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15q25.2-q25.3CNV Type: Deletion


Largest CNV size: 1058276 bp

Statistics Box:
Number of Reports: 9



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
Structural variation of chromosomes in autism spectrum disorder.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Deletion
NA
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.
Deletion
Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families.
Deletion
NA
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 718458
 1
 0
 1
 girirajan_13a_DD_discovery_cases
 Data from individuals with developmental delay derived from two published reports (Cooper et al., 2011 & Kaminsky et al., 2011)
 31518
 Developmental delay
 NA
 NA
 1050000
 5
 1
 6
 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
 792711
 1
 0
 1
 leppa_16_ASD_discovery_cases
 Children affected with ASD from 1,464 families from the Autism Genetic Resource Exchange (AGRE)
 1764
 Diagnosis according to ADOS and ADI-R
 N/A
 N/A
 600000
 1
 0
 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
 
 
 1058276
 1
 0
 1
 pinto_14_ASD_discovery_cases
 ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
 1359
 Cases classified according to ADOS and ADI-R
 N/A
 N/A
 807813
 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
 613811
 1
 0
 1
 sajan_13_ACC/CBLH/PMG_discovery_cases
 Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
 487
 Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
 N/A
 N/A
 614863
 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
 868117
 1
 0
 1
 schuch_19_ASD_discovery_cases
  NA NA
 Childen of European descent diagnosed with idiopathic ASD
 40
 Cases diagnosed with ASD according to DSM-IV criteria: 55% with autistic disorder, 45% with PDD-NOS, 5% with Asperger syndrome.
 Mean, 7.83 2.95 yrs.
 90.00% Male
 558000
 1
 0
 1

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
 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
 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)
 613811
 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.
 
 818759
 1
 0
 1

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 girirajan_13a_DD_discovery_cases
  NA
 N/A
  N/A
 
 
 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
 leppa_16_ASD_discovery_cases
  N/A
 Solid phase hybridization
  Illumina 550v1 and 550v3, Omni-1.0-B and -H, Omni 2.5
 PennCNV, QuantiSNP, GNOSIS
 GenomeStudio, CNVision
 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
 pinto_14_ASD_discovery_cases
  Predominantly European
 Solid phase hybridization
  Illumina 1M (v.1 and v.3)
 
 
 qPCR, MLPA, long-range PCR
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 sajan_13_ACC/CBLH/PMG_discovery_cases
  81.31% Caucasian
 Solid phase hybridization
  Illumina InfiniumII HumanHap610
 PennCNV
 
 qPCR
 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
 
 
 schuch_19_ASD_discovery_cases
  European
 aCGH
  Agilent 8x60K
 ADM-2
 Agilent Feature Extraction v.9.5.1, Agilent Cytogenomics v.2.7.8.0
 None

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
 
  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
 
 
  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
  digregorio_17_DD/ID_discovery_cases-DECIPHER_300045
  NA NA
 N/A
 M
 Developmental delay/intellectual disability
 
 
 84609517
 85327974
  718458
 GRCh38
 Deletion
 Yes
  girirajan_13a_DD_discovery_cases-DDcase204
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 No
  girirajan_13a_DD_discovery_cases-DDcase205
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 No
  girirajan_13a_DD_discovery_cases-DDcase206
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 No
  girirajan_13a_DD_discovery_cases-DDcase207
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 No
  girirajan_13a_DD_discovery_cases-DDcase208
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Deletion
 No
  girirajan_13a_DD_discovery_cases-DDcase209
 N/A
 N/A
 Developmental delay
 N/A
 N/A
 84165244
 85330765
  1165522
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004121
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 84391435
 85185613
  794179
 GRCh38
 Deletion
 Yes
  leppa_16_ASD_discovery_cases-AU056103
 N/A
 M
 ASD
 
