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3q25.32CNV Type: Deletion


Largest CNV size: 11573 bp

Statistics Box:
Number of Reports: 6



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
Refinement and discovery of new hotspots of copy-number variation associated with 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
Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families.
Duplication
Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.
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
 81619
 0
 1
 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
 648859
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 112494
 0
 1
 1
 larson_17_ASD_discovery_cases
  NA NA
 Participants with a dual diagnosis of ASD and psychosis that were recruited from clinical services in the public and independent sectors in the United Kingdom, as well as from charities and an Asperger's syndrome social networking website (study took place from January 2011 and April 2014)
 116
 All cases with a dual diagnosis of ASD and psychosis (affective, schizophrenic, and atypical)
 N/A
 N/A
 34385
 0
 1
 1
 pfundt_16_nonNDD_discovery_cases
 Subset of a cohort of 2,603 patients affected by genetic disorders for which exome seqeuncing was performed in a diagnostic setting
 1430
 Craniofacial anomalies (n=31), disorders of sexual development (n=38), immunodeficiency (n=24), metabolic disorders (n=34), hereditary cancer (n=74), renal disorders (n=56), complex phenotypes (n=183), mitochondrial disorders (n=142), muscle disorders (n=171), deafness (n=223), movement disorders (n=217), or blindness (n=237)
 N/A
 N/A
 403139
 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
 11573
 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
 112494
 1
 1
 2
 larson_17_ASD_discovery_controls
  NA NA
 Entries listed in the Database of Genomic Variants (up to October 2017)
 N/A
 Control
 N/A
 N/A
 34385
 0
 1
 1
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 12247
 1
 0
 1

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
 aCGH (NimbleGen 135K array)
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 larson_17_ASD_discovery_cases
  United Kingdom
 Array SNP
  Affymetrix CytoScan HD 2.8M, Affymetrix Cytogenetics
 SNP-FASST2 Segmentation
 Nexus Copy Number 7 (BioDiscovery), Affymetrix ChAS
 None
 pfundt_16_nonNDD_discovery_cases
  N/A
 WES
  Solid5500xl, IlluminaHiSeq2000
 
 CoNIFER
 No
 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
  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)
  larson_17_ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
 
  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
  egger_14_ASD_discovery_cases-caseA27
 19 yrs. (born 1995)
 M
 ASD
 Diagnosis: atypical autism. Co-morbidities/additional features: horseshoe kidney, hypermetropia +5dpt. Family history: brother has ADHD. 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.
 Cognitive impairment (IQ 60-80)
 157357799
 157439417
  81619
 GRCh38
 Duplication
 No
  girirajan_13a_ASD_discovery_cases-12215.p1
 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
 158431768
 159080627
  648860
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case13858.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 158592433
 158704927
  112495
 GRCh38
 Duplication
 Yes
  larson_17_ASD_discovery_cases-case45
  NA NA
 N/A
 N/A
 ASD and psychosis
 No additional clinical information available. Patient carries CNV that is present in DGV (less than 1.5%) but was not present in 1124 ASD cases without psychosis from the Simons Simplex Collection.
 
 158625138
 158659523
  34386
 GRCh38
 Duplication
 No
  pfundt_16_nonNDD_discovery_cases-case81
 N/A
 N/A
 Non-NDD
 Disease cohort: movement disorder. Description: GFM1 deletion
 
 158666303
 159069442
  403140
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11001.p1
 7.8
 M
 Autism
 NA
 Full-scale IQ, 124; non-verbal IQ, 123; verbal IQ, 113
 158686478
 158698051
  11574
 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-control13916.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  158592433
  158704927
  112495
  GRCh38
  Duplication
  Yes
  krumm_15_ASD_discovery_controls-control13982.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  158704775
  158713859
  9085
  GRCh38
  Deletion
  Yes
  sanders_11_ASD_discovery_controls-12153.s1
  16.5
  F
  Control (matched sibling)
  NA
  NA
  158029134
  158041381
  12248
  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-caseA27
 
 
 Unknown
 Multiplex for NDD (brother with ADHD)
 Unknown
 PTX3,VEPH1
 
 girirajan_13a_ASD_discovery_cases-12215.p1
 aCGH (NimbleGen 135K array)
 
 Paternal
 Simplex
 Unknown
 MTAPP1,GPR79,GFM1,LXN,MFSD1,MLF1,RARRES1,IQCJ,RSRC1,IQCJ-SCHIP1
 
 krumm_15_ASD_discovery_cases-case13858.p1
 Omni2.5-4v1
 
 Paternal
 Simplex
 Segregated
 MTAPP1,GFM1,LXN,MLF1,RARRES1
 
 larson_17_ASD_discovery_cases-case45
 
 
 Unknown
 
 Unknown
 GFM1,LXN
 
 pfundt_16_nonNDD_discovery_cases-case81
 
 
 
 
 
 GPR79,GFM1,LXN,MFSD1,RARRES1,IQCJ,IQCJ-SCHIP1
 
 sanders_11_ASD_discovery_cases-11001.p1
 
 
 Unknown
 Simplex (trio)
 NA
 GFM1,RARRES1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_15_ASD_discovery_controls-control13916.s1
  Omni2.5-4v1
 
  Paternal
 
 
  MTAPP1,GFM1,LXN,MLF1,RARRES1
 
krumm_15_ASD_discovery_controls-control13982.s1
  Omni2.5-4v1
 
  Maternal
 
 
  RARRES1
 
sanders_11_ASD_discovery_controls-12153.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 

No Animal Model Data Available
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