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3q13.31CNV Type: Deletion-Duplication


Largest CNV size: 301000 bp

Statistics Box:
Number of Reports: 17



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
Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
Deletion
Structural variation of chromosomes in autism spectrum disorder.
Duplication
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
A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic...
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Neurodevelopmental disorders associated with dosage imbalance of ZBTB20 correlate with the morbidity spectrum of ZBTB20 candidate target genes.
Deletion
Excess of rare, inherited truncating mutations in autism.
Deletion
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
Deletion

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
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Deletion
Transmission disequilibrium of small CNVs in simplex autism.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
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
Refining analyses of copy number variation identifies specific genes associated with developmental delay.
Deletion
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Deletion
NA
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 coe_14_ASD/DD/ID_discovery_cases
 Primarily pediatric cases with intellectual disability, developmental delay, and/or ASD (cohort consists of 13,318 previously unpublished cases and 15,767 cases originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
 29085
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 410000
 9
 0
 9
 digregorio_17_DD/ID_discovery_cases
  NA NA
 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
 487000
 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
 1946940
 1
 1
 2
 krumm_13_ASD_discovery_cases
 Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 81.265% Male
 31640
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 31640
 1
 0
 1
 levy_11_ASD_discovery_cases
 Autistic probands from 887 families from the Simons Simplex Collection (SSC)
 858
 ASD
 
 87.06% Male
 47470
 1
 0
 1
 marshall_08_ASD_discovery_cases
 Cohort of ASD families (237 simplex, 189 mulitplex) recruited from the Hospital for Sick Children, McMaster Univ., Memorial Univ., and other sites
 427
 ASD
 
 
 98301
 0
 1
 1
 molin_12_DD/ASD_discovery_cases
 14 novel patients carrying microscopic or submicroscopic deletions in the 3q12.3-q21.3 region, and 1 previously reported 3q-deletion patient (Ogilvie et al. 1998).
 15
 Developmental delay present in 13/15 cases; 5/15 cases with attention deficits; 3/15 cases with autism.
 Range, 1 yr. 6 mos.-19 yrs. 6 mos.
 66.67% Male
 1180000
 2
 0
 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
 913035
 1
 0
 1
 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
 
 
 192185
 1
 0
 1
 poultney_13_ASD_discovery_cases
 ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
 299
 Cases diagnosed with ASD
 N/A
 79.86% Male (before filtering)
 31644
 2
 0
 2
 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
 10004
 1
 0
 1
 rasmussen_14_ASD/DD/ID_discovery_cases
 Patient referred for genetic evaluation due to autism and psychomotor developmental delay
 1
 Diagnosis of autism using ADI-R. Developmental delay and intellectual disability assessed suing Griffith Mental Development Scales 1st Edition.
 3 yrs. 11 mos.
 Male
 1300000
 1
 0
 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
 36365
 2
 0
 2
 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
 43730
 6
 0
 6
 szatmari_07_ASD_discovery_cases
 ASD patients from 173 families with at least two affected individuals from AGP
 196
 Patients diagnosed with ASD based on ADI-R and ADOS
 
 
 301000
 2
 0
 2
 yin_16_ASD_discovery_cases
 Discovery cohort of ASD cases recruited from the Department of Psychiatry of National Taiwan University Hospital (NTUH), Chang Gung Memorial Hospital (CGMH), Taoyuan, and Taoyuan Mental Hospital (TMH), Taiwan.
 335
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R. Cases' autistic behaviors assessed by Social Responsiveness Scale (SRS), and cognitive functions assessed by the Weschler Intelligence Scale for Children-Third Edition (WISC-III) and the Wisconsin Card Sorting Test (WCST).
 Mean, 9.39 4.04 yrs.
 89.3% Male
 45849
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 coe_14_ASD/DD/ID_discovery_controls
 Adult population controls (cohort consists of 11,255 new controls and 8329 controls originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
 19584
 Control
 N/A
 N/A
 410000
 0
 0
 0
 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_13_ASD_discovery_controls
 Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
 411
 Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 46.47% Male
 31640
 1
 0
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 31640
 1
 0
 1
 levy_11_ASD_discovery_controls
 Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
 863
 Control
 
 47.97% Male
 232823
 1
 1
 2
 marshall_08_ASD_discovery_controls_1
 German PopGen project and entries from Database of Genomic Variants
 500
 Controls
 
 
 0
 0
 0
 0
 marshall_08_ASD_discovery_controls_2
 Non-disease controls from Ontario population
 1152
 Controls
 
 
 0
 0
 0
 0
 poultney_13_ASD_discovery_controls
 Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
 260
 Control
 N/A
 47.49% Male (before filtering)
 31644
 2
 0
 2
 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)
 10004
 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.
 
