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4q13.1-q13.2CNV Type: Duplication


Largest CNV size: 39746 bp

Statistics Box:
Number of Reports: 4



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
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
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.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 262823
 0
 1
 1
 quintela_17_DD/ID_discovery_cases
 Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
 573
 All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
 Range, 3 months-18 years
 60.38% Male
 3846405
 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
 39746
 0
 12
 12
 yuen_17_ASD_discovery_cases
 ASD genomes (1745 ASD probands, 879 ASD-affected siblings, 1 ASD-affected father, and 1 ASD-affected grandfather) from AGRE (n=730), the AGRE; Autism Treatment Network cohort (n=192) ,the ASD: Genomes to Outcomes Study cohort (n=1421), the Baby Siblings Research Consortium (n=43), the Baby Siblings Research Consortium; The Autism Simplex Collection cohort (n=6), the Infant Sibling Study (n=62), th
 2626
 ASD diagnosis of research quality when meeting criteria on one (n=437) or both (n=1361) of the diagnostic measures ADI-R and ADOS; clinical diagnosis of ASD (n=819) when given by expert clinician according to DSM-IV or DSM-5
 N/A
 78.71% Male
 3846000
 0
 1
 1

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)
 262823
 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.
 
 39746
 11
 0
 11

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None
 quintela_17_DD/ID_discovery_cases
  North West Spain
 Array SNP
  Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
 
 Affymetrix ChAS v.1.2.2
 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
 
 
 yuen_17_ASD_discovery_cases
  N/A
 WGS
  Complete Genomics, Illumina HiSeq 2000, HiSeq X
 
 
 aCGH (Agilent 1M), array SNP (Affymetrix 6.0, Affymetrix CytoScan HD), solid phase hybridization (Illumina 1M, Illumina OMNI 2.5M)

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
  prasad_12_ASD_discovery_cases-case133399
 NA
 F
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 66155007
 66417829
  262823
 Unknown
 Duplication
 No
  quintela_17_DD/ID_discovery_cases-caseID_191
 9 yrs.
 M
 Developmental delay/intellectual disability
 Patient originally reported in Quintela et al., 2015d (P1 in this report). CNV inherited from affected parent.
 
 64870306
 68716710
  3846405
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11251.p1
 7.3
 M
 Autism
 NA
 Full-scale IQ, 84; non-verbal IQ, 84; verbal IQ, 88
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11343.p1
 8.3
 M
 ASD
 NA
 Full-scale IQ, 87; non-verbal IQ, 90; verbal IQ 87
 65731139
 65763257
  32119
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11615.p1
 12.6
 M
 Autism
 NA
 Full-scale IQ, 83; non-verbal IQ, 83; verbal IQ, 89
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11616.p1
 10.3
 M
 Autism
 NA
 Full-scale IQ, 127; non-verbal IQ, 129; verbal IQ, 113
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11691.p1
 14.7
 M
 Autism
 NA
 Full-scale IQ, 59; non-verbal IQ, 62; verbal IQ, 54
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11794.p1
 8.3
 M
 Autism
 NA
 Full-scale IQ, 36; non-verbal IQ, 40; verbal IQ, 33
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11869.p1
 10.1
 M
 Autism
 NA
 Full-scale IQ, 98; non-verbal IQ, 104; verbal IQ, 86
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12020.p1
 17.3
 M
 Autism
 NA
 Full-scale IQ, 116; non-verbal IQ, 115; verbal IQ, 114
 65731139
 65763257
  32119
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12492.p1
 15.4
 M
 Autism
 NA
 Full-scale IQ, 26; non-verbal IQ, 30; verbal IQ, 19
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12671.p1
 12.8
 M
 Autism
 NA
 Full-scale IQ, 101; non-verbal IQ, 98; verbal IQ, 108
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12735.p1
 10.7
 M
 ASD
 NA
 Full-scale IQ, 55; non-verbal IQ, 53; verbal IQ, 59
 65723511
 65763257
  39747
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12784.p1
 4.4
 M
 Autism
 NA
 Full-scale IQ, 99; non-verbal IQ, 106; verbal IQ, 87
 65731139
 65763257
  32119
 GRCh38
 Duplication
 No
  yuen_17_ASD_discovery_cases-case2-1275-003
 N/A
 N/A
 ASD
 Case cohort: ASD: Genomes to Outcome Study. Clinical description: ADHD; Tourette's; lactose intolerant
 
 64430282
 68276282
  3846001
 GRCh38
 Duplication
 Yes

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-11193.s1
  4.8
  F
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11251.s1
  4.9
  M
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11333.s1
  6.9
  M
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11450.s1
  12.5
  F
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11616.s1
  6.8
  M
  Control (matched sibling)
  NA
  NA
  65731139
  65763257
  32119
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11794.s1
  4.3
  F
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11954.s1
  6.8
  F
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12020.s1
  13.8
  M
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12690.s1
  10.6
  M
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12735.s1
  9.1
  M
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13162.s1
  6.7
  F
  Control (matched sibling)
  NA
  NA
  65723511
  65763257
  39747
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 prasad_12_ASD_discovery_cases-case133399
 
 
 Unknown
 Unknown
 Unknown
 EPHA5,LOC100144602
 
 quintela_17_DD/ID_discovery_cases-caseID_191
 
 Maternal
 Maternal
 Multi-generational
 Possibly segregated
 RNU2-40P,MIR1269A,RPS23P3,RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,MT2P1,UGT2B29P,EPHA5-AS1,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,APOOP4,YTHDC1,TMPRSS11E,UGT2B15,EFL1P2,EPHA5,CENPC,UBA6,UBA6-AS1,UGT2B17,LINC02232
 
 sanders_11_ASD_discovery_cases-11251.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11343.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-11615.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11616.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11691.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11794.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-11869.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12020.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12492.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12671.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12735.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12784.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 yuen_17_ASD_discovery_cases-case2-1275-003
 Illumina OMNI 2.5M
 
 Maternal
 Simplex
 Unknown
 DPP3P1,MTCO3P27,MTCYBP16,MTND6P16,MTND5P13,MTND4LP31,MTND3P24,MTCO3P28,RNU2-40P,MIR1269A,RPS23P3,RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,EPHA5-AS1,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,EFL1P2,EPHA5,CENPC,UBA6,UBA6-AS1,LINC02232
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11193.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11251.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11333.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11450.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11616.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11794.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11954.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12020.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12690.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12735.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-13162.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 

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