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15q13.2CNV Type: Deletion-Duplication


Largest CNV size: 693884 bp

Statistics Box:
Number of Reports: 15



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
Functional impact of global rare copy number variation in autism spectrum disorders.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
Dysfunction of SHANK2 and CHRNA7 in a patient with intellectual disability and language impairment supports genetic epistasis of the two loci.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.
Deletion
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Duplication
Rare deletions at the neurexin 3 locus in autism spectrum disorder.
Duplication
Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
Deletion
Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures.
Deletion
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion-Duplication
Analysis of CHRNA7 rare variants in autism spectrum disorder susceptibility.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Recurrent copy number variations as risk factors for Autism Spectrum Disorders: analysis of the clinical implications.
Deletion
Two de novo variations identified by massively parallel sequencing in 13 Chinese families with children diagnosed with autism spectrum disorder.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 bacchelli_15_ASD_discovery_cases
 ASD cases screened for 15q13.3 CNVs from 133 families recruited at the Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry (Calambrone, Pisa, Italy)
 135
 ASD diagnosis based on ADI-R and ADOS
 N/A
 N/A
 55000
 1
 0
 1
 celestino-soper_11_ASD_discovery_cases
 ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
 99
 ASD
 
 87.88% Male
 35270
 1
 0
 1
 chilian_13_DD/ID_discovery_cases
 Patient, born to healthy non-consanguineous parents with no family history of ID, referred at 18 months of age for marked psychomotor and developmental delay; patient carries balanced de novo triple translocation t(11;17;19)(q13.3;q25.1;q13.42)dn with breakpoint disrupting the SHANK2 gene.
 1
 Severe DD/ID, language impairment, behavioral abnormalities
 5 yrs.
 Male
 152124
 1
 0
 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
 693883
 13
 2
 15
 gai_11_ASD_discovery_cases
 Discovery case samples derived from AGRE set 4 (most recent patient recruitment)
 631
 Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
 
 
 130921
 1
 0
 1
 gregory_09_ASD_discovery_cases
 Probands from multiplex autism families
 119
 Idiopathic autism, minimum IQ equivalent of 35 or Vineland Adaptive Behavior Scale age equivalent of 18 months
 
 78.15% Male
 182240
 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
 229181
 1
 1
 2
 leblond_12_ASD_discovery_cases
 ASD cases recruited by the PARIS (Paris Autism Research International Sibpair) study at specialized centers disposed in France, Sweden, Germany, Finland, and the UK.
 260
 171 cases with autism, 20 cases with atypical autism, 69 cases with Asperger syndrome (ADOS and either ADI-R or DISCO-10 used for diagnosis). 79 cases with IQ>70, 133 cases with IQ<70, 48 cases with unknown IQ.
 
 74.6% Male
 49767
 1
 0
 1
 leblond_12_ASD_replication_cases
 Dataset featuring ASD patients from the Autism Genome Project carrying de novo SHANK2 deletions previously identified by Pinto et al. 2010. CNV validation information taken from Pinto report.
 2
 1 patient diagnosed with autism, 1 patient diagnosed with PDD-NOS.
 NA
 100% Male
 23517
 1
 0
 1
 lionel_13_ASD/SCZ/EP_discovery_cases
 Patient cohort composed of 1158 Canadian ASD patients, 72 Austrian ASD patients, 450 Canadian schizophrenia patients, and a clinical dataset of 3704 individuals with primary diagnosis of ASD and/or seizure disorder referred for clinical microarray testing at the Mayo Clinic cytogenetics laboratory.
 5384
 ASD (n=1230), schizophrenia (n=450), and ASD and/or seizure disorder (n=3704). Canadian and Austrian ASD patients met criteria for ASD diagnosis based on ADI-R and/or ADOS.
 NA
 NA
 159633
 1
 0
 1
 li_18_ASD_discovery_cases
 Children from 13 ASD trio families recruited at the Department of Pediatrics of the Chinese PLA General Hospital for Autism Research
 13
 Diagnosis of ASD made according to DSM-IV
 Mean age, 4.56 0.97 years
 92.31% Male
 104599
 1
 0
 1
 oikonomakis_16_ASD_discovery_cases
 ASD cases evaluated with chromosomal microarray (CMA) from 2008-2015
 195
 Cases assessed for ASD according to DSM-IV behavioral criteria
 Range, 1-38 yrs.
 64.61% Male
 498800
 2
 0
 2
 pinto_10_ASD_discovery_cases
 Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
 996
 ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
 
