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15q22.31CNV Type: Deletion-Duplication


Largest CNV size: 119692 bp

Statistics Box:
Number of Reports: 11



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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References

Major Reports

Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Duplication
A common cognitive, psychiatric, and dysmorphic phenotype in carriers of NRXN1 deletion.
Deletion
Excess of rare, inherited truncating mutations in autism.
Deletion
NA
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
NA
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 13000
 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
 109927
 0
 1
 1
 girirajan_13a_ASD_discovery_cases
 1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
 2588
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 NA
 NA
 103757
 0
 1
 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
 1526743
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 6190
 1
 0
 1
 nord_11_ASD_discovery_cases
 Youth with ASD (as part of mother-father-child trios)
 41
 ASD
 
 85.4% Male
 15810
 1
 0
 1
 peycheva_18_ID/EP_discovery_cases
  NA NA
 Patients referred by clinicians from major neurologic clinics in Bulgaria (47 cases with positive family history for developmental delay/intellectual disability and/or seizures, 45 sporadic cases)
 92
 Cases primarily presented with intellectual disability (99%) and epilepsy/seizures (96%), with some exhibiting behavioral abnormalities (43%), dysmorphic features (52%), delayed or absent speech (45%), microcephaly (15%), motor disorders (37%), and brain structural abnormalities (31%)
 Range, 1-22 years
 54.35% Male
 1320000
 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
 
 
 109928
 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
 8120
 1
 0
 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
 119692
 2
 1
 3
 vinas-jornet_14_ASD/ID/ADHD/BPD/EP_discovery_cases
 Three unrelated patients with 2p16.3/NRXN1 deletions seen at the Service for Mental Health and Intellectual Disability at the Parc Hospitalari Marti I Julia (Girona, Catalunya, Spain) and referred to the Clinical Genetics Department at the Corporacio Sanitaria Parc Tauli (Sabasell, Catalunya, Spain).
 3
 All three cases present with intellectual disability; additional diagnoses of bipolar disorder (case 1), ASD (case 2) and ADHD (case 3). Psychopathological evaluation tests: PASS-ADD, Compulsive behavior checklist, and Y-BOCS (cases 1 and 2). Cognitive evaluation tests: K-BIT, FCRO, Color Trail Test 1 and 2, PIEN-ID, BRIEF, ADOS, and Tower of London (cases 1 and 2); WISC-IV, Bayley II, and Reynell (case 3). Behavioral evaluation tests: ABC scale, ABS-RC:2 (cases 1 and 2).
 Range, 11-21 yrs.
 66.67% Male
 33000
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 brandler_18_ASD_replication_controls
 Unaffected individuals from the Simons Simplex 2 (SSC2) cohort (584 controls from simplex quad families)
 584
 Control (unaffected siblings from simplex quad families)
 N/A
 N/A
 3257
 1
 0
 1
 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
 0
 0
 0
 0
 girirajan_13a_ASD_discovery_controls1
 NIMH control cohort consisting of 207 DNA samples obtained from Rutgers Univ. Cell and DNA Repository, and 373 individuals from ClinSeq study of artherosclerotic disease
 580
 Control. Individuals from NIMH control cohort negative for DSM-IV criteria for major depression and history of bipolar disorder or psychosis.
 NA
 NA
 0
 0
 0
 0
 girirajan_13a_ASD_discovery_controls2
 Controls characterized through the Wellcome Trust Case-Control Consortium (WTCCC) for smaller hotspot regions and candidate-gene events
 2090
 Control
 NA
 NA
 0
 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_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 32593
 0
 1
 1
 nord_11_ASD_discovery_controls
 Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
 123
 Controls (no history of psychiatric symptoms by self-report)
 30 yrs.
 
 0
 0
 0
 0
 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)
 8120
 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.
 
 44805
 3
 0
 3

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 engchuan_15_ASD_discovery_cases
  Caucasian
 Solid phase hybridization
  Illumina 1M
 
 
 None
 girirajan_13a_ASD_discovery_cases
  NA
 aCGH
  Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
 ADM-2
 Agilent Genomic Workbench
 aCGH (NimbleGen 135K array)
 kaminsky_11_DD/ID/ASD_discovery_cases
  NA
 aCGH
  Agilent 44K, Agilent 105K
 
 Feature Extraction, DNA Analytics
 FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 nord_11_ASD_discovery_cases
  29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
 aCGH
  NimbleGen HD2
 Sliding-window algorithm, ~10 kb minumum size threshold
 
 None
 peycheva_18_ID/EP_discovery_cases
  Bulgarian
 aCGH
  Agilent SurePrint G3 Human CGH Microarray Kit, Agilent 4x180K, Agilent SurePrint G3 Unrestricted CGH ISCA v2 4x180K
 
