Xq13.2CNV Type: Duplication
Largest CNV size: 152396 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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Duplication
Copy number variation in Han Chinese individuals with autism spectrum disorder.
Deletion-Duplication
RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features
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.
Duplication
Phenotypic spectrum associated with duplication of Xp11.22-p11.23 includes Autism Spectrum Disorder.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
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
chung_11_ASD_discovery_cases
Autistic female proband; second child of healthy, non-consanguineous parents (first child developmentally normal)
1
ASD (ADI-R and ADOS, Module 3)
12
Female
143459
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
44107
0
1
1
gazzellone_14_ASD_discovery_cases
ASD-affected individuals referred to the Children Development and Behavior Research Center (CDRBC) at Harbin Medical University, China, between January 2007 and June 2011.
104
Diagnosis of ASD made using Autism Behavior Checklist (ABC) and Childhood Autism Rating Scale (CARS)
Mean age at enrollment, 4.31 1.80 yrs.
87.5% Male
33484
2
1
3
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
4252
1
0
1
palmer_20_ASD/ADHD/DD/ID_discovery_cases
14 males from 9 families with duplications at the Xq13.2-q13.3 locus affecting the RLIM gene
14
Cases presented with developmental delay, intellectual disability (12/14), ASD or autistic features (8/14), ADHD (3/14), and seizure disorder (2/14)
Range, 3-60 yrs.
100.0% Male
933755
0
3
3
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
54986
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
144325
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
152396
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
246687
0
2
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)
144325
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.
152396
0
1
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chung_11_ASD_discovery_cases
Scottish-Canadian
Array SNP
Affymetrix 6.0
HMM
Affymetrix Genotyping Console v.2.1, Birdseed v.2
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
gazzellone_14_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix CytoScan HD
ChAS, iPattern, Nexus, Partek
qPCR, Taqman assay
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
palmer_20_ASD/ADHD/DD/ID_discovery_cases
Australia (n=8), France (n=4), United Kindgom (n=1), and United States (n=1)
aCGH, solid phase hybridization
Agilent SurePrint G3 Human 2x400K, Agilent 44K, Agilent 180K, Illumina HumanCyto SNP-12 Beadchip, Illumina CytoSNP 850K Genome Wide
qPCR
pinto_14_ASD_discovery_cases
Predominantly European
Solid phase hybridization
Illumina 1M (v.1 and v.3)
qPCR, MLPA, long-range PCR
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
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
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
chung_11_ASD_discovery_cases-proband
12
F
ASD
Diagnosed with ASD at 8 using ADI-R & ADOS, Module 3. Moderate language delay. Comorbid behavior includes anxiety disorders, aggressive behaviors, self-injurious behaviors, sleep disturbances, & trichotillomania. No history of developmental regression. No history of seizures; normal EEG. Dysmorphic features: high anterior hairline, long face with prognathism, long nose, broad nasal bridge with underdeveloped alae nasi, asymmetic ears, narrow mouth. Camptodactyly, mild 2/3 cutaneous syndactyly, flat narrow feet, shortened 5th toes. Normal eyes and eyebrows. Prominent hypotonia. Brain MRI at 5 revealed mild prominence of Virchow-Robin spaces without any structural abnormalities. Growth parameters: height, weight, & head circumference all >97th %ile.
WISC-IV assessment: at 7 yrs., 32nd %ile (average range); at 9 yrs., 2nd-8th %ile (borderline range)
73088075
73231536
143462
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case8617_201
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
73087110
73131217
44108
GRCh38
Duplication
No
gazzellone_14_ASD_discovery_cases-case502-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
73652953
73678719
25767
GRCh38
Duplication
No
gazzellone_14_ASD_discovery_cases-case552-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
73100068
73133552
33485
GRCh38
Deletion
Yes
gazzellone_14_ASD_discovery_cases-case663-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
73112239
73133552
21314
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002443
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
73835373
73839625
4253
GRCh38
Deletion
Yes
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam4-III:1
8 yrs.
M
ASD, developmental delay, and intellectual disability
Birth/neonatal history: born at 29 weeks gestation via emergency caesarean section following a pregnancy complicated by antenatal hemorrhage; birth weight 1.5 kg. Developmental milestones: gross motor delay (walking at 18 months), speech delay (two words at 3 years). Motor and musculoskeletal evaluation: hypotonia, easy fatigability. Behavioral/psychiatric evaluation: ASD, short attention span (easily distracted), disordered sleep initiation and maintenance. Additional medical history: myopia, hernia. Dysmorphic features: almond-shaped eyes, flat midface. Growth parameters: head circumference 25th %ile (height and weight N/D).
Mild intellectual disability
74260461
74627838
367378
GRCh38
Duplication
No
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam4-III:2
5 yrs.