 236993
 3
 1
 4
 stamouli_18_ASD/NDD_discovery_controls
  NA NA
 Unaffected individuals from 100 twin pairs (69 monozygotic, 31 dizygotic), corresponding to 97 families, that were enriched for neurodevelopmental disorders from the Roots of Autism and ADHD Study in Sweden (RATSS)
 100 twin pairs
 Control (unaffected) individual following evaluation using standard diagnostic tools [a psychosocial and anamnestic interview, the Autism Diagnosis Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule Second Edition (ADOS-2), the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS), or the Diagnostic Interview for ADHD in Adults (DIVA)]; Wechsler Intelligence Scale for Children or Adults, Fourth Edition (WISC-IV) or the Leiter-revised scales in combination with the Peabody Picture Vocabulary Test, Third Edition, and the parent-based Adaptive Behavior Assessment Scale, 2nd Edition (ABAS-2) were also used to evaluate adaptive, cognitive, and verbal abilities and
 N/A
 N/A
 40962
 1
 0
 1
 yin_16_ASD_discovery_controls
 Individuals from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
 1093
 Controls
 Mean, 68.07 10.12 yrs.
 48.0% Male
 45849
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 coe_14_ASD/DD/ID_discovery_cases
  N/A
 aCGH
  N/A
 
 
 None
 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
 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_13_ASD_discovery_cases
  N/A
 WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
 DNACopy, CGHCall
 CoNIFER
 None
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 levy_11_ASD_discovery_cases
 
 aCGH
  NimbleGen HD2
 HMM
 
 
 marshall_08_ASD_discovery_cases
  90% European, 4.5% European-mixed, 4.5% Asian, 0.07% African
 Array SNP, karotyping
  Affymetrix 500K
 dChip, CNAG, GEMCA
 
 qPCR, qmPCR
 molin_12_DD/ASD_discovery_cases
  NA
 aCGH, array SNP
  Affymetrix GeneChip 250K Nsp, Affymetrix 6.0, 1 Mb clone array, Agilent 400K, Agilent 44K, BlueGnome CytoChip V2, SpectralChip CC4-V0.3
 
 
 FISH
 mosca_16_DCD_discovery_cases
  Canada
 Solid phase hybridization
  Illumina HumanOmni2.5-Quad BeadChip
 iPattern, PennCNV, QuantiSNP, CNVPartition
 
 qPCR
 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)
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 None
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 qPCR
 rasmussen_14_ASD/DD/ID_discovery_cases
  Portuguese
 aCGH
  Agilent Human Genome 180K
 
 
 FISH
 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
 
 
 szatmari_07_ASD_discovery_cases
 
 Array SNP
  Affymetrix 10K (v2)
 HMM
 dChip
 Karyotyping, qPCR, aCGH, array SNP, overlap with Mendelian genotype errors
 yin_16_ASD_discovery_cases
  Han Chinese
 Array SNP
  Affymetrix 6.0
 
 Affymetrix Genotyping Console v.4.1
 None

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  coe_14_ASD/DD/ID_discovery_controls
  N/A
  aCGH, solid phase hybridization
  Multiple platforms used (including HumanHap, Illumina, and Human610-Quad)
 
 
  None
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  krumm_13_ASD_discovery_controls
  N/A
  WES
  Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
  DNACopy, CGHCall
  CoNIFER
  Solid phase hybridization (Illumina 1M), aCGH (Agilent SurePrint G3 4x180K), or confirmed by manual inspection
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  levy_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  HMM
 
 
  marshall_08_ASD_discovery_controls_1
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  marshall_08_ASD_discovery_controls_2
  European
  Array SNP, karotyping
  Affymetrix 500K
  dChip, CNAG, GEMCA
 
