12q23.3CNV Type: Deletion-Duplication
Largest CNV size: 141887 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
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, ...
Deletion
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Identifying autism loci and genes by tracing recent shared ancestry.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare de novo and transmitted copy-number variation in autistic spectrum disorders.
Duplication
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion-Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
battaglia_13_DD/ID/ASD_discovery_cases
Patients affected by DD/ID/ASD/dysmorphic features of unknown origin observed at the Stella Maris Institute (Pisa, Italy) between May 2004 & December 2011
349
34 cases with borderline intellectual disability, 237 cases with mixed intellectual disability, 78 cases with intellectual disability and ASD (cases referred with a provisional diagnosis of ASD evaluated with ADI-R and ADOS-G)
Range, 5 mos.-19 yrs.
63.9% Male
550000
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
2753
1
1
2
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
106507
1
1
2
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
2015137
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
33963
2
1
3
levy_11_ASD_discovery_cases
Autistic probands from 887 families from the Simons Simplex Collection (SSC)
858
ASD
87.06% Male
141887
0
1
1
morrow_08_ASD_discovery_cases
Affected individuals from 70 families (52 simplex, 18 multiplex) recruited by Homozygosity Mapping Collaborative for Autism (HMCA) used in CNV analysis. This cohort was selected from an original population of affected individuals from 104 families (79 simplex, 25 multiplex; 82.7% male); 88 of these pedigrees have cousin marriages.
94
ASD (based on DSM-IV-TR diagnoses when research scales not available in native language)
36000
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)
185974
0
8
8
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
138652
4
2
6
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
98518
2
2
4
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
kanduri_15_ASD_discovery_controls
Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
269
Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
N/A
N/A
222247
1
0
1
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
2536
1
0
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
12270
3
0
3
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
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.
182996
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)
310507
0
2
2
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
77632
3
0
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
battaglia_13_DD/ID/ASD_discovery_cases
Italy
aCGH, array SNP
BACs aCGH, Agilent 44K, Agilent 180K, Affymetrix 6.0
FISH, qPCR
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
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
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_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
morrow_08_ASD_discovery_cases
Arabic Middle East, Turkey, and Pakistan
Array SNP
Affymetrix 500K
BRLMM
dChip
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
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
kanduri_15_ASD_discovery_controls
Finnish
Solid phase hybridization
Illumina Infinium HD Human610-Quad BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
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
None
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
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
battaglia_13_DD/ID/ASD_discovery_cases-case2
4 yrs.
M
Developmental delay/intellectual disability
Autism: no. Epilepsy: no. Dysmorphic features: yes.
Moderate-mild DD/ID
104113778
104663373
549596
GRCh38
Deletion
Yes
celestino-soper_11_ASD_discovery_cases-11303
NA
M
ASD
NA
NA
108536471
108536629
159
GRCh38
Duplication
No
celestino-soper_11_ASD_discovery_cases-11510
NA
M
ASD
NA
NA
103982872
103985625
2754
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case14297_4180
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
104451954
104558461
106508
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4045_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
108011986
108089618
77633
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001860
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
104550262
106565399
2015138
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case11565.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
105195260
105229223
33964
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12096.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
108006080
108018350
12271
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case14495.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
103956630
103989577
32948
GRCh38
Deletion
Yes
levy_11_ASD_discovery_cases-11565.p1
NA
M
ASD
NA
NA
105191354
105333240
141887
GRCh38
Duplication
No
morrow_08_ASD_discovery_cases-case3605
NA
ASD
NA
NA
104681000
104717000
36000
Unknown
Deletion
No
poultney_13_ASD_discovery_cases-case03HI2580A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0924301; NDAR ID NDAR_INVCE056PE7)
103980891
104135455
154565
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
103594393
103780366
185974
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
108524314
108701320
177007
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
103759131
103798679
39549
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
106971103
107022194
51092
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
107699371
107752211
52841
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
104066165
104120481
54317
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI1144B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU020404; NDAR ID NDAR_INVPN168CVH)
105026543
105122240
95698
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11233.p1
6.3
F
Autism
NA
Full-scale IQ, 57; non-verbal IQ, 60; verbal IQ, 65
108011986
108099368
87383
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11565.p1
10.8
M
Autism
NA
Full-scale IQ, 113; non-verbal IQ, 114; verbal IQ, 109
105190099
105328751
138653
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11609.p1
5.3
M
Autism
NA
Full-scale IQ, 78; non-verbal IQ, 79; verbal IQ, 83
104512902
104523570
10669
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12096.p1
11.7
M
Autism
NA
Full-scale IQ, 119; non-verbal IQ, 119; verbal IQ, 114
108011986
108089618
77633
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12097.p1
4.8
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 115; verbal IQ, 145
105549177
105583628
34452
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13007.p1
13.6
M
Autism
NA
Full-scale IQ, 91; non-verbal IQ, 107; verbal IQ, 67
104470949
104476739
5791
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
engchuan_15_ASD_discovery_controls-controlB404708_0067942623
N/A
N/A
Control
No previous psychiatric history
108011986
108089618
77633
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB522577_1007840898
N/A
N/A
Control
No previous psychiatric history
108011986
108089618
77633
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_900064_900064
N/A
N/A
Control
No previous psychiatric history
104128342
104226860
98519
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900308_900308
N/A
N/A
Control
No previous psychiatric history
107875173
107910311
35139
GRCh38
Duplication
No
kanduri_15_ASD_discovery_controls-control_split140
N/A
N/A
Control
Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
103974255
104196501
222247
Unknown
Deletion
No
krumm_13_ASD_discovery_controls-control13832.s1
N/A
F
Control
Unaffected sibling from SSC quad family 13832. SRS score of 38.
