15q23-q24.1CNV Type: Deletion
Largest CNV size: 5057128 bp
Statistics Box:
Number of Reports: 9
Number of Reports: 9
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critic...
Deletion
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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Deletion
Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism.
Deletion
Diagnostic yield of array CGH in patients with autism spectrum disorder in Hong Kong.
Deletion
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_replication_cases
Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
1979
Cases diagnosed with ASD
N/A
N/A
5051820
1
0
1
girirajan_11_ASD_discovery_cases
ASD cases with sporadic autism from the Simons Simplex Collection (SSC)
336
Diagnosis of ASD based on meeting criteria on ADOS, ADI-R, and expert clinical judgment. 246 cases with no intellectual disability, 90 cases with intellectual disability. Exclusion criteria: significant hearing, vision, or motor problems; significant birth complications; a diagnosis of ASD-related disorders, such as Fragile X; or having a relative (up to 3rd degree) with ASD or sibling showing ASD-related symptoms.
5090833
1
0
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
5047547
1
0
1
girirajan_13a_DD_discovery_cases
Data from individuals with developmental delay derived from two published reports (Cooper et al., 2011 & Kaminsky et al., 2011)
31518
Developmental delay
NA
NA
0
0
0
0
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
4992764
1
1
2
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
5052436
1
0
1
mcinnes_10_ASD_discovery_cases
Sporadic ASD cases from an isolated founder population in the Central Valley of Costa Rica
173
ASD
88.4% Male
3060000
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
5057128
1
0
1
siu_15_ASD_discovery_cases
Adult group of 41 ASD cases (39 males, 2 females; age range of 22-33 years, median age 27 years) and pediatric group of 25 ASD cases (21 males, 6 females; age range 2-15 years, median age 5 years)
66
All cases diagnosed with ASD. Diagnosis of ASD in adult group confirmed with the Developmental, Dimensional and Diagnostic Interview; adult cohort also assessed with Wechseler Adult Intelligence Scale-Third Edition (WAIS-III). Pediatric group assessed using ADI-R to confirm ASD diagnosis; 13 patients in this group also had developmental delay.
Range, 2-33 yrs.
89.39% Male
1970000
1
0
1
siu_16_ASD_discovery_cases
41 adult ASD cases (39 males, 2 females, age range of 22-33 years, median age of 27 years) recruited from a cohort of a local study on the adult outcome of children with autism with normal intelligence, and 27 pediatric ASD cases (21 males, 6 females, age range of 2-15 years, median age of 5 years) assessed in the Department of Paediatrics and Adolescent Medicine of Princess Margaret Hospital or T
68
Diagnosis of ASD in cases from the adult cohort was made during childhood (before the year 1990) using Diagnostic and Statistical Manual of Mental Disorders, Third Revised Edition and was confirmed with the developmental, dimensional and diagnostic interview during adulthood; diangosis of ASD in cases from the pediatric cohort was confirmed using ADI-R. IQ of cases in the adult cohort was assessed by Wechsler Adult Intelligence Scale-Third edition (WAIS-III) Chinese version. Developmental delay reported in 13/27 (52.0%) of cases in the pediatric cohort.
Range, 2-33 yrs. (median age of 25 yrs.)
88.23% Male
1970000
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
girirajan_11_ASD_discovery_controls
Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
337
Control. Individuals screened specifically for eight mental health disorders.
5090833
0
0
0
girirajan_13a_ASD_discovery_controls3
Controls assessed for CNVs within 120 SD-mediated hotspots; includes 2090 controls from Wellcome Trust Case-Control Consortium (girirajan_13_ASD_discovery_controls2)
8329
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
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
0
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.
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_replication_cases
N/A
WGS
Illumina HiSeq X10
ForestSV, Lumpy, Manta, Mobster, SV2
None
girirajan_11_ASD_discovery_cases
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
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)
girirajan_13a_DD_discovery_cases
NA
N/A
N/A
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
levy_11_ASD_discovery_cases
aCGH
NimbleGen HD2
HMM
aCGH (Agilent 244K)
mcinnes_10_ASD_discovery_cases
Costa Rican
Array SNP
Affymetrix NspI 250K arrays
aCGH, 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
qPCR
siu_15_ASD_discovery_cases
Han Chinese
aCGH
NimbleGen CGX-135K
DEVA (Roche), Genoglyphix (Signature Genomics)
siu_16_ASD_discovery_cases
Hong Kong
aCGH
NimbleGen CGX-135K
DEVA, Genoglyphix
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
girirajan_11_ASD_discovery_controls
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
girirajan_13a_ASD_discovery_controls3
NA
Array SNP
N/A
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
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
brandler_18_ASD_replication_cases-caseSSC00263
N/A
F
ASD
Case from SSC_phase2 cohort
68807392
73859209
5051818
GRCh38
Deletion
No
girirajan_11_ASD_discovery_cases-Si169
9
F
Autism
ADOS score: 10. Vineland composite score: 57.
Mild mental retardation/intellectual disability. Full-scale IQ, 57; Verbal IQ, 65; Non-verbal IQ, 60.