 
 693884
 2
 0
 2
 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
 277810
 3
 2
 5
 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
 71183
 0
 2
 2
 vaags_11_ASD_replication_cases_2
 Replication cohort consisting of patients referred to the Mayo Clinic
 1796
 Autism or pervasive developmental disorder (PDD)
 NA
 NA
 536758
 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
 418512
 15
 2
 17
 gregory_09_ASD_discovery_controls
 Samples from 27 sex-mismatched hybridizations
 54
 Controls
 
 50% Male
 374451
 1
 0
 1
 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
 kanduri_15_ASD_discovery_controls
 Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
 269
 Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 N/A
 N/A
 152159
 4
 0
 4
 sanders_11_ASD_discovery_controls
 Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
 872
 Controls
 Mean, 10.0 yrs.
 
 49943
 2
 0
 2

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 bacchelli_15_ASD_discovery_cases
  Italian
 Solid phase hybridization
  Illumina 1M-Duo
 
 QuantiSNP, PennCNV
 None
 celestino-soper_11_ASD_discovery_cases
 
 aCGH
  Agilent 1M
 ADM-2
 Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
 Solid phase hybridization (Illumina 1M SNP)
 chilian_13_DD/ID_discovery_cases
  Germany
 aCGH
  Agilent Human Genome CGH Microarray 244A
 
 
 qPCR
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 gai_11_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium II HumanHap550 BeadChip
 
 BeadStudio 3.0
 None
 gregory_09_ASD_discovery_cases
 
 aCGH
  BACs aCGH
 BioDiscovery RSA
 Bluefuse, Nexus
 
 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
 leblond_12_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina Human 1M-Dup BeadChip
 QuantiSNP, PennCNV
 
 None
 leblond_12_ASD_replication_cases
  1 Canadian, 1 French
 Solid phase hybridization
  Illumina 1M SNP array
 QuantiSNP, PennCNV
 
 None
 lionel_13_ASD/SCZ/EP_discovery_cases
  NA
 aCGH, array SNP
  Agilent ISCA 44K, Agilent 180K, Affymetrix 6.0
 
 Agilent DNA Analytics, Birdsuite, iPattern, Affymetrix Genotyping Console
 None
 li_18_ASD_discovery_cases
  Chinese
 Low-coverage WGS
  Illumina HiSeq 2000 or 2500 analyzers
 PSCC
 
 None
 oikonomakis_16_ASD_discovery_cases
  Greece
 aCGH
  Agilent 244K, 4x180K, or 4x180K (SurePrint G3 arrays)
 
 
 None
 pinto_10_ASD_discovery_cases
  European
 Solid phase hybridization
  Illumina Infinium 1M SNP microarray
 QuantiSNP, iPattern
 
 qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
 sajan_13_ACC/CBLH/PMG_discovery_cases
  81.31% Caucasian
 Solid phase hybridization
  Illumina InfiniumII HumanHap610
 PennCNV
 
 None (not tested or failure to confirm by 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
 
 
 vaags_11_ASD_replication_cases_2
  NA
 aCGH
  Agilent 44K & 244K
 
 
 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
  gregory_09_ASD_discovery_controls
 