 
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
  None
  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
 
 
  stamouli_18_ASD/NDD_discovery_controls
  Swedish
  Solid phase hybridization
  Illumina Infinium PsychArray-24 v1.1
  PennCNV, QuantiSNP, iPattern, iPsychCNV
 
  None
  yin_16_ASD_discovery_controls
  Han Chinese
  Array SNP
  Affymetrix 6.0
 
  Affymetrix Genotyping Console v.4.1
  None

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  coe_14_ASD/DD/ID_discovery_cases-case610
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case611
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case612
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case613
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case614
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case615
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case616
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case617
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  coe_14_ASD/DD/ID_discovery_cases-case618
 N/A
 N/A
 Intellectual disability, developmental delay, and/or ASD
 N/A
 N/A
 115518463
 115928463
  410001
 GRCh38
 Deletion
 No
  digregorio_17_DD/ID_discovery_cases-DECIPHER_299972
  NA NA
 N/A
 M
 Developmental delay/intellectual disability
 CNV locus incorrectly reported as 3p26.3 in the original report
 
 116694018
 117180983
  486966
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002775
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 114530663
 115439099
  908437
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005324
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 114649022
 116595962
  1946941
 GRCh38
 Deletion
 Yes
  krumm_13_ASD_discovery_cases-case13162.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 13162. SRS score of 90.
 Full-scale IQ (FSIQ) score of 74.
 113869506
 113901146
  31641
 GRCh38
 Deletion
 No (not tested)
  krumm_15_ASD_discovery_cases-case13162.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 113869506
 113901146
  31641
 GRCh38
 Deletion
 Yes
  levy_11_ASD_discovery_cases-12297.p1
 NA
 M
 ASD
 NA
 NA
 113853363
 113900832
  47470
 GRCh38
 Deletion
 No
  marshall_08_ASD_discovery_cases-NA0018-000
 NA
 M
 ASD
 NA
 NA
 116637163
 116735463
  98301
 GRCh38
 Duplication
 Yes
  molin_12_DD/ASD_discovery_cases-case13
 9 yrs. 6 mos.
 F
 Developmental delay and autism
 DECIPHER ID: NA. Birth parameters: weight (g), 3490 (50-85th %ile); length (cm), NA; OFC (cm), NA. Delayed speech: yes. Behavioral problems: autism, short attention span. Hypotonia: no. Brain/CNS abnormalities: none reported. Skull abnormalities: brachycephaly. Skeletal abnormalities: flexion contracture of digiti V left hand op., pes planus, mild sandal gap digiti IV-V. Other malformations: none reported. Eye abnormalities: ptosis. Dysmorphic features: short philtrum, large ears. Growth parameters: weight (kg), 29.4 (50th %ile); height (cm), 135 (50th %ile); OFC (cm), 54.5 (90th %ile). Family history: brother with autism and IQ of 68 (karyotype of 47, XXY; lacks 3q13.31 deletion)
 Developmental delay; IQ 55
 114133819
 114715311
  581493
 GRCh38
 Deletion
 No
  molin_12_DD/ASD_discovery_cases-case14
 5 yrs. 6 mos.
 M
 Developmental delay
 DECIPHER ID: 252520. Birth parameters: weight (g), NA; length (cm), NA; OFC (cm), NA. Delayed speech: none reported. Behavioral problems: none reported. Hypotonia: none reported. Brain/CNS abnormalities: none reported. Skull abnormalities: none reported. Skeletal abnormalities: none reported. Other malformations: none reported. Eye abnormalities: none reported. Dysmorphic features: none reported. Growth parameters: weight (kg), NA; height (cm), NA; OFC (cm), NA.
 Developmental delay
 115721125
 116896653
  1175529
 GRCh38
 Deletion
 Yes
  mosca_16_DCD_discovery_cases-case116003
 N/A
 M
 DCD/ADHD
 Ancestry: European. Family history: maternal diagnosis unaffected; paternal diagnosis unaffected; sibling diagnosis unaffected.
 
