12q24.11CNV Type: Deletion-Duplication
Largest CNV size: 13817 bp
Statistics Box:
Number of Reports: 11
Number of Reports: 11
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Paternally inherited cis-regulatory structural variants are associated with autism.
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
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion-Duplication
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Chromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of cou...
Duplication
Copy number variation analysis of patients with intellectual disability from North-West Spain.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
733
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
331
1
1
2
egger_14_ASD_discovery_cases
ASD probands from Austria (71 simplex, 2 multiplex) recruited from the catchment area of Styria using three recruitment sites (Institute of Human Genetics, Medical University of Graz, Club Libelle, Center for Autism, Styria, and Children's Hospital, University Hospital Graz).
73
Diagnosis of ASD made using ADOS and ADI-R according to DSM-IV or DSM-V categories
N/A
80.82% Male
39659
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
112073
0
2
2
iourov_12_ASD/ID/EP_discovery_cases
Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012
54
Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies
Range, 3 mos.-11 yrs.
NA
215508
0
1
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
19760
0
2
2
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
135000
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)
169818
0
2
2
quintela_17_DD/ID_discovery_cases
Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
573
All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
Range, 3 months-18 years
60.38% Male
347363
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
13817
1
0
1
xu_16_ASD/DD/ID_discovery_cases
Patients referred to the Duke Autism Genetics Clinic for clinical genetic evaluation of ASD and DD/ID from 2010-2014
115
66 cases with confirmed primary diagnosis of ASD (DSM-IV, DSM-5, ADOS, and ADI-R used to support ASD diagnosis), 49 cases with primary diagnosis of DD or ID (based on IQ and DQ scores).
Range, 18 months-15.1 years (mean age, 5.7 years)
72.17% Male
100000
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
egger_14_ASD_discovery_controls
CNV data from POPGEN (n=1,123) and the Ottawa Heart Institute (n=1,234)
2357
Control
N/A
N/A
0
0
0
0
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
116769
0
3
3
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
2470
1
0
1
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
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.
85263
0
1
1
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)
97032
0
4
4
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
14533
0
1
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
celestino-soper_11_ASD_discovery_cases
aCGH
Agilent 1M
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
None
egger_14_ASD_discovery_cases
68 European, 2 Asian, 1 African, 1 Turkish, 1 Egyptian
Array SNP
Affymetrix 6.0
Birdsuite, iPattern, Affymetrix Genotyping Console
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
iourov_12_ASD/ID/EP_discovery_cases
Russian
aCGH
BACs aCGH
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
quintela_17_DD/ID_discovery_cases
North West Spain
Array SNP
Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
Affymetrix ChAS v.1.2.2
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
xu_16_ASD/DD/ID_discovery_cases
N/A
aCGH, array SNP
BlueGnome CytoChip v2, Affymetrix 6.0, Affymetrix Cytoscan HD
Affymeytrix Genotyping Console v3.0.2
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
egger_14_ASD_discovery_controls
European
N/A
N/A
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
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
None
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
brandler_18_ASD_discovery_cases-caseSSC10364
N/A
M
ASD
Case from SSC cohort
109536027
109536760
734
GRCh38
Deletion
Yes
celestino-soper_11_ASD_discovery_cases-11399
NA
M
ASD
NA
NA
111034113
111034444
332
GRCh38
Deletion
No
celestino-soper_11_ASD_discovery_cases-11461
NA
M
ASD
NA
NA
109188029
109188172
144
GRCh38
Duplication
No
egger_14_ASD_discovery_cases-caseA16
N/A
N/A
ASD
CNV: high stringency genic CNV call (2 or more algorithms), with no overlapping calls in 2,357 POPGEN and OHI controls, and <50% overlap in DGV.
109165689
109205347
39659
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case3097_4
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
109113703
109225776
112074
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4341_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
109073339
109158046
84708
GRCh38
Duplication
No
iourov_12_ASD/ID/EP_discovery_cases-case19
2 yrs. 7 mos.
NA
Intellectual disability
Speech delay, autistic features, kidney malformation
Intellectual disability
110573785
110789293
215509
GRCh38
Duplication
No
krumm_15_ASD_discovery_cases-case13150.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
108892981
108912741
19761
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case13634.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
108892981
108912741
19761
GRCh38
Duplication
Yes
maini_18_ASD/DD/ID_discovery_cases-case_unknown20
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
110333224
110468313
135090
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
110326388
110496205
169818
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
109961611
110036330
74720
GRCh38
Duplication
No
quintela_17_DD/ID_discovery_cases-caseID_19
11 yrs.
