12q24.13CNV Type: Deletion
Largest CNV size: 32936 bp
Statistics Box:
Number of Reports: 7
Number of Reports: 7
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum 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
Global increases in both common and rare copy number load associated with autism.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
girirajan_13b_ASD_discovery_cases
Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)
243
Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol
N/A
N/A
302210
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
415436
0
2
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
107437
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
121560
0
1
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)
19497
0
1
1
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
32936
9
0
9
schmitz-abe_20_ASD_discovery_cases
ASD probands rom 187 families from the Homozygosity Mapping Collaborative of Autism (HMCA); 22% of families had more than one affected child, and 66% of families were consanguineous.
255
Diagnosis of autism or ASD made by a neurologist, child psychiatrist, or psychologist; DSM-IV-R criteria confirmed in all individuals with an Autism diagnosis
N/A
N/A
5601
2
0
2
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_controls
Unaffected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (112 individuals from 311 families) and the Simons Simplex 1 (SSC1) cohort (518 controls from simplex quad families)
630
Control
N/A
N/A
7268
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
297834
0
2
2
girirajan_13b_ASD_discovery_controls
Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)
223
Control
N/A
N/A
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_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
0
0
0
0
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
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)
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.
32936
3
0
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
girirajan_13b_ASD_discovery_cases
133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American
aCGH
Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
DNA Copy Number v1.6
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)
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
schmitz-abe_20_ASD_discovery_cases
Middle Eastern
Array SNP
Affymetrix 6.0, Affymetrix 500K
qPCR
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_controls
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
None
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_13b_ASD_discovery_controls
116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American
aCGH
Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
DNA Copy Number v1.6
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
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
girirajan_13b_ASD_discovery_cases-28504101060
N/A
N/A
Autism
Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Hispanic
N/A
113807584
114109794
302211
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001722
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
112307532
112722967
415436
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002120
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
112303430
112676526
373097
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case13322.p1
N/A
M
ASD
ASD proband from SSC quad family 13322. SRS score of 77.
Full-scale IQ (FSIQ) score of 59.
113858790
113966227
107438
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_cases-case13322.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
113844667
113966227
121561
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
113268740
113288236
19497
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11216.p1
4.7
M
ASD
NA
Full-scale IQ, 77; non-verbal IQ, 97; verbal IQ, 57
113213463
113232741
19279
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11447.p1
6.6
M
Autism
NA
Full-scale IQ, 89; non-verbal IQ, 97; verbal IQ, 82
113410729
113434639
23911
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11918.p1
9.8
F
Autism
NA
Full-scale IQ, 48; non-verbal IQ, 59; verbal IQ, 39
113130992
113150326
19335
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12219.p1
7.2
M
Autism
NA
Full-scale IQ, 121; non-verbal IQ, 110; verbal IQ, 136
113231058
113263994
32937
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12582.p1
6.3
M
Autism
NA
Full-scale IQ, 57; non-verbal IQ, 73; verbal IQ, 45
113134361
113156910
22550
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12596.p1
4.9
M
Autism
NA
Full-scale IQ, 61; non-verbal IQ, 89; verbal IQ, 32
113134361
113158204
23844
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12597.p1
6.4
M
Autism
NA
Full-scale IQ, 70; non-verbal IQ, 77; verbal IQ, 66
113130992
113158204
27213
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12941.p1
4.5
M
Autism
NA
Full-scale IQ, 92; non-verbal IQ, 93; verbal IQ, 96
113134361
113156910
22550
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13056.p1
4.6
M
Autism
NA
Full-scale IQ, 64; non-verbal IQ, 65; verbal IQ, 58
113134361
113136469
2109
GRCh38
Deletion
No
schmitz-abe_20_ASD_discovery_cases-caseAU-19601
N/A
M
ASD
Proband born to non-consanguineous parents of Middle Eastern descent from the HMCA cohort. Homozygous deletion segregated with ASD in this family.
111995070
112000670
5601
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_discovery_controls-controlSSC00082
N/A
F
Control
Control from SSC_phase1 cohort
112478880
112486148
7269
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB475222_1007872252
N/A
N/A
Control
No previous psychiatric history
113823248
114121082
297835
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB884573_1007852580
N/A
N/A
Control
No previous psychiatric history
111902039
112039251
137213
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11216.s1
6.4
M
Control (matched sibling)
NA
NA
113213463
113231058
17596
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12219.s1
11.4
F
Control (matched sibling)
NA
NA
113231058
113263994
32937
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12798.s1
8.1
F
Control (matched sibling)
NA
NA
113134361
113159115
24755
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
girirajan_13b_ASD_discovery_cases-28504101060
Unknown
Unknown
Unknown
GLULP5,HAUS8P1,RBM19
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001722
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
MIR1302-1,RPL6,PTPN11,RPH3A,HECTD4
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002120
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPL6,PTPN11,RPH3A,HECTD4
krumm_13_ASD_discovery_cases-case13322.p1
Maternal
Simplex
Segregated
RBM19
krumm_15_ASD_discovery_cases-case13322.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
RBM19
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
TPCN1
sanders_11_ASD_discovery_cases-11216.p1
Maternal
Simplex (quad-proband matched)
Not segregated
IQCD,TPCN1
sanders_11_ASD_discovery_cases-11447.p1
Unknown
Simplex (quad-proband matched)
Segregated
SDS,SDSL
sanders_11_ASD_discovery_cases-11918.p1
Maternal
Simplex (quad-proband matched)
Not segregated
CFAP73,RASAL1
sanders_11_ASD_discovery_cases-12219.p1
Paternal
Simplex (quad-proband matched)
Not segregated
TPCN1
sanders_11_ASD_discovery_cases-12582.p1
Paternal
Simplex (quad-proband matched)
Not segregated
CFAP73,RASAL1
sanders_11_ASD_discovery_cases-12596.p1
Maternal
Simplex (quad-proband matched)
Not segregated
CFAP73,DDX54,RASAL1
sanders_11_ASD_discovery_cases-12597.p1
Unknown
Simplex (quad-proband matched)
Not segregated
CFAP73,DDX54,RASAL1
sanders_11_ASD_discovery_cases-12941.p1
Maternal
Simplex (trio)
NA
CFAP73,RASAL1
sanders_11_ASD_discovery_cases-13056.p1
Maternal
Simplex (trio)
NA
RASAL1
schmitz-abe_20_ASD_discovery_cases-caseAU-19601
qPCR
Both parents
Simplex
Segregated
TMEM116
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC00082
Not available
Maternal
PTPN11
engchuan_15_ASD_discovery_controls-controlB475222_1007872252
Unknown
GLULP5,HAUS8P1,RBM19
engchuan_15_ASD_discovery_controls-controlB884573_1007852580
Unknown
ADAM1B,SLC25A3P2,MIR3657,MAPKAPK5,ERP29,TMEM116,NAA25
sanders_11_ASD_discovery_controls-11216.s1
Maternal
Simplex (quad)
NA
IQCD,TPCN1
sanders_11_ASD_discovery_controls-12219.s1
Paternal
Simplex (quad)
NA
TPCN1
sanders_11_ASD_discovery_controls-12798.s1
Unknown
Simplex (quad)
NA
CFAP73,MIR7106,DDX54,RASAL1
No Animal Model Data Available