 Agilent Feature Extraction v12.0.1.1, OGT Cytosure Interpret v4.3
 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)
 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
 
 
 vinas-jornet_14_ASD/ID/ADHD/BPD/EP_discovery_cases
  Spain
 aCGH
  Agilent 400K
 
 Agilent Workbench 5.0, Cytogenetics software, BioDiscovery Nexus 6.1
 MLPA

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  brandler_18_ASD_replication_controls
  N/A
  WGS
  Illumina HiSeq X10
  ForestSV, Lumpy, Manta, Mobster, SV2
 
  None
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  None
  girirajan_13a_ASD_discovery_controls1
  NA
  aCGH
  Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
  ADM-2
  Agilent Genomic Workbench
  None
  girirajan_13a_ASD_discovery_controls2
  NA
  Solid phase hybridization
  Illumina 1.2M SNP microarray
 
 
  None
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  nord_11_ASD_discovery_controls
 
  aCGH
  NimbleGen HD2
  Sliding-window algorithm, ~10 kb minumum size threshold
 
  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
 
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  digregorio_17_DD/ID_discovery_cases-DECIPHER_299892
  NA NA
 N/A
 F
 Developmental delay/intellectual disability
 
 
 66536449
 66549503
  13055
 GRCh38
 Deletion
 No
  engchuan_15_ASD_discovery_cases-case1956_302
 N/A
 N/A
 ASD
 Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
 
 64994508
 65104435
  109928
 GRCh38
 Duplication
 No
  girirajan_13a_ASD_discovery_cases-11734.p1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 N/A
 66296273
 66400030
  103758
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002155
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 64448836
 65975439
  1526604
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case11055.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 66325830
 66332020
  6191
 GRCh38
 Deletion
 Yes
  nord_11_ASD_discovery_cases-223-1
 
 
 ASD
 
 
 62546091
 62561900
  15810
 Unknown
 Deletion
 No
  peycheva_18_ID/EP_discovery_cases-case409
  NA NA
 16 yrs.
 M
 ID and epilepsy
 Language and communication evaluation: stuttering, dyslexia. Behavioral/psychiatric evaluation: attention deficit, hyperactivity, aggressive behavior. Epilepsy/seizures: generalized tonic-clonic seizures. Brain imaging: calcifications in the left cerebellar hemisphere. Visual evaluation: unilateral convergent strabismus. Dysmorphic features: caf au lait macules. Family history: mother with epilepsy (negative for 15q22.31 deletion)
 Moderate intellectual disability
 63950631
 65277924
  1327294
 GRCh38
 Deletion
 Yes
  pinto_10_ASD_discovery_cases-case1956_302
 NA
 M
 Autism
 Low functioning autism, non verbal
 MR (untestable by Ravens)
 64994508
 65104435
  109928
 GRCh38
 Duplication
 Yes
  prasad_12_ASD_discovery_cases-case47560
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 62464282
 62472401
  8120
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11734.p1
 13.8
 F
 Autism
 NA
 Full-scale IQ, 84; non-verbal IQ, 81; verbal IQ, 95
 66284705
 66404397
  119693
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11894.p1
 5.4
 M
 ASD
 NA
 Full-scale IQ, 114; non-verbal IQ, 104; verbal IQ, 125
 65466105
 65484867
  18763
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12894.p1
 6.8
 M
 Autism
 NA
 Full-scale IQ, 77; non-verbal IQ, 80; verbal IQ, 79
 64475944
 64482803
  6860
 GRCh38
 Deletion
 No
  vinas-jornet_14_ASD/ID/ADHD/BPD/EP_discovery_cases-case2
 20 yrs.
 M
 ASD and intellectual disability
 Diagnosis of atypical autism; performance on ADOS placed case within the ASD range. Birth/neonatal history: uneventful pregnancy, full-term and dystocic delivery; birth weight of 2790 g and OFC of 33.5 cm; no congenital abnormalities or feeding difficulties observed at birth. Motor and musculoskeletal evaluation: dorsal kyphosis, finger rigidity. Behavioral/psychiatric evaluation: nonspecified psychotic disorder with hypochondriac delusions; behavior inlcuded explosive temper tantrums, violence, and property destruction with a diagnosis of verbal and physically aggressive destructive behavior; also presented with obsessive-compulsive behavior. Dysmorphic features: long face, deep set eyes, hypotelorism, low set ears, prominent premaxilla, high palate. Growth parameters: height of 167 cm (3th-10th %ile), weight of 65.5 kg (25th %ile), and OFC of 54 cm (-1.5 SD). Family history: mother (positive for NRXN1 deletion) and brother (negative for NRXN1 deletion) with a history of behavioral disorders; mother also with a history of borderline IQ.
 Mild intellectual disability (IQ of 62); neuropsychological tests showed complex cognitive profile, which included concretism and severe impairment of executive functioning, mainly in relation to working memory, difficulty in classifying information correctly, and deficit of abstract reasoning
 65037600
 65070546
  32947
 GRCh38
 Deletion
 Yes

