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Xq27.1CNV Type: Deletion-Duplication


Largest CNV size: 706000 bp

Statistics Box:
Number of Reports: 8



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
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Clinical genetic testing for patients with autism spectrum disorders.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
NA
Duplication

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
 186000
 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
 167336
 0
 1
 1
 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
 1626357
 1
 4
 5
 pinto_10_ASD_discovery_cases
 Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
 996
 ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
 
 
 167337
 0
 1
 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
 36723
 1
 1
 2
 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
 123133
 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
 261211
 2
 1
 3
 shen_10_ASD_discovery_cases
 Patients from original discovery case cohort that were subsequently used in chromosomal microarray analysis (CMA). Original discovery case cohort (n=933) was 80.9 % male and consisted of 461 patients recruited through Autism Consortium (AC) & 472 patients added through samples from Children's Hospital Boston DNA Diagnostic laboratory (CHB).
 848
 ASD (initial case cohort of 933 cases consisted of 447 patients diagnosed with autistic disorder, 454 with PDD-NOS, 31 with Asperger disorder, and 1 with CDD. AC Cohort: 54 patients with secondary diagnosis of mental retardation, 36 with seizures, and 16 with multiple congenital anomalies)
 
 
 706000
 1
 0
 1

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
 535692
 0
 4
 4
 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
 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)
 36723
 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.
 
 38153
 1
 1
 2
 stamouli_18_ASD/NDD_discovery_controls
  NA NA
 Unaffected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
 100 twin pairs
 Control (unaffected) individual following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities and
 N/A
 N/A
 626258
 0
 2
 2

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
 None
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 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
 pinto_10_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium 1M SNP microarray
 QuantiSNP, iPattern
 
 qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
 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
 
 None (not tested or failure to confirm by 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
 
 
 shen_10_ASD_discovery_cases
 
 aCGH, array SNP
  Agilent 244A, Affymetrix NspI, Affymetrix SytI, Affymetrix 5.0
 BRLMM, CNAT4, Partek Genomic Suite
 CGH Analytics, DNA Analytics software
 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
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  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
 
 
  stamouli_18_ASD/NDD_discovery_controls
  Swedish
  Solid phase hybridization
  Illumina Infinium PsychArray-24 v1.1
  PennCNV, QuantiSNP, iPattern, iPsychCNV
 
  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
  digregorio_17_DD/ID_discovery_cases-DECIPHER_301179
  NA NA
 N/A
 F
 Developmental delay/intellectual disability
 
 
 139744127
 139930619
  186493
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case6239_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 139639501
 139806837
  167337
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001638
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 139333024
 140959375
  1626352
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001759
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 140247565
 140694868
  447304
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002017
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 139605696
 140302516
  696821
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002591
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 140265414
 140661089
  395676
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005400
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 139199307
 139682289
  482983
 GRCh38
 Duplication
 Yes
  pinto_10_ASD_discovery_cases-case6239_3
 NA
 M
 Autism
 No language, strabism, no dysmorphic features, no epilepsy
 Severe MR
 139639501
 139806837
  167337
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case115745L
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 138858916
 138865831
  6916
 Unknown
 Deletion
 No
  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
 
 139867785
 139904507
  36723
 Unknown
 Duplication
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-case1599-0
 N/A
 N/A
 ACC-CBLH
 Diagnosis of agenesis of the corpus callosum (ACC) and cerebellar hypoplasia (CBLH). ASD: no. Seizures: no.
 Developmental delay: yes. Intellectual disability: unknown.
 140646066
 140769198
  123133
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12008.p1
 7.3
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 106; verbal IQ, 128
 140847050
 140849253
  2204
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12192.p1
 6.9
 M
 Autism
 NA
 Full-scale IQ, 127; non-verbal IQ, 130; verbal IQ, 115
 140794655
 141043845
  249191
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13327.p1
 12.6
 M
 Aspergers
 NA
 Full-scale IQ, 103; non-verbal IQ, 95; verbal IQ, 118
 140847050
 140849253
  2204
 GRCh38
 Deletion
 No
  shen_10_ASD_discovery_cases-ASD-09-080
 NA
 M
 PDD-NOS
 NA
 NA
 139520119
 140226554
  706436
 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-control110036020774_
  N/A
  N/A
  Control
  No previous psychiatric history
 