  aCGH
  BACs aCGH
  BioDiscovery RSA
  Bluefuse, Nexus
 
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  kanduri_15_ASD_discovery_controls
  Finnish
  Solid phase hybridization
  Illumina Infinium HD Human610-Quad BeadChip
  QuantiSNP, PennCNV
  Illumina BeadStudio
  None
  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
  bacchelli_15_ASD_discovery_cases-case3474_3
 13 yrs.
 M
 Autism
 Diagnosis of autism based on meeting ADI-R and ADOS criteria. Birth and neonatal history: no exposure of history of alcohol, tobacco, or drug abuse during pregnancy; born at term by C-section; birth weight of 3550 g (50th %ile) and length of 50 cm (50th %ile); breast-fed with good suction. Developmental milestones: sat unaided at age of 8 months, started walking independently at 16 months; babbling noted at age of 9 months, pronounced first words at 12 months; regression of language skills at age 18 months associated with refusal of physical contact, selective feeding, and hyperactivity. Language and communication evaluation: able to pronounce only single words with reduced gesture repertoire; limited comprehension. Epilepsy/seizures: developed complex partial seizures with secondary generalization at age of 13 years. EEG: reported to be normal at age of 5 years 5 months. Brain imaging: brain MRI reported to be normal. Dysmorphic features: bilateral epicanthal folds, broad-hypoplastic nasal bride, prominent digit pads. Growth parameters: weight of 26 kg (97th %ile), height of 114 cm (50th-75th %ile), and OFC of 55.5 cm (>90th %ile) at age of 5 years 5 months. Family history: only child of healthy non-consanguineous parents; paternal grandfather's sister affected by intellectual disability; paternal grandfather's brother had speech delay.
 Moderate cognitive impairment
 N/A
 N/A
  55000
 GRCh37
 Deletion
 No
  celestino-soper_11_ASD_discovery_cases-11178
 NA
 M
 ASD
 NA
 NA
 30361443
 30396713
  35271
 GRCh38
 Deletion
 Yes
  chilian_13_DD/ID_discovery_cases-case1
 5 yrs.
 M
 Developmental delay/intellectual disability
 Patient referred at 18 months for marked psychomotor and developmental delay. Karyotype: 46, XY, t(11;17;19)(q13.3;q25.1;q13.42)dn; translocation with breakpoints within the SHANK2 and UBE2O genes. Birth/neonatal history: duing pregnancy mother had cervical cancer (treated after birth), born at 39 weeks gestation by C-section; birth weight -0.23 SD, length -0.83 SD, OFC +0.7 SD; uneventful perinatal adaption; ventricular septal defect diagnosed at 2 months. Developmental milestones: psychomotor retardation noted at 1.5 years; sat independently at 8 months, began to walk with support at 2.5 years, independent walking at 3.5 years, not toilet trained at 5 years of age. Language and communication evaluation: no spoken language. Motor and musculoskeletal evaluation: ataxia, able to stand with support. Behavioral/psychiatric evaluation: anxious, exhibited habit disorder with stereotypic movements, decreased sensitivity to pain, often caused self-injury. EEG: increased irregular activity. Brain imaging: normal by ultrasound. Visual and auditory evaluation: normal. Sleep disturbances: serious sleeping disturbances. Other features: elevated alkaline phosphatase, lactate dehydrogenase, and serum magnesium levels. Dysmorphic features: coarse face with facial dysmorphism, broad thorax, clinodactyly of 2nd and 3rd toes. Growth parameters: weight of 19.3 kg (+0.1 SD), length of 105 cm (-1.0 SD) and OFC of 51 cm (0 SD) at 5 years of age. Family history: second child of healthy non-consanguineous parents; no family history of miscarriages, ID, or alcohol exposure in utero.
 Severe DD/ID. Evaluation at age of 1.5 years: Brunet-Lezine development test showed delay in movements, coordination, communication, and social skills; psychomotor development corresponded to 9 months, development quotient of 48; Bayley Scales of Infant Development gave Developmental Index score of 84.
 30527262
 30679386
  152125
 GRCh38
 Deletion
 Yes
  engchuan_15_ASD_discovery_cases-case1231_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30108393
 30802276
  693884
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case14022_460
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30606930
 30816586
  209657
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case14143_2410
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30635314
 30675803
  40490
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case20164_1684001
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30651309
 30683173
  31865
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case20165_1702001
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30621004
 30683173
  62170
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case2303_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30644082
 30683173
  39092
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case3474_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30621004
 30675803
  54800
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case3607_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30578492
 30814623
  236132
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4177_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30606930
 30705755
  98826
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4238_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30606930
 30705755
  98826
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4301_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30606930
 30730116
  123187
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case4534_1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30626045
 30693848
  67804
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case5248_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30635007
 30675803
  40797
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case5277_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30561883
 30802276
  240394
 GRCh38
 Duplication
 No
  engchuan_15_ASD_discovery_cases-case5320_3
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 30626045
 30720374
  94330
 GRCh38
 Deletion
 No
  gai_11_ASD_discovery_cases-AU1390301
 
 
 Autism
 
 
 28723577
 28854497
  130921
 Unknown
 Deletion
 No
  gregory_09_ASD_discovery_cases-19981880
 NA
 