 115533011
 116446045
  913035
 GRCh38
 Deletion
 Yes
  pinto_10_ASD_discovery_cases-case5245_3
 NA
 M
 Autism
 Language delay, below average language (1%ile), apraxia, abnormal sleep EEG without seizures; born at 29 wks, intraventricular hemorrhage, mild cerebral palsy; alopecia areata, no dysmorphic features
 Below average nonverbal IQ (<1%ile)
 117285007
 117477191
  192185
 Unknown
 Deletion
 Yes
  poultney_13_ASD_discovery_cases-case98HI0158A
 N/A
 M
 ASD
 ASD case from AGRE (AGRE ID AU010904; NDAR ID NDAR_INVWN987FMF)
 
 113869505
 113901148
  31644
 GRCh38
 Deletion
 No
  poultney_13_ASD_discovery_cases-case98HI0361A
 N/A
 M
 ASD
 ASD case from AGRE (AGRE ID AU002704; NDAR ID NDAR_INVXF645EXZ)
 
 113869505
 113901148
  31644
 GRCh38
 Deletion
 No
  prasad_12_ASD_discovery_cases-case52026
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 116104105
 116114108
  10004
 Unknown
 Deletion
 Yes
  rasmussen_14_ASD/DD/ID_discovery_cases-case1
 3 yrs. 11 mos.
 M
 ASD and DD/ID
 Case was diagnosed with autism using ADI-R. Birth/neonatal history: born at 40 weeks gestation; birth weight of 3160 g (50th %ile), birth length of 49 cm (50th %ile), and birth OFC of 34.5 cm (50th %ile). Language and communication evaluation: moderate speech delay (Hearing and Speech Developmental Quotient of 34). Dysmorphic features: tall forehead, downslanted palpebral fissures, bilateral epicanthus, full cheeks, thick lips, gun hypertrophy, grooved chin, large prominent ears. Growth parameters: weight of 16 kg (50th %ile), height of 105 cm (50th-85th %ile), and OFC of 49.4 cm (25th-50th %ile) at age of 3 years 11 months.
 Mild intellectual disability (based on neuropsychological evaluation using Griffiths Mental Development Scales 1st Edition); mild developmental delay (Global Developmental Quotient of 54).
 114850895
 116149589
  1298695
 GRCh38
 Deletion
 Yes
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseDP96-053_LP
 N/A
 N/A
 CBLH
 Diagnosis of cerebellar hypoplasia (CBLH).
 
 114942209
 114978573
  36365
 GRCh38
 Deletion
 No
  sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR02-417a1
 N/A
 N/A
 CBLH
 Diagnosis of cerebellar hypoplasia (CBLH).
 
 114942209
 114978573
  36365
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11630.p1
 10.6
 M
 Autism
 NA
 Full-scale IQ, 104; non-verbal IQ, 105; verbal IQ, 106
 115760416
 115766547
  6132
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12297.p1
 15
 M
 Autism
 NA
 Full-scale IQ, 97; non-verbal IQ, 102; verbal IQ, 89
 113857767
 113901497
  43731
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12315.p1
 5.8
 M
 ASD
 NA
 Full-scale IQ, 53; non-verbal IQ, 54; verbal IQ, 61
 113857767
 113901497
  43731
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12739.p1
 6.8
 M
 ASD
 NA
 Full-scale IQ, 98; non-verbal IQ, 112; verbal IQ, 77
 116130484
 116172844
  42361
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13150.p1
 8.1
 F
 Autism
 NA
 Full-scale IQ, 46; non-verbal IQ, 47; verbal IQ, 50
 115760416
 115766547
  6132
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13162.p1
 9.8
 M
 Autism
 NA
 Full-scale IQ, 74; non-verbal IQ, 78; verbal IQ, 72
 113857767
 113901497
  43731
 GRCh38
 Deletion
 No
  szatmari_07_ASD_discovery_cases-NAAR072-G5-HI0615
 NA
 
 ASD
 NA
 NA
 116771463
 117072463
  301001
 GRCh38
 Deletion
 Yes
  szatmari_07_ASD_discovery_cases-NAARCP2-D11-HI0615
 NA
 
 ASD
 NA
 NA
 116771463
 117072463
  301001
 GRCh38
 Deletion
 Yes
  yin_16_ASD_discovery_cases-case120
 N/A
 N/A
 ASD
 Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
 
 114780894
 114826742
  45849
 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
  krumm_13_ASD_discovery_controls-control13162.s1
  N/A
  F
  Control
  Unaffected sibling from SSC quad family 13162. SRS score of 36.
 