103777828
103780364
2537
GRCh38
Deletion
No (not tested)
krumm_15_ASD_discovery_controls-control12096.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
108006080
108018350
12271
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control13832.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
103777828
103780384
2557
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_controls-control14391.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
108006080
108018350
12271
GRCh38
Deletion
Yes
nord_11_ASD_discovery_controls-04C28227
Control
104591119
104774114
182996
Unknown
Duplication
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
103590895
103733184
142290
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
106686882
106997388
310507
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11049.s1
9.8
F
Control (matched sibling)
NA
NA
105549177
105583628
34452
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11909.s1
5.7
M
Control (matched sibling)
NA
NA
104453536
104453934
399
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12096.s1
9.7
M
Control (matched sibling)
NA
NA
108011986
108089618
77633
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
battaglia_13_DD/ID/ASD_discovery_cases-case2
FISH or qPCR
De novo
Unknown
Unknown
RNA5SP370,LINC02385,RPL18AP3,EID3,MIR3922,NFYB,TXNRD1,CHST11
celestino-soper_11_ASD_discovery_cases-11303
Unknown
Simplex
NA
SART3
celestino-soper_11_ASD_discovery_cases-11510
Unknown
Simplex
NA
TDG
engchuan_15_ASD_discovery_cases-case14297_4180
Unknown
CHST11
engchuan_15_ASD_discovery_cases-case4045_1
Unknown
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001860
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
MIR3922,KRT18P20,ST13P3,RNU7-94P,ALDH1L2,APPL2,KCCAT198,CASC18,NUAK1,TCP11L2,CHST11,C12orf45,WASHC4,C12orf75,CKAP4,POLR3B,SLC41A2
krumm_15_ASD_discovery_cases-case11565.p1
Illumina 1M
Paternal
Simplex
Segregated
APPL2
krumm_15_ASD_discovery_cases-case12096.p1
Illumina 1MDuo
Paternal
Simplex
Not segregated (CNV in unaffected sibling)
krumm_15_ASD_discovery_cases-case14495.p1
Omni2.5-4v1
De novo
Simplex
Segregated
C12orf73,TDG,GLT8D2
levy_11_ASD_discovery_cases-11565.p1
Paternal
Simplex
Segregated
APPL2,KCCAT198,C12orf75
morrow_08_ASD_discovery_cases-case3605
Unknown
Multiplex
NA
3' end of NUAK1
poultney_13_ASD_discovery_cases-case03HI2580A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
RNA5SP370,TDG,GLT8D2,NFYB,HCFC2
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
STAB2,NT5DC3
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
FICD,ISCU,MIR4496,RNU7-169P,TMEM119,SELPLG,SART3,CORO1C
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
STAB2,NT5DC3
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
MTERF2,TMEM263,CRY1
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
PWP1,PRDM4
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
NFYB,HCFC2
poultney_13_ASD_discovery_cases-case99HI1144B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
ALDH1L2,C12orf45,WASHC4
sanders_11_ASD_discovery_cases-11233.p1
Maternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-11565.p1
Paternal
Simplex (quad-proband unmatched)
Unknown
APPL2,KCCAT198,C12orf75
sanders_11_ASD_discovery_cases-11609.p1
Maternal
Simplex (trio)
NA
CHST11
sanders_11_ASD_discovery_cases-12096.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12097.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-13007.p1
Paternal
Simplex (quad-proband matched)
Not segregated
CHST11
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB404708_0067942623
Unknown
engchuan_15_ASD_discovery_controls-controlB522577_1007840898
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900064_900064
Unknown
LINC02385,NFYB,TXNRD1
engchuan_15_ASD_discovery_controls-controlHABC_900308_900308
Unknown
kanduri_15_ASD_discovery_controls-control_split140
Unknown
NT5DC3,STAB2
krumm_13_ASD_discovery_controls-control13832.s1
Paternal
Simplex
NT5DC3
krumm_15_ASD_discovery_controls-control12096.s1
Illumina 1MDuo
Paternal
krumm_15_ASD_discovery_controls-control13832.s1
Omni2.5-4v1
Paternal
NT5DC3
krumm_15_ASD_discovery_controls-control14391.s1
Omni2.5-4v1
Maternal
nord_11_ASD_discovery_controls-04C28227
0 genes
poultney_13_ASD_discovery_controls-control05C44621
Unknown
STAB2
poultney_13_ASD_discovery_controls-control05C44621
Unknown
EEF1B2P4,RPL30P12,MTERF2,TMEM263,RFX4,RIC8B,CRY1
sanders_11_ASD_discovery_controls-11049.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11909.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12096.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available