Xp22.33-p22.31CNV Type: Deletion
Largest CNV size: 5825311 bp
Statistics Box:
Number of Reports: 7
Number of Reports: 7
Summary Information
Summary statement in development
Additional Locus Information
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-Duplication
Genome-wide copy number variation analysis in a Chinese autism spectrum disorder cohort.
Deletion
Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders an...
Deletion
Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
guo_17_ASD_discovery_cases
ASD subjects (with 343 trios) screened for rare, large (>1 Mb) CNVs
546
Diagnosis of ASD based on DSM-IV-TR criteria
Mean, 5.065 years
N/A
3536295
1
0
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
8407842
4
1
5
kushima_22_BPD_discovery_cases
Japanese bipolar disorder probands evaluated for copy number variation from an initial cohort of 1,843 probands before quality control.
1818
Cases diagnosed with bipolar disorder (BPD) according to DSM-5 criteria.
Median age, 48 yrs.
46.7% Male
4658800
1
0
1
mahjani_22_OCD/CTD_discovery_cases
Subjects from the Epidemiology and Genetics of Obsessive-Compulsive Disorder and Chronic Tic Disorders in Sweden (EGOS) cohort from an initial cohort of 1249 affected individuals after quality control.
1210
993 cases diagnosed with obsessive-compulsive disorder (OCD) and 217 cases diagnosed with chronic tic disorder (CTD) according to ICD-10 crtieria (note: 91 cases were diagnosed with both OCD and CTD). A subset of cases in this cohort had additional diagnoses of autism spectrum disorder (ASD) and ADHD (according to ICD-10 criteria).
Age of at least 16 yrs. (in the year 1997).
42.15% Male
5143660
0
1
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
5825311
1
0
1
tammimies_15_ASD_discovery_cases
Consecutively ascertained unrelated children with ASD recruited between 2008 and 2013 in Newfoundland and Labrador, Canada
258
Diagnosis of ASD based on DSM-IV-TR criteria and confirmed by ADOS and ADI-R assessments
4.5 2.8 yrs.
83.72% Male
5838878
1
0
1
willemsen_12_DD/ID_discovery_cases
Individuals referred between Jan. 2003 and August 2010 to diagnostic center at Dept. of Human Genetics, Radboud Univ. Mijmegen Medical Centre, Nijmegen, The Netherlands for genome-wide array analysis (emphasis on X chromosome CNVs)
4407
Majority of cases: indication of developmental delay/intellectual disability [with or without other neuropsychiatric disorders (ASD, ADHD, etc.) and/or congenital anomalies]. Minority of cases: congenital anomalies or behavioral problems without DD/ID.
2/3 of cases: age range of 1-18 yrs.
54.5% Male
8500000
3
0
3
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
guo_17_ASD_discovery_controls
Control subjects screened for rare, large (>1 Mb) CNVs
988
No history of ASD or any other psychiatric diseases; no family history of psychiatric, neurological or autoimmune diseases
Mean, 34.3 years
N/A
0
0
0
0
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
kushima_22_ASD/BPD/SCZ_discovery_controls
Psychiatrically normal control individuals selected from the general population evaluated for copy number variation from an initial cohort of 2,713 control individuals before quality control.
2671
Controls were psychiatrically normal and had no history of mental disorders based on responses to questionnaires or self-reporting.
Median age, 36 yrs.
47.8% Male
0
0
0
0
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
guo_17_ASD_discovery_cases
Chinese Han
Solid phase hybridization
Illumina 370K or 660K BeadChip
PennCNV
qPCR
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
kushima_22_BPD_discovery_cases
Japan
aCGH
Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
mahjani_22_OCD/CTD_discovery_cases
Sweden
Solid phase hybridization
Illumina Infinium Global Screening Array
QuantiSNP, PennCNV, cnvPartition v.3.2.1
CNVision, Illumina GenomeStudio v.2.0
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
tammimies_15_ASD_discovery_cases
Canada
aCGH, array SNP, solid phase hybridization
One or more of the following: Affymetrix 6.0, Illumina Omni2.5M-Quad, Illumina 1M, Agilent 1M, Affymetrix CytoScan HD, Illumina 1M Duo, custom Agilent 4x44K, or custom OGT 4x180K
QuantiSNP, PennCNV, iPattern, DNAcopy, Partek
Affymetrix ChAS, Agilent DNA Analytics v 4.0 or v4.0.85, Nexus BioDiscovery, Agilent Feature Extract
None
willemsen_12_DD/ID_discovery_cases
Netherlands
aCGH, array SNP
Agilent 32K BAC array, Affymetrix 250K
CNAG V2.0 (SNP array)
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
guo_17_ASD_discovery_controls
Chinese Han
Solid phase hybridization
Illumina 610K BeadChip
PennCNV
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
kushima_22_ASD/BPD/SCZ_discovery_controls
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
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
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
guo_17_ASD_discovery_cases-caseM8590
N/A
F
ASD
Diagnosis of ASD based on DSM-IV-TR criteria; no other clinical information available
4016164
7552458
3536295
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001161
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
10679
7515914
7505236
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002541
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
2782275
8961059
6178785
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004013
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
26102
8495903
8469802
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004699
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
10679
6495923
6485245
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005192
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
10679
8480277
8469599
GRCh38
Duplication
Yes
kushima_22_BPD_discovery_cases-caseBD0757
NA
NA
Bipolar disorder
Diagnosis of bipolar disorder according to DSM-5 criteria.