M
Intellectual disability and ADHD
ADHD, congenital heart disease
Intellectual disability
109100884
109448246
347363
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12424.p1
4.2
M
ASD
NA
Full-scale IQ, 69; non-verbal IQ, 77; verbal IQ, 65
110607577
110621394
13818
GRCh38
Deletion
No
xu_16_ASD/DD/ID_discovery_cases-case28
N/A
N/A
Developmental delay
Primary diagnosis of developmental delay based on DQ scores.
110579135
110681560
102426
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-controlHABC_900301_900301
N/A
N/A
Control
No previous psychiatric history
109110668
109227437
116770
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900930_900930
N/A
N/A
Control
No previous psychiatric history
109195511
109227437
31927
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900930_900930
N/A
N/A
Control
No previous psychiatric history
109113703
109166126
52424
GRCh38
Duplication
No
krumm_13_ASD_discovery_controls-control11895.s1
N/A
M
Control
Unaffected sibling from SSC quad family 11895. SRS score of 47.
108897005
108899475
2471
GRCh38
Deletion
Yes
nord_11_ASD_discovery_controls-04C27933
Control
108051589
108136851
85263
Unknown
Duplication
poultney_13_ASD_discovery_controls-control04C27933A
N/A
M
Control
NIMH Control (NIMH ID 38427)
109109827
109206858
97032
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C36026A
N/A
F
Control
NIMH Control (NIMH ID 68324)
110485076
110487945
2870
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C36026A
N/A
F
Control
NIMH Control (NIMH ID 68324)
110722133
110731903
9771
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
110326388
110388625
62238
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12977.s1
5.3
M
Control (matched sibling)
NA
NA
108899544
108914077
14534
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC10364
SNP VCF
De novo
UBE3B
celestino-soper_11_ASD_discovery_cases-11399
Unknown
Simplex
NA
CUX2
celestino-soper_11_ASD_discovery_cases-11461
Unknown
Simplex
NA
ACACB
egger_14_ASD_discovery_cases-caseA16
Unknown
Unknown
ACACB
engchuan_15_ASD_discovery_cases-case3097_4
Unknown
ACACB
engchuan_15_ASD_discovery_cases-case4341_1
Unknown
ALKBH2,UNG,ACACB,USP30
iourov_12_ASD/ID/EP_discovery_cases-case19
Unknown
Unknown
Unknown
RN7SL387P,PPTC7,HVCN1,PPP1CC,TCTN1
krumm_15_ASD_discovery_cases-case13150.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
DAO,SVOP
krumm_15_ASD_discovery_cases-case13634.p1
1M-Duov3
Maternal
Simplex
Not segregated (CNV in unaffected sibling)
DAO,SVOP
maini_18_ASD/DD/ID_discovery_cases-case_unknown20
Paternal
Unknown
Unknown
RN7SL769P,HMGA1P3,RPL31P49,ATP2A2,ANAPC7,ARPC3,GPN3
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
RN7SL769P,HMGA1P3,RPL31P49,ATP2A2,ANAPC7,ARPC3,GPN3,FAM216A,VPS29
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
ANKRD13A,C12orf76,TCHP,GIT2
quintela_17_DD/ID_discovery_cases-caseID_19
Unknown
Unknown
LINC01486,UNG,FOXN4,ACACB,MYO1H
sanders_11_ASD_discovery_cases-12424.p1
Maternal
Simplex (quad-proband matched)
Segregated
TCTN1
xu_16_ASD/DD/ID_discovery_cases-case28
Maternal
RN7SL387P,PPTC7,HVCN1,TCTN1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900301_900301
Unknown
UNG,ACACB
engchuan_15_ASD_discovery_controls-controlHABC_900930_900930
Unknown
ACACB
engchuan_15_ASD_discovery_controls-controlHABC_900930_900930
Unknown
ACACB
krumm_13_ASD_discovery_controls-control11895.s1
aCGH (Agilent SurePrint G3 4x180K)
Maternal
Simplex
DAO
nord_11_ASD_discovery_controls-04C27933
ACACB
poultney_13_ASD_discovery_controls-control04C27933A
Unknown
UNG,ACACB
poultney_13_ASD_discovery_controls-control04C36026A
Unknown
FAM216A
poultney_13_ASD_discovery_controls-control04C36026A
Unknown
PPP1CC
poultney_13_ASD_discovery_controls-control05C44621
Unknown
RN7SL769P,ATP2A2,ANAPC7
sanders_11_ASD_discovery_controls-12977.s1
Maternal
Simplex (quad)
NA
DAO,SVOP
No Animal Model Data Available