Xq13.3CNV Type: Deletion
Largest CNV size: 90882 bp
Statistics Box:
Number of Reports: 12
Number of Reports: 12
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...
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
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
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.
Deletion
Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...
Deletion-Duplication
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
Duplication
Chromosomal microarray in clinical diagnosis: a study of 337 patients with congenital anomalies and developmental delays or intellectual disability.
Duplication
NEXMIF encephalopathy: an X-linked disorder with male and female phenotypic patterns
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chehbani_22_ASD_discovery_cases
Patients recruited between January and April 2017 at the Child and Adolescent Psychiatry Clinic of the Department of Psychiatry, Fattouma Bourguiba University Hospital (Monastir, Tunisia); 91 patients were from simplex families, and 7 from multiplex families.
98
Clinical diagnosis of ASD based on DSM-IV and confirmed by ADI-R and ADOS.
Range, 3-18 yrs.
84.69% Male
201822
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
201670
2
4
6
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
166433
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
188323
0
3
3
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
4770
0
1
1
lesca_12_EP_discovery_cases
Epilepsy patients collected at four French hospitals from 2009: Strasbourg Univ. Hospital (n=40), Lyons Univ. Hospital (n=18), Henri Gastaut Hospital (St. Paul Centre) in Marseille (n=2), and Reims American Memorial Hospital (n=1).
61
Epilepsy/epileptic encephalopathy. 41 patients with continuous spike and wave during slow-wave sleep syndrome (CSWSS), 20 patients with Landau-Kleffner syndrome (LKS). 12 (out of 57) patients displayed autistic features; ADHD features (hyperactivity, attention deficit and/or aggressiveness) reported in 41/58 patients,
Mean age of diagnosis: 5.6 yrs. (range, 1-14 yrs.)
61% Male
57000
1
1
2
mosca_16_DCD_discovery_cases
Participants recruited as part of a multidisciplinary study at the Alberta Children's Hospital (Calgary, Alberta, Canada)
82
All cases met diagnostic criteria for developmental coordination disorder (DCD) with or without co-occurring ADHD and/or reading disorder.
Range, 8-17 years (Mean, 10.06 2.92 yrs.)
N/A
192852
0
1
1
pinto_14_ASD_discovery_cases
ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
1359
Cases classified according to ADOS and ADI-R
N/A
N/A
60666
0
1
1
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
129256
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
90882
1
0
1
sansovic_17_DD/ID/ASD_discovery_cases
Unrelated patients from Croatia referred to the Department of Medical Genetics and Reproductive Health, Children's Hospital Zagreb, University of Zagreb School of Medicine
337
Cases diagnosed by clinical geneticists or pediatricians to have developmental delay/intellectual disability (DD/ID), ASD, congenital anomalies, or a combination of those features
Mean, 7 years (range, 1 month-25 years)
N/A
187000
0
1
1
stamberger_20_DD/ID_discovery_cases
Patient with NEXMIF encephalopathy recruited through the Epilepsy Genetics Research program at the University of Melbourne and a NEXMIF European collaboration
1
Case presented with developmental delay, intellectual disability, and epilepsy
26 yrs.
Female
77391
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
227486
2
4
6
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
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
136509
0
2
2
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
188770
1
2
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chehbani_22_ASD_discovery_cases
Tunisia
aCGH
Agilent SurePrint G3
ADM-2
Agilent Cytogenomic v.4.0.3.12.
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
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
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
lesca_12_EP_discovery_cases
France
aCGH
Agilent SurePrint G3 Human CGH Microarray 4x180K
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent Genomic WORKBENCH v5.0.14
None
mosca_16_DCD_discovery_cases
Canada
Solid phase hybridization
Illumina HumanOmni2.5-Quad BeadChip
iPattern, PennCNV, QuantiSNP, CNVPartition
None
pinto_14_ASD_discovery_cases
Predominantly European
Solid phase hybridization
Illumina 1M (v.1 and v.3)
qPCR, MLPA, long-range PCR
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
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
sansovic_17_DD/ID/ASD_discovery_cases
Croatia
aCGH
Agilent SurePrint G3 Unrestricted CGH ISCA v2
Agilent Feature Extraction (v12.0), Agilent CytoGenomics (v3.0 and v4.0)
None
stamberger_20_DD/ID_discovery_cases
NA
NA
NA
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
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
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
chehbani_22_ASD_discovery_cases-case87
NA
F
ASD and intellectual disability
Case diagnosed with ASD based on DSM-IV criteria and confirmed by ADI-R and ADOS-2.
