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3q25.2CNV Type: Deletion


Largest CNV size: 163051 bp

Statistics Box:
Number of Reports: 3



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
Excess of rare, inherited truncating mutations in 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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 96292
 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
 50226
 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
 163051
 8
 0
 8

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 0
 0
 0
 0
 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)
 50226
 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.
 
 158206
 12
 0
 12

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 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
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, 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
  krumm_15_ASD_discovery_cases-case12119.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 155084167
 155180459
  96293
 GRCh38
 Deletion
 Yes
  prasad_12_ASD_discovery_cases-case139353L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 155120860
 155171085
  50226
 Unknown
 Duplication
 No
  sanders_11_ASD_discovery_cases-11289.p1
 6
 M
 Autism
 NA
 Full-scale IQ, 82; non-verbal IQ, 98; verbal IQ, 62
 153885505
 153895675
  10171
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11473.p1
 11.5
 M
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 109; verbal IQ, 105
 152629693
 152637456
  7764
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11543.p1
 16.9
 M
 Autism
 NA
 Full-scale IQ, 63; non-verbal IQ, 81; verbal IQ, 31
 152732544
 152739403
  6860
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11839.p1
 4
 M
 ASD
 NA
 Full-scale IQ, 100; non-verbal IQ, 101; verbal IQ, 99
 152629693
 152637456
  7764
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11918.p1
 9.8
 F
 Autism
 NA
 Full-scale IQ, 48; non-verbal IQ, 59; verbal IQ, 39
 154573689
 154736740
  163052
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12631.p1
 17.2
 M
 Autism
 NA
 Full-scale IQ, 80; non-verbal IQ, 87; verbal IQ, 76
 152629693
 152637456
  7764
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12817.p1
 9.4
 M
 Autism
 NA
 Full-scale IQ, 36; non-verbal IQ, 34; verbal IQ, 37
 152629693
 152637456
  7764
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13070.p1
 8.9
 M
 Autism
 NA
 Full-scale IQ, 86; non-verbal IQ, 96; verbal IQ, 85
 152629693
 152637456
  7764
 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
  sanders_11_ASD_discovery_controls-11017.s1
  5.7
  F
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11196.s1
  10
  M
  Control (matched sibling)
  NA
  NA
  154626161
  154645439
  19279
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11233.s1
  4.7
  M
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11289.s1
  8
  M
  Control (matched sibling)
  NA
  NA
  153885505
  153895675
  10171
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11543.s1
  18.1
  F
  Control (matched sibling)
  NA
  NA
  152732544
  152739403
  6860
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11567.s1
  7.7
  M
  Control (matched sibling)
  NA
  NA
  154930939
  154955060
  24122
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11810.s1
  4.4
  F
  Control (matched sibling)
  NA
  NA
  153952749
  153953768
  1020
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11916.s1
  6.9
  F
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11918.s1
  12.3
  M
  Control (matched sibling)
  NA
  NA
  154573689
  154731895
  158207
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11990.s1
  13.4
  M
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12817.s1
  15.7
  F
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13070.s1
  11.6
  M
  Control (matched sibling)
  NA
  NA
  152629693
  152637456
  7764
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 krumm_15_ASD_discovery_cases-case12119.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 MME-AS1,MME
 
 prasad_12_ASD_discovery_cases-case139353L
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sanders_11_ASD_discovery_cases-11289.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 LINC02006
 
 sanders_11_ASD_discovery_cases-11473.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11543.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11839.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11918.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 SYPL1P1,DYNLL1P5,RPL9P15
 
 sanders_11_ASD_discovery_cases-12631.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12817.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-13070.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11017.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11196.s1
 
 
  Unknown
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11233.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11289.s1
 
 
  Maternal
  Simplex (quad)
  NA
  LINC02006
 
sanders_11_ASD_discovery_controls-11543.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11567.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11810.s1
 
 
  Paternal
  Simplex (quad)
  NA
  LINC02006
 
sanders_11_ASD_discovery_controls-11916.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11918.s1
 
 
  Paternal
  Simplex (quad)
  NA
  SYPL1P1,DYNLL1P5,RPL9P15
 
sanders_11_ASD_discovery_controls-11990.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12817.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-13070.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 

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