Controls

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  brandler_18_ASD_replication_controls-controlSSC01043
  N/A
  F
  control
  Control from SSC_phase2 cohort
 
  63734012
  63737268
  3257
  GRCh38
  Deletion
  No
  krumm_15_ASD_discovery_controls-control13564.s1
  N/A
  Male
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  66532246
  66564839
  32594
  GRCh38
  Duplication
  Yes
  sanders_11_ASD_discovery_controls-11055.s1
  11.3
  F
  Control (matched sibling)
  NA
  NA
  66326004
  66329008
  3005
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-11101.s1
  6.7
  F
  Control (matched sibling)
  NA
  NA
  65659204
  65704009
  44806
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12894.s1
  4.9
  F
  Control (matched sibling)
  NA
  NA
  64475944
  64482803
  6860
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 digregorio_17_DD/ID_discovery_cases-DECIPHER_299892
 
 
 Unknown
 
 
 ZWILCH,LCTL
 
 engchuan_15_ASD_discovery_cases-case1956_302
 
 
 Unknown
 
 
 SLC51B,RASL12,KBTBD13,UBAP1L,MTFMT
 
 girirajan_13a_ASD_discovery_cases-11734.p1
 aCGH (NimbleGen 135K array)
 
 Maternal
 Simplex
 Unknown
 SCARNA14,RPL9P25,TIPIN,DIS3L,MAP2K1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002155
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 GAPDHP61,RNU6-549P,MIR1272,PIF1,SLC51B,RNU6-686P,SNORA24B,RNU5A-1,RNU5B-1,RNU6-19P,SNORD13E,MIR4511,HNRNPA1P44,TRIP4,OAZ2,PLEKHO2,ANKDD1A,SPG21,RASL12,KBTBD13,UBAP1L,PDCD7,CLPX,CILP,IGDCC3,DPP8,INTS14,SLC24A1,ZNF609,RBPMS2,PARP16,IGDCC4,HACD3,DENND4A,RAB11A,MTFMT,MEGF11
 
 krumm_15_ASD_discovery_cases-case11055.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Segregated
 DIS3L
 
 nord_11_ASD_discovery_cases-223-1
 
 
 Paternal
 
 
 0 genes
 
 peycheva_18_ID/EP_discovery_cases-case409
 qPCR
 Maternal
 Unknown
 Multi-generational
 Not segregated
 SNX22,GAPDHP61,RNU6-549P,MIR1272,PIF1,SLC51B,RNU6-686P,CIAO2A,PPIB,PCLAF,TRIP4,OAZ2,PLEKHO2,ANKDD1A,SPG21,RASL12,KBTBD13,UBAP1L,PDCD7,CLPX,CILP,SNX1,CSNK1G1,ZNF609,RBPMS2,PARP16,DAPK2,MTFMT
 
 pinto_10_ASD_discovery_cases-case1956_302
 Illumina550-Paternal
 
 paternal
 NA
 NA
 SLC51B,RASL12,KBTBD13,UBAP1L,MTFMT
 
 prasad_12_ASD_discovery_cases-case47560
 
 
 Unknown
 Unknown
 Unknown
 TRIP4
 
 sanders_11_ASD_discovery_cases-11734.p1
 
 
 Maternal
 Simplex (trio)
 NA
 SCARNA14,RPL9P25,TIPIN,DIS3L,MAP2K1
 
 sanders_11_ASD_discovery_cases-11894.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 DPP8
 
 sanders_11_ASD_discovery_cases-12894.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 ZNF609
 
 vinas-jornet_14_ASD/ID/ADHD/BPD/EP_discovery_cases-case2
 MLPA
 Maternal
 Maternal
 Multi-generational
 Unknown
 SLC51B,RASL12
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_replication_controls-controlSSC01043
  No validation step reported
 
  Paternal
 
 
  HERC1
 
krumm_15_ASD_discovery_controls-control13564.s1
  1M-Duov3
 
  Paternal
 
 
  ZWILCH,LCTL
 
sanders_11_ASD_discovery_controls-11055.s1
 
 
  Maternal
  Simplex (quad)
  NA
  DIS3L
 
sanders_11_ASD_discovery_controls-11101.s1
 
 
  Unknown
  Simplex (quad)
  NA
  SNORD13E,SLC24A1,DENND4A
 
sanders_11_ASD_discovery_controls-12894.s1
 
 
  Paternal
  Simplex (quad)
  NA
  ZNF609
 

No Animal Model Data Available
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