 ASD
 NA
 NA
 30095831
 30278071
  182241
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001105
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 30662523
 30891704
  229182
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002644
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 30639641
 30746551
  106911
 GRCh38
 Deletion
 Yes
  leblond_12_ASD_discovery_cases-AUGB038_3
 11.05 yrs.
 M
 Autism
 ADI-R domain scores (at 11 yrs.): social, 24; communication, 23; behavior, 6. Birth/neonatal history: normal pregnancy and delivery, at term; height 48 cm, weight 2500 g, HC 31 cm; Apgar scores of 7 and 10; no mention of signs of hypotonia in first year. Developmental milestones: apparently normal motor acquisition, severe speech delay; age of sitting, 6 months; age of walking, 18 months; age of first words, 48 months; age of first sentences, 78 months; no regression during development. Language and communication evaluation: expressive language limited to restrictive sentences, mainly dyssyntaxic. Neurological evaluation: normal neurological exam. Epilepsy/seizures: none. EEG: no significant epileptic event reported. Brain imaging: ND. Other exams: karyotype, fragile X, and metabolic screening normal. Other comorbid conditions: inguinal hernia, operated at 2 months of age; hypermetropia and astigmatism. Dysmorphic features: prominent chin, no other dysmorphic features. Family history: non-consanguineous parents, no relevant personal and familial history of psychiatric or medical illness.
 Composite score on Kaufman Assessment Battery for Children/K-ABC (age at evaluation, 11.05 years) of 40 (moderate ID)
 30644082
 30693848
  49767
 GRCh38
 Deletion
 No
  leblond_12_ASD_replication_cases-Pintocase5237_3
 NA
 M
 Autism
 Diagnosis of autism based on ADI-R and ADOS. Language and communication evaluation: below average language (<1st %ile). Epilepsy/seizures: no history of epilepsy. Dysmorphic features: minor, including 5th finger clinodactyly and several curled toes.
 Below average non-verbal IQ (<1st %ile)
 30440634
 30675803
  235170
 GRCh38
 Deletion
 No
  lionel_13_ASD/SCZ/EP_discovery_cases-proband5
 24 yrs.
 M
 Schizophrenia
 Diagnosis of chronic schizophrenia confirmed through use of detailed psychiatric assessment, including use of a modified version of Strructed Clinical Interviews for DSM-III-R for Axis I disorder. Developmental milestones: no evidence of developmental delay. Behavioral/psychiatric evaluation: increasing anxiety, preoccupation, and paranoia at 23 years (responded well ti a few months of treatment with chloropromazine); admitted to hospital for schizophrenia at 24 years of age; improved with electroconvulsive therapy and was discharged for two months; following two additional hospitalizations, case has been relatively stable on standard antipsychotic medication regiment with an adjuvant antidepressant for many years. no evidence of autistic features. Epilepsy/seizures: no history of seizures. Dysmorphic features: no significant dysmorphology. Family history: non-consanguineous parents; no known history of neuropsychiatric illness or seizures in parents or siblings; significant history of schizophrenia in paternal extended family.
 Full Scale IQ of 92 (Wechsler Adult Intelligence Scale/WAIS) at 24 years of age.
 30297594
 30457226
  159633
 GRCh38
 Deletion
 No
  li_18_ASD_discovery_cases-case4601
 N/A
 M
 ASD
 Diagnosis of ASD made according to DSM-IV
 
 30591968
 30696567
  104600
 GRCh38
 Deletion
 No
  oikonomakis_16_ASD_discovery_cases-case543
 3 yrs.
 F
 ASD
 Case was assessed for ASD according to DSM-IV behavioral criteria. Clinical characteristics other than ASD: growth deficiency, stereotypic movements, frontal bossing, arched upper lip, macrostomia, open mouth, microcephaly
 
 30097818
 30596650
  498833
 GRCh38
 Deletion
 No
  oikonomakis_16_ASD_discovery_cases-case673
 4 yrs.
 M
 ASD
 Case was assessed for ASD according to DSM-IV behavioral criteria. Clinical characteristics other than ASD: hypospadias
 