68802337
73893169
5090833
GRCh38
Deletion
No
girirajan_13a_ASD_discovery_cases-11233.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
68811476
73859022
5047547
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000800
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
68830574
73823337
4992764
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001996
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
72058544
72481033
422490
GRCh38
Duplication
Yes
levy_11_ASD_discovery_cases-11233.p1
NA
F
ASD
NA
NA
68807208
73859642
5052435
GRCh38
Deletion
Yes
mcinnes_10_ASD_discovery_cases-AU008
5
M
Autism
Behavioral abnormalities: developmental regression, constant smiling, hyperactivity, aggressiveness, sleep disturbances. Neurological abnormalities: minimal cortical atrophy on CT, hypotonia not reported but probable. Growth: low birth weight, no persistent growth retardation, obesity, or low head circumference. Facial dysmorphism: high anterior hair line, long narrow face, hypertelorism, broad medial eyebrows, epicanthus, full lower lip, widely spaced teeth, protuberant ears. Eye abnormalities: nystagmus. Digital abnormalities: right single palmar crease, left 2-3 syndactyly of toes. Mild scoliosis and joint laxity, polyhydramminos, recurrent infections.
Moderate intellectual disability; language regression, 2 words at 5 yrs
71758583
74817543
3058961
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_cases-11233.p1
6.3
F
Autism
NA
Full-scale IQ, 57; non-verbal IQ, 60; verbal IQ, 65
68807678
73864805
5057128
GRCh38
Deletion
Yes
siu_15_ASD_discovery_cases-case1
26 yrs.
M
Autism
Case diagnosed with autism at age of 3 years (diagnosis confirmed with Developmental, Dimensional and Diagnostic Interview during adulthood). Birth/neonatal history: born at full-term without complications. Developmental milestones: developmental delays; could not walk independently until 24 months old, spoke first meaningful words after 24 months of age. Language and communication evaluation: impairments in social interactions and communication with other people. Motor and musculoskeletal evaluation: no abnormalities affecting digits or skeletal system. Behavioral/psychiatric evaluation: described as having a difficult temper; displayed stereotypies, including clapping and hand scratching. Epilepsy/seizures: none. Dysmorphic features: mild hypertelorism, broad nasal bade, mild facial asymmetry. Family history: non-consanguineous parents; father was 32 and mother 29 at time of birth; father N/A for testing; both unaffected mother and younger sister are negative for deletion; no other autistic family members.
Mild intellectual disability
71391645
73360338
1968694
GRCh38
Deletion
No
siu_16_ASD_discovery_cases-patient3
Adult (22-33 yrs.)
M
ASD
Diagnosis of ASD made during childhood (before the year 1990) using Diagnostic and Statistical Manual of Mental Disorders, Third Revised Edition and confirmed with the developmental, dimensional and diagnostic interview during adulthood. Additional clinical features: subtle facial dysmorphism.
IQ of 85 [as determined by Wechsler Adult Intelligence Scale-Third edition (WAIS-III) Chinese version]
71391645
73360338
1968694
GRCh38
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_replication_cases-caseSSC00263
No validation step reported
De novo
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,ANP32A,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
girirajan_11_ASD_discovery_cases-Si169
De novo
Simplex
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,TBC1D21,ANP32A,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
girirajan_13a_ASD_discovery_cases-11233.p1
aCGH (NimbleGen 135K array)
De novo
Simplex
Possibly segregated
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,ANP32A,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000800
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001996
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
HEXA-AS1,RPL12P35,PHBP20,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,MYO9A,PKM,ARIH1,HEXA
levy_11_ASD_discovery_cases-11233.p1
aCGH (Agilent 244K)
De novo
Simplex
Segregated
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,ANP32A,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
mcinnes_10_ASD_discovery_cases-AU008
aCGH, qPCR
Paternal
Simplex
NA
RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,DNM1P33,RN7SL429P,ISLR,PPIAP46,MIR6881,CYP1A1,CYP1A2,MIR4513,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,TBC1D21,LOXL1,STOML1,PML,GOLGA6A,ISLR2,CYP11A1,LINC02255,SEMA7A,UBL7-AS1,CLK3,EDC3,CSK,LMAN1L,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,LOXL1-AS1,STRA6,CCDC33,ARID3B,THSD4,HEXA,UBL7
sanders_11_ASD_discovery_cases-11233.p1
qPCR
De Novo
Simplex (quad-proband matched)
Segregated
RPLP1,MIR629,RNU6-745P,LINC02205,SALRNA3,SALRNA2,RPL29P30,KRT8P9,THAP10,RPL5P3,CT62,HMGB1P6,RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,MRPS15P1,NPTN-IT1,KIF23,TLE3,LINC02204,UACA,LARP6,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,NPTN,CD276,INSYN1,INSYN1-AS1,ANP32A,SPESP1,NOX5,EWSAT1,PAQR5,DRAIC,LRRC49,THSD4-AS1,MYO9A,PKM,ARIH1,LINC02259,NEO1,REC114,GLCE,THSD4,HEXA
siu_15_ASD_discovery_cases-case1
Unknown (not maternal)
Simplex
Unknown
RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,MYO9A,PKM,ARIH1,LINC02259,NEO1,THSD4,HEXA
siu_16_ASD_discovery_cases-patient3
Unknown
Unknown
Unknown
RNA5SP399,EIF5A2P1,RNU2-65P,HEXA-AS1,RPL12P35,PHBP20,MIR630,RN7SL853P,NPM1P42,FKBP1AP2,NPM1P43,NR2E3,SENP8,GRAMD2A,PARP6,CELF6,TMEM202,TMEM202-AS1,GOLGA6B,HIGD2B,BBS4,ADPGK,ADPGK-AS1,HCN4,MYO9A,PKM,ARIH1,LINC02259,NEO1,THSD4,HEXA
Controls
No Control Data Available
No Animal Model Data Available