 
 84570769
 85185769
  615001
 GRCh38
 Deletion
 No
  marshall_08_ASD_discovery_cases-NA0064-000
 NA
 M
 ASD
 NA
 NA
 84113665
 85287462
  1173798
 GRCh38
 Deletion
 Yes
  pinto_14_ASD_discovery_cases2-case5537_3
 N/A
 M
 ASD
 Case previously reported in Marshall et al., 2008 (subject NA0064-000). Asperger syndrome, meets ADI-R criteria for autism, advanced language skills, ADHD, obsessive behaviors, nocturnal generalized tonic-clonic seizure disorder resolved at age 8, Dysmorphic features: marfanoid looking, long palpebral fissures, long face with malar hypoplasia, high arched palate and dental crowding (prior to orthodontic work), long neck. Family history: mother was very shy as child and had depression at 40 y (physical exam showed no dysmorphism , not marfanoid); 1 sister (#61018) without social concerns without CNV, 1 brother (#61114) with ADHD diagnosed at 6 y and autism diagnosed at 13 y with CNV.
 WISC-III FSIQ 103
 84262270
 85185603
  923334
 GRCh38
 Deletion
 Yes
  prasad_12_ASD_discovery_cases-case63582-L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 82907012
 83520822
  613811
 Unknown
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-case1124-0
 N/A
 N/A
 ACC-CBLH
 Diagnosis of agenesis of the corpus callosum (ACC) and cerebellar hypoplasia (CBLH). ASD: unknown. Seizures: yes.
 Developmental delay: yes. Intellectual disability: unknown.
 84570741
 85185603
  614863
 GRCh38
 Deletion
 Yes
  sanders_11_ASD_discovery_cases-11348.p1
 7.8
 M
 Autism
 NA
 Full-scale IQ, 77; non-verbal IQ, 84; verbal IQ, 64
 84393201
 85262785
  869585
 GRCh38
 Deletion
 No
  schuch_19_ASD_discovery_cases-case8
  NA NA
 N/A
 M
 ASD
 Autism, self-injurious behavior, mood instability, repetitive movements.
 
 84581311
 85139000
  557690
 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-11348.s1
  9.2
  F
  Control (matched sibling)
  NA
  NA
  84252414
  85186694
  934281
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 digregorio_17_DD/ID_discovery_cases-DECIPHER_300045
 qPCR
 
 Maternal
 
 
 EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase204
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase205
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase206
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase207
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase208
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 girirajan_13a_DD_discovery_cases-DDcase209
 
 
 Unknown
 
 
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004121
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
 leppa_16_ASD_discovery_cases-AU056103
 
 
 Paternal
 Multiplex
 Not segregated (CNV not present in affected siblings)
 EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
 marshall_08_ASD_discovery_cases-NA0064-000
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 DNM1P41,RN7SL331P,GOLGA6L4,UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,EFL1P1,UBE2Q2L,CSPG4P11,GOLGA2P7,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 pinto_14_ASD_discovery_cases2-case5537_3
 Affy 500K, Illumina 2.5M, qPCR
 
 Maternal
 Multiplex
 Segregated [1 sister (#61018) without social concerns without DEL, 1 brother (#61114) with ADHD and autism with DEL]
 RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
 prasad_12_ASD_discovery_cases-case63582-L
 
 
 Unknown
 Unknown
 Unknown
 SEC11A,ALPK3,SLC28A1,UBE2Q2P1,LOC100506874,ZNF592,SCAND2,NMB,WDR73,PDE8A,ZSCAN2
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-case1124-0
 qPCR
 
 Maternal
 Unknown
 Unknown
 EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 
 sanders_11_ASD_discovery_cases-11348.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,RN7SL428P,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,GOLGA6L3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,CSPG4P12,ADAMTS7P4,SLC28A1
 
 schuch_19_ASD_discovery_cases-case8
 
 
 Unknown
 Unknown
 Unknown
 EGLN1P1,RNU6-339P,RNU6-796P,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,SEC11A,ZNF592,PDE8A,SLC28A1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11348.s1
 
 
  Maternal
  Simplex (quad)
  NA
  UBE2Q2P8,RN7SL417P,CSPG4P5,UBE2Q2P11,EGLN1P1,RNU6-339P,RNU6-796P,NIFKP8,UBE2Q2P12,GOLGA6L5P,LINC00933,ZSCAN2,SCAND2P,WDR73,NMB,ALPK3,DNM1P51,UBE2Q2P1,SEC11A,ZNF592,PDE8A,SLC28A1
 

No Animal Model Data Available
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