER_296509
  NA NA
 N/A
 M
 Developmental delay
 Global developmental delay (CNV locus reported as 3p21.1-p14.3 in the report)
 
 53228280
 54324330
  1096051
 GRCh38
 Duplication
 Yes
  engchuan_15_ASD_discovery_cases-case14222_3560
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 52993967
 53026621
  32655
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case20187_1464001
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 53858526
 54145559
  287034
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case4219_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 52993967
 53026621
  32655
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4330_100
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 52993967
 53026621
  32655
 GRCh38
 Deletion
 No
  girirajan_11_ASD_discovery_cases-Si109
 8
 M
 Autism
 ADOS score: 6. Vineland composite score: 62.
 Mild mental retardation/intellectual disability. Full-scale IQ, 65; Verbal IQ, 79; Non-verbal IQ, 64.
 52058589
 52529568
  470980
 GRCh38
 Duplication
 No
  leblond_12_ASD_replication_cases-Pintocase6319_3
 NA
 M
 PDD-NOS
 ADI-R domain scores: social, 14; communication, 8; behaviors, 2; age at first symptoms <36 months. Developmental milestones: delayed langauge (1st words at 24 months, 1st sentences at 48 months); no history of regression. Language and communication evaluation: delayed but functional language. Epilepsy/seizures: no history of epilepsy. Neurological examination: normal. Dysmorphic features: large and prominent ears, flat feet. Other comorbid medical conditions: hypermetropia.
 Mild intellectual disability (ID). WISC-III IQ scores: full-scale IQ, 60; performance IQ, 60; verbal IQ, 67.
 52993967
 53020711
  26745
 GRCh38
 Homozygous deletion
 No
  sanders_11_ASD_discovery_cases-11350.p1
 9.1
 M
 Autism
 NA
 Full-scale IQ, 80; non-verbal IQ, 92; verbal IQ, 93
 52082698
 52110166
  27469
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11676.p1
 7.1
 F
 Autism
 NA
 Full-scale IQ, 78; non-verbal IQ, 79; verbal IQ, 83
 52082698
 52110166
  27469
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12558.p1
 10.5
 M
 Autism
 NA
 Full-scale IQ, 81; non-verbal IQ, 95; verbal IQ, 51
 51702328
 51715522
  13195
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12710.p1
 4
 M
 Autism
 NA
 Full-scale IQ, 88; non-verbal IQ, 81; verbal IQ, 105
 51701459
 51715522
  14064
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13097.p1
 9.9
 M
 Autism
 NA
 Full-scale IQ, 34; non-verbal IQ, 37; verbal IQ, 27
 54191973
 54282728
  90756
 GRCh38
 Deletion
 No
  yin_16_ASD_discovery_cases-case101
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 52562382
 52647106
  84725
 GRCh38
 Deletion
 No
  yin_16_ASD_discovery_cases-case102
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 52916375
 52988839
  72465
 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
  engchuan_15_ASD_discovery_controls-controlB137135_1007853656
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52988392
  53026621
  38230
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB476509_1007853948
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52993967
  53026621
  32655
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB667434_1007854745
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52993967
  53026621
  32655
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB772297_1007873646
  N/A
  N/A
  Control
  No previous psychiatric history
 
  53928107
  54070158
  142052
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB782997_1007853703
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52993967
  53026621
  32655
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB916764_1007873302
  N/A
  N/A
  Control
  No previous psychiatric history
 
  52993967
  53026621
  32655
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11798.s1
  7.2
  F
  Control (matched sibling)
  NA
  NA
  53447270
  53455063
  7794
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11869.s1
  5.5
  F
  Control (matched sibling)
  NA
  NA
  51881397
  51928065
  46669
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13097.s1
  12.4
  F
  Control (matched sibling)
  NA
  NA
  54191973
  54292604
  100632
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 brandler_18_ASD_discovery_cases-caseMT_26.3
 PCR or SNP data validation
 
 Maternal
 
 
 CACNA1D
 
 digregorio_17_DD/ID_discovery_cases-DECIPHER_296509
 qPCR
 
 De novo
 
 
 CABYRP1,TKT,CHDH,IL17RB,SELENOK,DCP1A,ACTR8,CACNA1D,CACNA2D3
 
 engchuan_15_ASD_discovery_cases-case14222_3560
 
 
 Unknown
 
 
 SFMBT1
 
 engchuan_15_ASD_discovery_cases-case20187_1464001
 
 
 Unknown
 
 
 CABYRP1,IL17RB,SELENOK,ACTR8,CACNA2D3
 
 engchuan_15_ASD_discovery_cases-case4219_1
 
 
 Unknown
 
 
 SFMBT1
 
 engchuan_15_ASD_discovery_cases-case4330_100
 
 
 Unknown
 
 
 SFMBT1
 
 girirajan_11_ASD_discovery_cases-Si109
 
 
 Unknown
 Simplex
 
 ALDOAP1,TLR9,MIRLET7G,GLYCTK,MIR135A1,BAP1,SEMA3G,TNNC1,POC1A,ALAS1,TWF2,PPM1M,WDR82,DNAH1,PHF7,NISCH,STAB1,NT5DC2,GLYCTK-AS1
 
 leblond_12_ASD_replication_cases-Pintocase6319_3
 
 
 Both parents
 
 
 SFMBT1
 
 sanders_11_ASD_discovery_cases-11350.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 POC1A
 
 sanders_11_ASD_discovery_cases-11676.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 POC1A
 
 sanders_11_ASD_discovery_cases-12558.p1
 
 
 Maternal
 Simplex (trio)
 NA
 TEX264,GRM2
 
 sanders_11_ASD_discovery_cases-12710.p1
 
 
 Maternal
 Simplex (trio)
 NA
 TEX264,GRM2
 
 sanders_11_ASD_discovery_cases-13097.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 CACNA2D3
 
 yin_16_ASD_discovery_cases-case101
 
 
 Unknown
 Unknown
 Unknown
 SMIM4,PBRM1
 
 yin_16_ASD_discovery_cases-case102
 
 
 Unknown
 Unknown
 Unknown
 SFMBT1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB137135_1007853656
 
 
  Unknown
 
 
  SFMBT1
 
engchuan_15_ASD_discovery_controls-controlB476509_1007853948
 
 
  Unknown
 
 
  SFMBT1
 
engchuan_15_ASD_discovery_controls-controlB667434_1007854745
 
 
  Unknown
 
 
  SFMBT1
 
engchuan_15_ASD_discovery_controls-controlB772297_1007873646
 
 
  Unknown
 
 
  CABYRP1
 
engchuan_15_ASD_discovery_controls-controlB782997_1007853703
 
 
  Unknown
 
 
  SFMBT1
 
engchuan_15_ASD_discovery_controls-controlB916764_1007873302
 
 
  Unknown
 
 
  SFMBT1
 
sanders_11_ASD_discovery_controls-11798.s1
 
 
  Both parents
  Simplex (quad)
  NA
  CACNA1D
 
sanders_11_ASD_discovery_controls-11869.s1
 
 
  Maternal
  Simplex (quad)
  NA
  IQCF1
 
sanders_11_ASD_discovery_controls-13097.s1
 
 
  Paternal
  Simplex (quad)
  NA
  CACNA2D3
 

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