M
Developmental delay and intellectual disability
Birth/neonatal history: born at 36 weeks gestation following a pregnancy complicated by threatened premature delivery; birth weight 3.65 kg. Developmental milestones: delayed motor development. Language and communication evaluation: speech articulation and grammatical difficulties, hard-to-understand speech at times. Motor and musculoskeletal evaluation: low muscle tone, small joint hypermobility. Behavioral/psychiatric evaluation: autistic features, poor concentration and sustained attention. Dysmorphic features: almond-shaped eyes, upslanted palpebral fissures, flat midface, epicanthus, tall forehead, broad nasal tip. Growth parameters: head circumference 75th-90th %ile (height and weight N/D).
Mild intellectual disability
74260461
74627838
367378
GRCh38
Duplication
No
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam6-II:1
NA
M
Developmental delay and learning difficulties
Birth/neonatal history: born at term with no prenatal or perinatal complications; birth weight 3.2 kg. Developmental milestones: speech delay; normal motor developmental milestones (walking at 17 months). Motor and musculoskeletal evaluation: short fifth fingers. Behavioral/psychiatric evaluation: hyperactivity. Dysmorphic features: round and small ears. Growth parameters: height 50th %ile, weight 25th-50th %ile, head circumference 2nd %ile.
Learning difficulties
73682743
74616497
933755
GRCh38
Duplication
Yes
pinto_14_ASD_discovery_cases2-case8617_201
N/A
M
ASD
Clinical profile: N/A.
Cognitive profile: N/A.
73076232
73131217
54986
GRCh38
Duplication
Yes
prasad_12_ASD_discovery_cases-case78681
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
72229814
72374138
144325
Unknown
Duplication
No
sanders_11_ASD_discovery_cases-11400.p1
8.3
M
Autism
NA
Full-scale IQ, 111; non-verbal IQ, 114; verbal IQ, 103
73165914
73318310
152397
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-control110036024081_
N/A
N/A
Control
No previous psychiatric history
73844952
74091639
246688
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-control110040001976_
N/A
N/A
Control
No previous psychiatric history
73844952
74091639
246688
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11400.s1
10.8
F
Control (matched sibling)
NA
NA
73165914
73318310
152397
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chung_11_ASD_discovery_cases-proband
Paternal
Simplex
NA
NAP1L6,NAP1L2,TOMM20P4
engchuan_15_ASD_discovery_cases-case8617_201
Unknown
NAP1L6
gazzellone_14_ASD_discovery_cases-case502-3
Unknown
Unknown
Unknown
CHIC1
gazzellone_14_ASD_discovery_cases-case552-3
qPCR or Taqman assay
De novo
Unknown
Possibly segregated
NAP1L6
gazzellone_14_ASD_discovery_cases-case663-3
Unknown
Unknown
Unknown
NAP1L6
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002443
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
XIST
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam4-III:1
Maternal
Multiplex
Segregated
MIR545,MIR374A,ZCCHC13,RPS6P26,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RLIM,FTX,SLC16A2
Increased RLIM mRNA and protein expression in patient LCLs compared to WT
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam4-III:2
Maternal
Multiplex
Segregated
MIR545,MIR374A,ZCCHC13,RPS6P26,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RLIM,FTX,SLC16A2
palmer_20_ASD/ADHD/DD/ID_discovery_cases-caseFam6-II:1
qPCR
Maternal
Simplex
Segregated
SEPHS1P4,RPSAP14,SHISA5P2,AARSD1P1,UHRF2P1,DDX3P2,MKRN5P,ATP5MDP1,MIR421,MIR374B,MIR374C,RN7SL648P,MIR545,MIR374A,ZCCHC13,RPS6P26,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,XIST,FXYD6P3,DDX3P1,RAB11FIP1P1,RLIM,CHIC1,TSIX,FTX,JPX,BMP2KL,SLC16A2
pinto_14_ASD_discovery_cases2-case8617_201
qPCR
Maternal (X-linked in a male)
Unknown
(not tested)
PABPC1L2A,NAP1L6
prasad_12_ASD_discovery_cases-case78681
Unknown
Unknown
Unknown
NAP1L2,NAP1L6
sanders_11_ASD_discovery_cases-11400.p1
Unknown
Simplex (quad-proband matched)
Segregated
NAP1L2,TOMM20P4,YWHAZP8
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036024081_
Unknown
RPSAP14,XIST,FXYD6P3,JPX,FTX
engchuan_15_ASD_discovery_controls-control110040001976_
Unknown
RPSAP14,XIST,FXYD6P3,JPX,FTX
sanders_11_ASD_discovery_controls-11400.s1
Maternal
Simplex (quad)
NA
NAP1L2,TOMM20P4,YWHAZP8
No Animal Model Data Available