Intellectual disability.
74731031
74932852
201822
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case13002_33
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
75283757
75485427
201671
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case14116_2080
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
76154115
76208215
54101
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case18113_302
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
75182793
75243458
60666
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case3563_4
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
75550141
75616125
65985
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case5274_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
75193235
75243458
50224
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5353_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
76629157
76669469
40313
GRCh38
Deletion
No
iourov_12_ASD/ID/EP_discovery_cases-case41
3 yrs.
F
Developmental delay
Severe speech delay, microcephaly, facial dysmorphisms, single transverse palmar crease. Karyotype: 9qh-.
Severe cognitive delay
75346477
75512910
166434
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001782
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
75012979
75197052
184074
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001982
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
75243091
75431414
188324
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005212
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
75243922
75372926
129005
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case11824.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
76173138
76177908
4771
GRCh38
Duplication
Yes
lesca_12_EP_discovery_cases-case15-211
NA
M
Epilepsy + autistic features
Phenotype: i-CSWSS. Seizure Characteristics: CPS. Autistic features: Yes. ADHD features: No. Other features: None.
Initial cognitive development: Normal. Cognitive regression: Yes.
75196996
75247115
50120
GRCh38
Duplication
No
lesca_12_EP_discovery_cases-caseDZ52
NA
F
Epilepsy
Phenotype: i-CSWSS. Seizure Characteristics: None. Autistic features: No. ADHD features: Yes. Other features: None.
Initial cognitive development: Normal. Cognitive regression: Yes.
76067425
76124526
57102
GRCh38
Deletion
No
mosca_16_DCD_discovery_cases-case101703
N/A
M
DCD (with or without ADHD and/or RD)
Ancestry: unknown. Family history: maternal diagnosis unknown; paternal diagnosis unknown.
75240526
75433377
192852
GRCh38
Duplication
No
pinto_14_ASD_discovery_cases2-case18113_302
N/A
F
ASD
Clinical profile: N/A.
Cognitive profile: N/A.
75182793
75243458
60666
GRCh38
Duplication
Yes
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-274
N/A
N/A
CBLH
Diagnosis of cerebellar hypoplasia (CBLH).
75298324
75427579
129256
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_cases-12158.p1
5.7
M
Autism
NA
Full-scale IQ, 86; non-verbal IQ, 81; verbal IQ, 100
75550141
75641023
90883
GRCh38
Deletion
No
sansovic_17_DD/ID/ASD_discovery_cases-case12
7 yrs.
M
Developmental delay/intellectual disability
Developmental delay/intellectual disability, Congenital anomalies, Dysmorphism
75243922
75431414
187493
GRCh38
Duplication
No
stamberger_20_DD/ID_discovery_cases-caseFamF31-p34
26 yrs.
F
Developmental delay, intellectual disability, and seizures
Birth/neonatal history: broken clavicle at birth. Developmental milestones: delayed speech and language development (sentences). Behavioral/psychiatric evaluation: liability for depression and anxiety. Epilepsy/seizures: seizures with onset at 16 months; seizure types included absence seizures with eyelid myoclonia, absence seizures, and a single episode of generalized tonic-clonic seizures. EEG: abnormal EEG (sharply contoured runs of alpha activity at times (prolonged eye blink) on interictal and ictal EEG). Additional medical history: gastroesophageal reflux as an infant. Growth parameters: overweight. Family history: patient was of Caucasian ancestry; family history was notable for a distant maternal cousin with generalized tonic-clonic seizures at 16 years and learning disability, a distant maternal relative with absence seizures in childhood, and the sister of the paternal grandmother with "drop seizures" and possible developmental delay.
