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Xq13.2CNV Type: Duplication


Largest CNV size: 152396 bp

Statistics Box:
Number of Reports: 8



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

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
 

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