Xq27.1CNV Type: Deletion-Duplication
Largest CNV size: 706000 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
Summary statement in development
Additional Locus Information
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
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
digregorio_17_DD/ID_discovery_cases
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
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
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
No Animal Model Data Available