Xq22.1CNV Type: Duplication
Largest CNV size: 250000 bp
Statistics Box:
Number of Reports: 9
Number of Reports: 9
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Duplication
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...
Duplication
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
3174
0
1
1
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
589000
0
1
1
han_22_ASD/DD/ID_discovery_cases
Probands with ASD or unexplained developmental delay/intellectual disability with or without other congenital anomalies from Shandong province in Northern China who were referred for genetic services from January 2014 to December 2018.
410
151 cases diagnosed with ASD (DSM-5 criteria, ADOS-2, confirmed by CARS score > 30) and 259 patients diagnosed with developmental delay/intellectual disability (DSM-5 criteria, confirmed by Gesell developmental scale DQ score < 75 and Wechsler Intelligence Scale for Children-Revised with IQ<70).
Mean age, 2 yrs. 11 mos.
68.78% Male
235821
0
2
2
iourov_12_ASD/ID/EP_discovery_cases
Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
54
Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
Range, 3 mos.-11 yrs.
NA
82516
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
385302
2
2
4
kucinska_24_ASD_discovery_cases
Patients referred from the Genetics Clinic and the Neurology Department of the Polish Mothers Memorial Hospital Research Institute from 20182021.
180
Cases diagnosed with ASD according to DSM-IV and DSM-5 criteria and assigned a disease code based on ICD-10 classification; a subset of cases also presented with motor and/or speech developmental delay, intellectual disability, and/or epilepsy.
Range, 2.4-17.9 yrs.
76.67% Male
2886
1
0
1
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
346000
1
0
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
30677
0
3
3
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
250000
0
1
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
273546
1
1
2
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)
30677
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.
562776
2
2
4
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
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
qPCR
han_22_ASD/DD/ID_discovery_cases
Han Chinese
Array SNP
Affymetrix SNP 6.0, Affymetrix CytoScan HD
iourov_12_ASD/ID/EP_discovery_cases
Russian
aCGH
BACs aCGH
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
kucinska_24_ASD_discovery_cases
Poland
aCGH
OGT CytoSure 4x180K
Agilent Feature Extraction v.12.1.0.3, CytoSure Interpret Software v.4.10.
aCGH or FISH
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
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
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
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
brandler_18_ASD_discovery_cases-caseSSC09326
N/A
M
ASD
Case from SSC cohort
102758857
102762031
3175
GRCh38
Duplication
Yes
digregorio_17_DD/ID_discovery_cases-DECIPHER_299932
N/A
F
DD, ID, and epilepsy/seizures
Global developmental delay, seizures
Cognitive impairment, intellectual disability
102496093
103084891
588799
GRCh38
Duplication
Yes
han_22_ASD/DD/ID_discovery_cases-case19D0589
1 yr. 11 mos.
F
Developmental delay
Developmental delay
101844971
101960388
115418
GRCh38
Duplication
No
han_22_ASD/DD/ID_discovery_cases-case19D0589
1 yr. 11 mos.
F
Developmental delay
Developmental delay
101602563
101838383
235821
GRCh38
Duplication
No
iourov_12_ASD/ID/EP_discovery_cases-case32
9 yrs. 10 mos.
F
Autism and intellectual disability
Autism, multiple hematomas, teeth anomalies. Karyotype: 1phqh, 9phqh.
Intellectual disability
100827193
100909709
82517
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001677
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
101323599
101596196
272598
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003822
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
100665849
101051159
385311
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004224
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
102510903
102866851
355949
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004292
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
101359634
101641294
281661
GRCh38
Duplication
Yes
kucinska_24_ASD_discovery_cases-case20
F
ASD and developmental regression
Autism spectrum disorders, regression of speech development, dyspraxia, hyperactivity
100366731
100369616
2886
GRCh38
Deletion
Yes
maini_18_ASD/DD/ID_discovery_cases-case216
3 yrs.
F
ASD and intellectual disability
Birth history: born at 39 weeks gestation, no reported pregnancy anomalies. Developmental milestones: motor delay, language delay. Language and communication evaluation: absent speech. Behavioral/psychiatric evaluation: ASD. Epilepsy/abnormal EEG: positive for epilepsy and/or abnormal EEG. Additional medical history: cerebral malformations, hearing loss. Dysmorphic features: posteriorly rotated ears. Growth parameters: normal head circumference, normal growth. Family history: negative for consanguineity, positive for familiarity, family history negative for NDDs.