 30527262
 30785630
  258369
 GRCh38
 Deletion
 No
  pinto_10_ASD_discovery_cases-case1231_3
 NA
 M
 Autism
 Verbal, delayed suture closure, complex partial seizures
 Normal IQ
 30108393
 30802276
  693884
 GRCh38
 Deletion
 Yes
  pinto_10_ASD_discovery_cases-case5320_3
 NA
 M
 ASD
 NA
 NA
 30626045
 30720374
  94330
 GRCh38
 Deletion
 Yes
  sajan_13_ACC/CBLH/PMG_discovery_cases-case1545-0
 N/A
 N/A
 ACC
 Diagnosis of agenesis of the corpus callosum (ACC). ASD: no. Seizures: no.
 Developmental delay: yes. Intellectual disability: no.
 30198235
 30377322
  179088
 GRCh38
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-274
 N/A
 N/A
 CBLH
 Diagnosis of cerebellar hypoplasia (CBLH).
 
 30167332
 30445141
  277810
 GRCh38
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR04-181
 N/A
 N/A
 PMG
 Diagnosis of polymicrogyria (PMG).
 
 30644082
 30810692
  166611
 GRCh38
 Duplication
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR08-019
 N/A
 N/A
 ACC-CBLH-PMG
 Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and polymicrogyria (PMG). ASD: N/A. Seizures: N/A.
 Developmental delay: N/A. Intellectual disability: N/A.
 30635007
 30810692
  175686
 GRCh38
 Duplication
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR08-279a2
 N/A
 N/A
 PMG
 Diagnosis of polymicrogyria (PMG).
 
 30658326
 30796240
  137915
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11370.p1
 14.6
 M
 Autism
 NA
 Full-scale IQ, 100; non-verbal IQ, 110; verbal IQ 102
 30440634
 30511817
  71184
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12044.p1
 5.6
 M
 Autism
 NA
 Full-scale IQ, 72; non-verbal IQ, 75; verbal IQ, 76
 30437332
 30491379
  54048
 GRCh38
 Duplication
 No
  vaags_11_ASD_replication_cases_2-probandF4-003
 3 yrs. 6 mos.
 M
 Autism
 Diagnosis of autism based on clinical diagnosis, C-TRF (Caregiver-Teacher Report Form), and DSM-Oriented Scales for Boys (>97th %ile). Aggression, anger, anxiety, temper tantrums, social avoidance, sucking and biting of hands and fingers, sleep-onset disorder, upper-body hypotonia, thumb-flexion difficulty, oppositional defiance, previous head banging, and prior speech delay
 Leiter-R IQ: incomplete (test attempted but proband failed to complete)
 30081191
 30617948
  536758
 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-control110036017473_
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635007
  30683173
  48167
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-control110036023653_
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30569581
  30675803
  106223
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-control110036024040_
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30606930
  30683173
  76244
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB250058_1007852610
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635007
  30683173
  48167
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB301469_1007854697
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635007
  30675803
  40797
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB365205_1007853975
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30490577
  30797323
  306747
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB419502_1007871739
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635007
  30693848
  58842
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB443041_1007873134
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30626045
  30693848
  67804
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB476720_1007853882
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635314
  30675803
  40490
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB549396_1007854239
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30606930
  30683173
  76244
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB980109_1007875790
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30626045
  30675803
  49759
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900499_900499
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30592457
  30657422
  64966
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_900976_900976
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30239163
  30520360
  281198
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902474_902474
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30635007
  30675803
  40797
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902607_902607
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30173945
  30592457
  418513
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902667_902667
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30621004
  30675803
  54800
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlHABC_902690_902690
  N/A
  N/A
  Control
  No previous psychiatric history
 
  30621004
  30675803
  54800
  GRCh38
  Deletion
  No
  gregory_09_ASD_discovery_controls-control5
  NA
 
  Control
  NA
  NA
 
 
  374451
  NCBI36
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split1055
  N/A
  N/A
  Control
  Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 
  30936285
  31088443
  152159
  Unknown
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split1785
  N/A
  N/A
  Control
  Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 
  30936285
  31088443
  152159
  Unknown
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split1797
  N/A
  N/A
  Control
  Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 
  30936285
  30964572
  28288
  Unknown
  Deletion
  No
  kanduri_15_ASD_discovery_controls-control_split341
  N/A
  N/A
  Control
  Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
 