Mild intellectual disability
74710688
74788078
77391
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-control110036024057_
N/A
N/A
Control
No previous psychiatric history
75243458
75430186
186729
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB356202_1007844561
N/A
N/A
Control
No previous psychiatric history
75243458
75470944
227487
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB653776_1007846516
N/A
N/A
Control
No previous psychiatric history
75243458
75458225
214768
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB656904_1007840969
N/A
N/A
Control
No previous psychiatric history
75552157
75608415
56259
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900522_900522
N/A
N/A
Control
No previous psychiatric history
75552157
75616125
63969
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_902520_902520
N/A
N/A
Control
No previous psychiatric history
75175011
75273467
98457
GRCh38
Duplication
No
krumm_15_ASD_discovery_controls-control11824.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
76173138
76177908
4771
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_controls-control13266.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
75293471
75429980
136510
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_controls-11620.s1
15.1
F
Control (matched sibling)
NA
NA
75193235
75243458
50224
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12624.s1
4.1
F
Control (matched sibling)
NA
NA
76274654
76286853
12200
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13266.s1
7.9
F
Control (matched sibling)
NA
NA
75243458
75432228
188771
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chehbani_22_ASD_discovery_cases-case87
Unknown
Simplex
NEXMIF
engchuan_15_ASD_discovery_cases-case13002_33
Unknown
RPL21P134,UPRT,ZDHHC15
engchuan_15_ASD_discovery_cases-case14116_2080
Unknown
PBDC1
engchuan_15_ASD_discovery_cases-case18113_302
Unknown
BUD31P2,RNU6-562P
engchuan_15_ASD_discovery_cases-case3563_4
Unknown
BRAFP1
engchuan_15_ASD_discovery_cases-case5274_3
Unknown
BUD31P2,RNU6-562P
engchuan_15_ASD_discovery_cases-case5353_3
Unknown
RNA5SP508,TRAPPC13P1,MIR325HG
iourov_12_ASD/ID/EP_discovery_cases-case41
Unknown
Unknown
Unknown
RPL21P134,ZDHHC15
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001782
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
ABCB7
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001982
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RPL21P134,UPRT,ZDHHC15
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005212
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
UPRT,ZDHHC15
krumm_15_ASD_discovery_cases-case11824.p1
Illumina 1MDuo
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
PBDC1
lesca_12_EP_discovery_cases-case15-211
Unknown
Unknown
Unknown
BUD31P2,RNU6-562P
lesca_12_EP_discovery_cases-caseDZ52
Unknown
Unknown
Unknown
mosca_16_DCD_discovery_cases-case101703
Unknown
Unknown
Unknown
RPL21P134,UPRT,ZDHHC15
pinto_14_ASD_discovery_cases2-case18113_302
qPCR
Paternal
Multiplex
1 affected sib with deletion of the same region, 1 affected sib with duplication of the same region
BUD31P2,RNU6-562P
sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-274
qPCR
Maternal
Unknown
Unknown
RPL21P134,UPRT,ZDHHC15
sanders_11_ASD_discovery_cases-12158.p1
Maternal
Simplex (trio)
NA
BRAFP1
sansovic_17_DD/ID/ASD_discovery_cases-case12
Maternal
RPL21P134,UPRT,ZDHHC15
stamberger_20_DD/ID_discovery_cases-caseFamF31-p34
De novo
NEXMIF
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036024057_
Unknown
RPL21P134,UPRT,ZDHHC15
engchuan_15_ASD_discovery_controls-controlB356202_1007844561
Unknown
RPL21P134,UPRT,ZDHHC15
engchuan_15_ASD_discovery_controls-controlB653776_1007846516
Unknown
RPL21P134,UPRT,ZDHHC15
engchuan_15_ASD_discovery_controls-controlB656904_1007840969
Unknown
BRAFP1
engchuan_15_ASD_discovery_controls-controlHABC_900522_900522
Unknown
BRAFP1
engchuan_15_ASD_discovery_controls-controlHABC_902520_902520
Unknown
BUD31P2,RNU6-562P
krumm_15_ASD_discovery_controls-control11824.s1
Illumina 1MDuo
Maternal
PBDC1
krumm_15_ASD_discovery_controls-control13266.s1
Illumina 1MDuo
Paternal
RPL21P134,UPRT,ZDHHC15
sanders_11_ASD_discovery_controls-11620.s1
Paternal
Simplex (quad)
NA
BUD31P2,RNU6-562P
sanders_11_ASD_discovery_controls-12624.s1
Both parents
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-13266.s1
Paternal
Simplex (quad)
NA
RPL21P134,UPRT,ZDHHC15
No Animal Model Data Available