Moderate intellectual disability
102496093
102843016
346924
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case44307
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
100941990
100972666
30677
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case59724-L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
101681244
101691407
10164
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case68257
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
101814951
101820759
5809
Unknown
Duplication
No
willemsen_12_DD/ID_discovery_cases-case29
M
Intellectual disability
Intellectual disability
Intellectual disability
100268346
100508347
240002
GRCh38
Duplication
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-controlHABC_900079_900079
N/A
N/A
Control
No previous psychiatric history
103333655
103607201
273547
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900254_900254
N/A
N/A
Control
No previous psychiatric history
100963792
101199557
235766
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11158.s1
11.6
M
Control (matched sibling)
NA
NA
100226686
100231287
4602
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11296.s1
14
M
Control (matched sibling)
NA
NA
100295885
100302906
7022
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11356.s1
9.3
M
Control (matched sibling)
NA
NA
99330744
99893520
562777
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-13322.s1
14.3
F
Control (matched sibling)
NA
NA
99791720
100217903
426184
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC09326
SNP VCF
De novo
digregorio_17_DD/ID_discovery_cases-DECIPHER_299932
qPCR
Unknown
ARMCX5,GPRASP1,RNU6-589P,BEND7P1,GPRASP2,MTND1P32,MTND2P2,MTCO1P19,MTCO2P19,MTATP6P19,MTCO3P19,MTND4P32,MTND5P26,MTND6P32,MTCYBP32,RAB40AL,BEX1,TMSB15A,FOXN3P1,NXF4,BHLHB9,LINC00630,NXF3,ARMCX5-GPRASP2
han_22_ASD/DD/ID_discovery_cases-case19D0589
Unknown
NXF5,ZMAT1,RNU6-345P
han_22_ASD/DD/ID_discovery_cases-case19D0589
Unknown
ARMCX3,ARMCX6,NXF5,GK4P,ARMCX3-AS1,RNU6-30P,RNU6-587P,ARMCX2
iourov_12_ASD/ID/EP_discovery_cases-case32
Unknown
Unknown
Unknown
HNRNPA1P26,HNRNPA1P27,CSTF2,NOX1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001677
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
RNU6-934P,NANOGNBP3,RPL21P132,TIMM8A,RPL36A,HNRNPH2,PPIAP90,ARMCX1,BTK,RPL36A-HNRNPH2,GLA,ARMCX4
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003822
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
PPIAP89,HNRNPA1P26,HNRNPA1P27,SYTL4,CSTF2,NOX1,ARL13A,TRMT2B,XKRX,TRMT2B-AS1,SRPX2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004224
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
ARMCX5,GPRASP1,RNU6-589P,BEND7P1,GPRASP2,MTND1P32,MTND2P2,MTCO1P19,MTCO2P19,MTATP6P19,MTCO3P19,MTND4P32,MTND5P26,MTND6P32,MTCYBP32,TMSB15A,FOXN3P1,NXF4,BHLHB9,LINC00630,ARMCX5-GPRASP2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004292
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPL36A,HNRNPH2,PPIAP90,ARMCX1,ARMCX7P,ARMCX6,ARMCX3,ARMCX3-AS1,RNU6-30P,BTK,RPL36A-HNRNPH2,GLA,ARMCX4
kucinska_24_ASD_discovery_cases-case20
aCGH or FISH
Paternal
PCDH19
maini_18_ASD/DD/ID_discovery_cases-case216
De novo
Simplex
Possibly segregated
ARMCX5,GPRASP1,RNU6-589P,BEND7P1,GPRASP2,MTND1P32,MTND2P2,MTCO1P19,MTCO2P19,MTATP6P19,MTCO3P19,MTND4P32,MTND5P26,MTND6P32,MTCYBP32,TMSB15A,FOXN3P1,NXF4,BHLHB9,LINC00630,ARMCX5-GPRASP2
prasad_12_ASD_discovery_cases-case44307
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case59724-L
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case68257
Unknown
Unknown
Unknown
ARMCX5-GPRASP2
willemsen_12_DD/ID_discovery_cases-case29
Unknown (not tested)
PCDH19
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900079_900079
Unknown
TCEAL9,BEX3,RAB40A,TCEAL4
engchuan_15_ASD_discovery_controls-controlHABC_900254_900254
Unknown
ARL13A,TRMT2B,TMEM35A,CENPI,TRMT2B-AS1
sanders_11_ASD_discovery_controls-11158.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11296.s1
Maternal
Simplex (quad)
NA
PCDH19
sanders_11_ASD_discovery_controls-11356.s1
Unknown
Simplex (quad)
NA
XRCC6P5,B3GNT2P1
sanders_11_ASD_discovery_controls-13322.s1
Paternal
Simplex (quad)
NA
B3GNT2P1,RPSAP8
No Animal Model Data Available