  30936285
  30964572
  28288
  Unknown
  Deletion
  No
  sanders_11_ASD_discovery_controls-11098.s1
  5.7
  F
  Control (matched sibling)
  NA
  NA
  30440634
  30490577
  49944
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11798.s1
  7.2
  F
  Control (matched sibling)
  NA
  NA
  30089917
  30118412
  28496
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 bacchelli_15_ASD_discovery_cases-case3474_3
 
 
 Paternal
 Possible multi-generational
 Unknown
 ARHGAP11B
 
 celestino-soper_11_ASD_discovery_cases-11178
 Solid phase hybridization (Illumina 1M SNP)
 
 De novo
 Simplex
 NA
 CHRFAM7A
 
 chilian_13_DD/ID_discovery_cases-case1
 qPCR
 
 Paternal
 Possibly simplex (no info on 1st child)
 Unknown
 RN7SL796P,DNM1P50,RN7SL628P,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case1231_3
 
 
 Unknown
 
 
 GOLGA8T,RN7SL469P,DNM1P30,RNU6-17P,RN7SL196P,RN7SL796P,DNM1P50,RN7SL628P,GOLGA8UP,RN7SL82P,ULK4P3,LINC02249,CHRFAM7A,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B,GOLGA8R
 
 engchuan_15_ASD_discovery_cases-case14022_460
 
 
 Unknown
 
 
 RN7SL628P,GOLGA8UP,RN7SL82P,GOLGA8H,ARHGAP11B,HERC2P10
 
 engchuan_15_ASD_discovery_cases-case14143_2410
 
 
 Unknown
 
 
 ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case20164_1684001
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case20165_1702001
 
 
 Unknown
 
 
 ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case2303_1
 
 
 Unknown
 
 
 
 
 engchuan_15_ASD_discovery_cases-case3474_3
 
 
 Unknown
 
 
 ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case3607_3
 
 
 Unknown
 
 
 RN7SL628P,GOLGA8UP,RN7SL82P,ULK4P2,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case4177_1
 
 
 Unknown
 
 
 RN7SL628P,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case4238_1
 
 
 Unknown
 
 
 RN7SL628P,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case4301_1
 
 
 Unknown
 
 
 RN7SL628P,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case4534_1
 
 
 Unknown
 
 
 ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case5248_3
 
 
 Unknown
 
 
 ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case5277_3
 
 
 Unknown
 
 
 DNM1P50,RN7SL628P,GOLGA8UP,RN7SL82P,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B
 
 engchuan_15_ASD_discovery_cases-case5320_3
 
 
 Unknown
 
 
 ARHGAP11B
 
 gai_11_ASD_discovery_cases-AU1390301
 
 
 Inherited
 
 
 ARHGAP11B
 
 gregory_09_ASD_discovery_cases-19981880
 
 
 Unknown
 NA
 NA
 DNM1P28,GOLGA8T,RN7SL469P,DNM1P30,RNU6-17P,ULK4P3,LINC02249
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001105
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 GOLGA8UP,RN7SL82P,HERC2P10
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002644
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 
 
 leblond_12_ASD_discovery_cases-AUGB038_3
 
 
 Maternal
 Simplex
 
 
 
 leblond_12_ASD_replication_cases-Pintocase5237_3
 
 
 Maternal
 
 
 RN7SL796P,DNM1P50,RN7SL628P,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B
 
 lionel_13_ASD/SCZ/EP_discovery_cases-proband5
 
 
 Unknown
 Simplex
 Unknown
 RN7SL196P,CHRFAM7A,GOLGA8R
 
 li_18_ASD_discovery_cases-case4601
 
 
 Unknown
 Simplex
 Unknown
 RN7SL628P,ULK4P2,GOLGA8H,ARHGAP11B
 
 oikonomakis_16_ASD_discovery_cases-case543
 
 
 Unknown
 
 
 DNM1P28,GOLGA8T,RN7SL469P,DNM1P30,RNU6-17P,RN7SL196P,RN7SL796P,DNM1P50,ULK4P3,LINC02249,CHRFAM7A,GOLGA8Q,ULK4P2,GOLGA8R
 
 oikonomakis_16_ASD_discovery_cases-case673
 
 
 Unknown
 
 
 RN7SL796P,DNM1P50,RN7SL628P,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B
 