1458743
6117542
4658800
GRCh38
Deletion
Yes
mahjani_22_OCD/CTD_discovery_cases-case14
NA
F
OCD
Case diagnosed with obsessive compulsive disorder (OCD).
3185014
8328673
5143660
GRCh38
Duplication
No
marshall_08_ASD_discovery_cases-NA0097-000
NA
F
ASD
Moderate speech unintelligibility, mild repetitive behavior
IQ/LOF 117
44419
6081953
6037535
GRCh38
Deletion
Yes
tammimies_15_ASD_discovery_cases-case3-0097-000
N/A
F
ASD
Dysmorphic features: prominent ears, telecanthus, long palpebral fissures, wide mouth.
Normal intelligence (IQ of 114)
253255
6090758
5837504
GRCh38
Deletion
No
willemsen_12_DD/ID_discovery_cases-case16
F
Intellectual disability
Hyperactivity, height -2 to -1 SD). Mother with learning difficulties; brother with moderate-severe ID.
Moderate-severe ID
283333
6481959
6198627
GRCh38
Deletion
No
willemsen_12_DD/ID_discovery_cases-case3
M
Intellectual disability
Short stature, hydrocephaly. Mother with learning difficulties; sister with moderate-severe ID.
Moderate-severe ID
283333
6481959
6198627
GRCh38
Deletion
No
willemsen_12_DD/ID_discovery_cases-case4
M
Intellectual disability
Kallman syndrome, ichthyosis
Intellectual disability
283333
8741959
8458627
GRCh38
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
guo_17_ASD_discovery_cases-caseM8590
qPCR
De novo
MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,NLGN4X,PUDP,STS
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001161
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,STS
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002541
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,DRAXINP1,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,FAM9A,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,ANOS1,STS
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004013
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,STS
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004699
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005192
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,STS
kushima_22_BPD_discovery_cases-caseBD0757
qRT-PCR
Unknown
ASMT,ARSD,ASS1P4,ARSL,ARSF,NLGN4X,DHRSX,P2RY8,ARSH,CD99P1,RPS27AP20,LINC01546,RPL24P9,CD99,HADHBP1,LINC00102,ARSD-AS1,GYG2-AS1,PRKX-AS1,PRKX,MIR6089,DHRSX-IT1,RN7SL578P,RNU6-146P,RNU6-114P,MTCYBP12,MTND6P12,SNORA48B,GYG2,XG,AKAP17A,RPS24P21,ZBED1,MXRA5
mahjani_22_OCD/CTD_discovery_cases-case14
Unknown
ASS1P4,STS,VCX,VCX3A,VCX2,NLGN4X,RPS27AP17,RPS5P8,MIR651,RPS27AP20,LINC01546,RPL24P9,HADHBP1,MIR4770,MIR4767,PRKX-AS1,PRKX,RNU6-146P,RNU6-114P,MTCYBP12,MTND6P12,SNORA48B,PNPLA4,PUDP,MXRA5
marshall_08_ASD_discovery_cases-NA0097-000
qPCR, qmPCR
De novo
Simplex-CHR
NA
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X
tammimies_15_ASD_discovery_cases-case3-0097-000
De novo
Unknown
Possibly segregated
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X
willemsen_12_DD/ID_discovery_cases-case16
Maternal
Maternal
Multiplex (brother with moderate-severe ID)
Segregated
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X
willemsen_12_DD/ID_discovery_cases-case3
Maternal
Maternal
Multiplex (sister with moderate-severe ID)
Segregated
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X
willemsen_12_DD/ID_discovery_cases-case4
Unknown (not tested)
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,ANOS1,STS
Controls
No Control Data Available
No Animal Model Data Available