  113869506
  113901146
  31641
  GRCh38
  Deletion
  Yes
  krumm_15_ASD_discovery_controls-control13162.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  113869506
  113901146
  31641
  GRCh38
  Deletion
  Yes
  levy_11_ASD_discovery_controls-11277.s1
  NA
  F
  Control
  NA
  NA
  115672284
  115905106
  232823
  GRCh38
  Duplication
  No
  levy_11_ASD_discovery_controls-12297.s1
  NA
  M
  Control
  NA
  NA
  113853363
  113900832
  47470
  GRCh38
  Deletion
  No
  poultney_13_ASD_discovery_controls-control04C28760A
  N/A
  M
  Control
  NIMH Control (NIMH ID 97777)
 
  113869505
  113901148
  31644
  GRCh38
  Deletion
  No
  poultney_13_ASD_discovery_controls-control04C30190A
  N/A
  M
  Control
  NIMH Control (NIMH ID 54326)
 
  113869505
  113901148
  31644
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11274.s1
  9.1
  M
  Control (matched sibling)
  NA
  NA
  117070604
  117162867
  92264
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11277.s1
  7.2
  F
  Control (matched sibling)
  NA
  NA
  115667724
  115904717
  236994
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12297.s1
  11.9
  M
  Control (matched sibling)
  NA
  NA
  113857767
  113907661
  49895
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-13162.s1
  6.7
  F
  Control (matched sibling)
  NA
  NA
  113857767
  113901025
  43259
  GRCh38
  Deletion
  No
  stamouli_18_ASD/NDD_discovery_controls-family25_Twin_1
  N/A
  N/A
  Control
  Control is from a dizygotic twin pair from the Discordant NDD diagnostic subgroup
 
  113865123
  113906084
  40962
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 coe_14_ASD/DD/ID_discovery_cases-case610
 
 
 De novo
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case611
 
 
 De novo
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case612
 
 
 De novo
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case613
 
 
 De novo
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case614
 
 
 Unknown
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case615
 
 
 Unknown
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case616
 
 
 Unknown
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case617
 
 
 Unknown
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 coe_14_ASD/DD/ID_discovery_cases-case618
 
 
 Unknown
 Unknown
 Unknown
 RN7SL815P,GAP43,LSAMP
 
 digregorio_17_DD/ID_discovery_cases-DECIPHER_299972
 
 
 Maternal
 
 
 MIR4447,LINC00901,RNU5E-8P,PTMAP8,TUSC7,LSAMP
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002775
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ZBTB20-AS2,MIR4796,ZBTB20-AS3,YBX1P3,ZBTB20-AS4,EIF4E2P2,ZBTB20
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005324
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 ZBTB20-AS2,MIR4796,ZBTB20-AS3,YBX1P3,ZBTB20-AS4,EIF4E2P2,RN7SL815P,LSAMP-AS1,RN7SL582P,GAP43,LINC00903,ZBTB20,LSAMP
 
 krumm_13_ASD_discovery_cases-case13162.p1
 
 
 Maternal
 Simplex
 Not segregated
 GRAMD1C
 
 krumm_15_ASD_discovery_cases-case13162.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Not segregated (CNV in unaffected sibling)
 GRAMD1C
 
 levy_11_ASD_discovery_cases-12297.p1
 
 
 Paternal
 Simplex
 Not segregated
 GRAMD1C
 
 marshall_08_ASD_discovery_cases-NA0018-000
 qPCR, qmPCR
 
 Unknown
 NA
 NA
 BZW1P2,TUSC7,LSAMP
 
 molin_12_DD/ASD_discovery_cases-case13
 
 
 De novo
 Multiplex
 Not segregated
 ZNF80,MIR568,ZBTB20-AS2,ZBTB20-AS1,ZBTB20-AS5,DRD3,ZBTB20,TIGIT
 
 molin_12_DD/ASD_discovery_cases-case14
 FISH
 
 Unknown (not maternal)
 Unknown
 Unknown
 RN7SL815P,LSAMP-AS1,RN7SL582P,BZW1P2,MIR4447,GAP43,LINC00903,TUSC7,LSAMP
 