 pinto_10_ASD_discovery_cases-case1231_3
 Illumina550-Paternal
 
 paternal
 NA
 NA
 GOLGA8T,RN7SL469P,DNM1P30,RNU6-17P,RN7SL196P,RN7SL796P,DNM1P50,RN7SL628P,GOLGA8UP,RN7SL82P,ULK4P3,LINC02249,CHRFAM7A,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B,GOLGA8R
 
 pinto_10_ASD_discovery_cases-case5320_3
 Agilent1M
 
 maternal
 NA
 NA
 ARHGAP11B
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-case1545-0
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 RNU6-17P,LINC02249,CHRFAM7A
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR03-274
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 RNU6-17P,RN7SL196P,LINC02249,CHRFAM7A,GOLGA8R
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR04-181
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 GOLGA8UP,RN7SL82P
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR08-019
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 GOLGA8UP,RN7SL82P,ARHGAP11B
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR08-279a2
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 GOLGA8UP
 
 sanders_11_ASD_discovery_cases-11370.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-12044.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Segregated
 
 
 vaags_11_ASD_replication_cases_2-probandF4-003
 
 
 Unknown
 Simplex
 Unknown
 GOLGA8J,RN7SL673P,DNM1P28,GOLGA8T,RN7SL469P,DNM1P30,RNU6-17P,RN7SL196P,RN7SL796P,DNM1P50,RN7SL628P,ULK4P3,LINC02249,CHRFAM7A,GOLGA8Q,ULK4P2,GOLGA8H,GOLGA8R
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-control110036017473_
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-control110036023653_
 
 
  Unknown
 
 
  DNM1P50,RN7SL628P,ULK4P2,GOLGA8H,ARHGAP11B
 
engchuan_15_ASD_discovery_controls-control110036024040_
 
 
  Unknown
 
 
  RN7SL628P,GOLGA8H,ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB250058_1007852610
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB301469_1007854697
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB365205_1007853975
 
 
  Unknown
 
 
  RN7SL796P,DNM1P50,RN7SL628P,GOLGA8UP,GOLGA8Q,ULK4P2,GOLGA8H,ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB419502_1007871739
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB443041_1007873134
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB476720_1007853882
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB549396_1007854239
 
 
  Unknown
 
 
  RN7SL628P,GOLGA8H,ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlB980109_1007875790
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlHABC_900499_900499
 
 
  Unknown
 
 
  RN7SL628P,ULK4P2,GOLGA8H,ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlHABC_900976_900976
 
 
  Unknown
 
 
  RNU6-17P,RN7SL196P,CHRFAM7A,GOLGA8R
 
engchuan_15_ASD_discovery_controls-controlHABC_902474_902474
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlHABC_902607_902607
 
 
  Unknown
 
 
  RNU6-17P,RN7SL196P,RN7SL796P,DNM1P50,LINC02249,CHRFAM7A,GOLGA8Q,ULK4P2,GOLGA8R
 
engchuan_15_ASD_discovery_controls-controlHABC_902667_902667
 
 
  Unknown
 
 
  ARHGAP11B
 
engchuan_15_ASD_discovery_controls-controlHABC_902690_902690
 
 
  Unknown
 
 
  ARHGAP11B
 
gregory_09_ASD_discovery_controls-control5
 
 
  Unknown
  NA
  NA
 
 
kanduri_15_ASD_discovery_controls-control_split1055
 
 
  Unknown
 
 
  LOC100288637 (non-coding RNA, exonic)
 
kanduri_15_ASD_discovery_controls-control_split1785
 
 
  Unknown
 
 
  LOC100288637 (non-coding RNA, exonic)
 
kanduri_15_ASD_discovery_controls-control_split1797
 
 
  Unknown
 
 
  LOC100288637 (non-coding RNA, exonic)
 
kanduri_15_ASD_discovery_controls-control_split341
 
 
  Unknown
 
 
  LOC100288637 (non-coding RNA, exonic)
 
sanders_11_ASD_discovery_controls-11098.s1
 
 
  Maternal
  Simplex (quad)
  NA
 
 
sanders_11_ASD_discovery_controls-11798.s1
 
 
  Unknown
  Simplex (quad)
  NA
  GOLGA8J,RN7SL673P,DNM1P28,ULK4P3
 

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