  140932346
  140998510
  66165
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB304127_0067942644
  N/A
  N/A
  Control
  No previous psychiatric history
 
  139719138
  140254824
  535687
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB585499_1007853979
  N/A
  N/A
  Control
  No previous psychiatric history
 
  139119181
  139222674
  103494
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB818952_1007874830
  N/A
  N/A
  Control
  No previous psychiatric history
 
  139573903
  139788579
  214677
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11563.s1
  9.3
  F
  Control (matched sibling)
  NA
  NA
  140958435
  140996588
  38154
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12347.s1
  7.3
  F
  Control (matched sibling)
  NA
  NA
  139541798
  139555357
  13560
  GRCh38
  Deletion
  No
  stamouli_18_ASD/NDD_discovery_controls-family10_Twin_1
  N/A
  N/A
  Control
  Control is from a monozygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
 
  139582456
  140208722
  626267
  GRCh38
  Duplication
  No
  stamouli_18_ASD/NDD_discovery_controls-family10_Twin_2
  N/A
  N/A
  Control
  Control is from a monozygotic twin pair from the Concordant typically developed (TD) diagnostic subgroup
 
  139582456
  140208722
  626267
  GRCh38
  Duplication
  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_301179
 
 
 Maternal
 
 
 RNU6ATAC23P,MIR505,ATP11C
 
 engchuan_15_ASD_discovery_cases-case6239_3
 
 
 Unknown
 
 
 MCF2,ATP11C
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001638
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Maternal
 Unknown
 Unknown
 SRD5A1P1,RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,RPS17P17,SOX3,CDR1,MIR320D2,SNURFL,F9,MCF2,ATP11C,LINC00632
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001759
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 RPS17P17,SOX3
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002017
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,MCF2,ATP11C
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002591
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 RPS17P17,SOX3
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005400
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 SRD5A1P1,SNURFL,F9,FGF13,MCF2
 
 pinto_10_ASD_discovery_cases-case6239_3
 qPCR-Maternal
 
 maternal
 Simplex
 NA
 MCF2,ATP11C
 
 prasad_12_ASD_discovery_cases-case115745L
 
 
 Unknown
 Unknown
 Unknown
 CXorf66
 
 prasad_12_ASD_discovery_cases-case133399
 
 
 Unknown
 Unknown
 Unknown
 0 genes
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-case1599-0
 qPCR (CNV not detected)
 
 Bi-parental
 Unknown
 Unknown
 LINC00632
 
 sanders_11_ASD_discovery_cases-12008.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12192.p1
 
 
 Unknown
 Simplex (trio)
 NA
 MIR320D2,SPANXB1
 
 sanders_11_ASD_discovery_cases-13327.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Segregated
 
 
 shen_10_ASD_discovery_cases-ASD-09-080
 
 
 Unknown
 NA
 NA
 RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,F9,MCF2,ATP11C
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036020774_
 
 
  Unknown
 
 
 
 
engchuan_15_ASD_discovery_controls-controlB304127_0067942644
 
 
  Unknown
 
 
  RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,ATP11C
 
engchuan_15_ASD_discovery_controls-controlB585499_1007853979
 
 
  Unknown
 
 
  FGF13
 
engchuan_15_ASD_discovery_controls-controlB818952_1007874830
 
 
  Unknown
 
 
  MCF2,ATP11C
 
sanders_11_ASD_discovery_controls-11563.s1
 
 
  Paternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-12347.s1
 
 
  Unknown
  Simplex (quad)
  NA
  F9
 
stamouli_18_ASD/NDD_discovery_controls-family10_Twin_1
 
 
  Unknown
  N/A (both twins typically developing)
 
  RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,MCF2,ATP11C
 
stamouli_18_ASD/NDD_discovery_controls-family10_Twin_2
 
 
  Unknown
  N/A (both twins typically developing)
 
  RNU6ATAC23P,MIR505,CXorf66,HNRNPA3P3,RN7SL727P,MCF2,ATP11C
 

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