 mosca_16_DCD_discovery_cases-case116003
 qPCR
 
 De novo
 Simplex
 Segregated
 RN7SL815P,LSAMP-AS1,GAP43,LSAMP
 
 pinto_10_ASD_discovery_cases-case5245_3
 qPCR, Agilent 1M
 
 De novo
 Multiplex
 Not segregated
 LSAMP exonic
 
 poultney_13_ASD_discovery_cases-case98HI0158A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 GRAMD1C
 
 poultney_13_ASD_discovery_cases-case98HI0361A
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 GRAMD1C
 
 prasad_12_ASD_discovery_cases-case52026
 qPCR
 
 Maternal
 Unknown
 Unknown
 ZBTB20
 
 rasmussen_14_ASD/DD/ID_discovery_cases-case1
 FISH
 
 De novo
 
 
 ZBTB20-AS3,YBX1P3,ZBTB20-AS4,EIF4E2P2,RN7SL815P,GAP43,ZBTB20,LSAMP
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseDP96-053_LP
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 ZBTB20
 
 sajan_13_ACC/CBLH/PMG_discovery_cases-caseLR02-417a1
 Not tested by qPCR
 
 Unknown
 Unknown
 Unknown
 ZBTB20
 
 sanders_11_ASD_discovery_cases-11630.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 
 
 sanders_11_ASD_discovery_cases-12297.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 GRAMD1C
 
 sanders_11_ASD_discovery_cases-12315.p1
 
 
 Paternal
 Simplex (trio)
 NA
 GRAMD1C
 
 sanders_11_ASD_discovery_cases-12739.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 LSAMP
 
 sanders_11_ASD_discovery_cases-13150.p1
 
 
 Maternal
 Simplex (trio)
 NA
 
 
 sanders_11_ASD_discovery_cases-13162.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 GRAMD1C
 
 szatmari_07_ASD_discovery_cases-NAAR072-G5-HI0615
 Karyotyping, qPCR, aCGH, array SNP, or overlap with Mendelian genotype errors
 
 Unknown
 NA
 NA
 MIR4447,LINC00901,RNU5E-8P,PTMAP8,LSAMP
 
 szatmari_07_ASD_discovery_cases-NAARCP2-D11-HI0615
 Karyotyping, qPCR, aCGH, array SNP, or overlap with Mendelian genotype errors
 
 Unknown
 NA
 NA
 MIR4447,LINC00901,RNU5E-8P,PTMAP8,LSAMP
 
 yin_16_ASD_discovery_cases-case120
 
 
 Unknown
 Unknown
 Unknown
 ZBTB20
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_13_ASD_discovery_controls-control13162.s1
  Solid phase hybridization (Illumina 1M) and aCGH (Agilent SurePrint G3 4x180K)
 
  Maternal
  Simplex
 
  GRAMD1C
 
krumm_15_ASD_discovery_controls-control13162.s1
  Illumina 1MDuo
 
  Maternal
 
 
  GRAMD1C
 
levy_11_ASD_discovery_controls-11277.s1
 
 
  Paternal
  Simplex
  NA
  RN7SL815P,GAP43,LSAMP
 
levy_11_ASD_discovery_controls-12297.s1
 
 
  Paternal
  Simplex
  NA
  GRAMD1C
 
poultney_13_ASD_discovery_controls-control04C28760A
 
 
  Unknown
 
 
  GRAMD1C
 
poultney_13_ASD_discovery_controls-control04C30190A
 
 
  Unknown
 
 
  GRAMD1C
 
sanders_11_ASD_discovery_controls-11274.s1
 
 
  Maternal
  Simplex (quad)
  NA
  LSAMP
 
sanders_11_ASD_discovery_controls-11277.s1
 
 
  Paternal
  Simplex (quad)
  NA
  RN7SL815P,GAP43,LSAMP
 
sanders_11_ASD_discovery_controls-12297.s1
 
 
  Paternal
  Simplex (quad)
  NA
  GRAMD1C
 
sanders_11_ASD_discovery_controls-13162.s1
 
 
  Maternal
  Simplex (quad)
  NA
  GRAMD1C
 
stamouli_18_ASD/NDD_discovery_controls-family25_Twin_1
 
 
  Unknown
  Simplex
 
  GRAMD1C
 

No Animal Model Data Available
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