12q13.2CNV Type: Deletion
Largest CNV size: 15515 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
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
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
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
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.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
bosch_23_DD_discovery_cases
Case with a de novo 12q13.2 microdeletion affecting the SMARCC2 gene (from an initial cohort of 41 novel individuals with SMARRC2 variants that were recruited through GeneMatcher and an international collaborative network).
1
Case presented with developmental delay (mildly delayed ability to walk) and Diamond-Blackfan anemia (deletion also involves the entire RPS26 gene)
20 mos.
Male
232171
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
255599
0
2
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
1882
0
1
1
nguyen_13_DD/ID/MCA/ASD_discovery_cases
Patients from the Developmental Gene Anatomy Project at Harvard Medical School (DGAP), the Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP), the National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS), the Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database, and DECIPHER
57365
Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD
N/A
N/A
N/A
1
2
3
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)
675083
0
6
6
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
101016
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
15515
4
0
4
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
36135
0
1
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
5276
0
1
1
nguyen_13_DD/ID/MCA/ASD_discovery_controls
Control data from the Database of Genomic Variants (DGV, n=12,145) and a published dataset of 8,329 individuals from Moriarty et al., 1998.
20474
Control
N/A
N/A
N/A
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)
68015
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.
3805
2
0
2
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
bosch_23_DD_discovery_cases
Turkey
CMA
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
nguyen_13_DD/ID/MCA/ASD_discovery_cases
N/A
aCGH
SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
N/A
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
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
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
nguyen_13_DD/ID/MCA/ASD_discovery_controls
N/A
N/A
N/A
N/A
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
bosch_23_DD_discovery_cases-case12
20 mos.
M
Developmental delay
Developmental milestones: mildly delayed ability to walk (16 months). Additional medical history: Diamond-Blackfan anemia (deletion also involves the entire RPS26 gene). Family history: unremarkable.
55960344
56192514
232171
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case13014_193
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
55087817
55159083
71267
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case14247_3710
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
55406929
55662528
255600
GRCh38
Duplication
No
krumm_15_ASD_discovery_cases-case11859.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
56100173
56102055
1883
GRCh38
Duplication
Yes
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient156
N/A
N/A
DD/ID/MCA
N/A
N/A
N/A
N/A
N/A
GRCh37
Deletion
N/A
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient157
N/A
N/A
DD/ID/MCA
N/A
N/A
N/A
N/A
N/A
GRCh37
Duplication
N/A
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient158
N/A
N/A
DD/ID/MCA
N/A
N/A
N/A
N/A
N/A
GRCh37
Duplication
N/A
poultney_13_ASD_discovery_cases-case00HI1663A
N/A
F
ASD
ASD case from AGRE (AGRE ID AU056708; NDAR ID NDAR_INVAC801FDF)
55129767
55552158
422392
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
55820258
55961465
141208
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
56137497
56181103
43607
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
56033190
56100247
67058
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0694B
N/A
F
ASD
ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
54573146
55248228
675083
GRCh38
Duplication
No
poultney_13_ASD_discovery_cases-case99HI0807A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU055105; NDAR ID NDAR_INVME794HY9)
55817664
55820397
2734
GRCh38
Duplication
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1022-0
N/A
N/A
ACC-CBLH
Diagnosis of agenesis of the corpus callosum (ACC) and cerebellar hypoplasia (CBLH). ASD: no. Seizures: yes.
Developmental delay: yes. Intellectual disability: no.
56383321
56484336
101016
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_cases-11939.p1
7.2
M
Autism
NA
Full-scale IQ, 89; non-verbal IQ, 91; verbal IQ, 88
55499179
55502266
3088
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12201.p1
13.3
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 131; verbal IQ, 116
55524002
55527807
3806
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12312.p1
5.5
M
Autism
NA
Full-scale IQ, 73; non-verbal IQ, 80; verbal IQ, 70
55328019
55343534
15516
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13233.p1
13.6
M
Autism
NA
Full-scale IQ, 90; non-verbal IQ, 95; verbal IQ, 84
55499179
55502266
3088
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-controlHABC_900060_900060
N/A
N/A
Control
No previous psychiatric history
56351525
56387660
36136
GRCh38
Duplication
No
krumm_15_ASD_discovery_controls-control11121.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
55837554
55842830
5277
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
56084993
56099747
14755
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C44621
N/A
M
Control
NIMH Control (NIMH ID 39000)
55937015
56005029
68015
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-11905.s1
8.6
F
Control (matched sibling)
NA
NA
55499179
55502266
3088
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12201.s1
12.1
M
Control (matched sibling)
NA
NA
55524002
55527807
3806
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
bosch_23_DD_discovery_cases-case12
De novo
Simplex
CDK2,ERBB3,IKZF4,ZC3H10,MYL6B,PA2G4,MYL6,RPL41,RPS26,RAB5B,SUOX,PMEL,SMARCC2,MYL6B-AS1,ESYT1
engchuan_15_ASD_discovery_cases-case13014_193
Unknown
OR9R1P,OR9K1P,OR9K2
engchuan_15_ASD_discovery_cases-case14247_3710
Unknown
PHC1P1,OR6C2,OR6C70,OR6C64P,OR6C4,OR6U2P,OR10P1,OR10AE3P,OR6C76,OR6C68,OR2AP1
krumm_15_ASD_discovery_cases-case11859.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
ERBB3
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient156
Unknown
Unknown
Unknown
Minimum CNV gene content: WIBG
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient157
Unknown
Unknown
Unknown
Minimum CNV gene content: WIBG
nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient158
Unknown
Unknown
Unknown
Minimum CNV gene content: WIBG
poultney_13_ASD_discovery_cases-case00HI1663A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
OR9R1P,OR10U1P,OR10A7,OR6C74,OR6C72P,OR6C1,OR6C3,OR6C7P,OR6C75,OR6C66P,OR6C73P,OR6C65,PHC1P1,OR6C2,OR6C70,OR6C64P,OR6C4,OR9K2,OR6C69P,OR6C6,OR6C71P,OR6C76,OR6C68,OR6C5P
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
DNAJC14,TMEM198B,OLA1P3,GSTP1P1,ORMDL2,PYM1,DGKA,MMP19,PMEL
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
MYL6B,MYL6,ESYT1,SMARCC2
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
RPS26,IKZF4,ERBB3
poultney_13_ASD_discovery_cases-case99HI0694B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
PPP1R1A,GLYCAM1,LACRT,DCD,VDAC1P5,NEUROD4,OR9R1P,OR10U1P,OR10A7,OR6C74,PDE1B,MUCL1,TESPA1,OR9K1P,OR9K2
poultney_13_ASD_discovery_cases-case99HI0807A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
SARNP,ORMDL2
sajan_13_ACC/CBLH/PMG_discovery_cases-case1022-0
qPCR
Paternal
Unknown
Unknown
TIMELESS,MIP,SPRYD4,GLS2
sanders_11_ASD_discovery_cases-11939.p1
Unknown
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12201.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12312.p1
Paternal
Simplex (trio)
NA
OR6C3,OR6C7P
sanders_11_ASD_discovery_cases-13233.p1
Both parents
Simplex (quad-proband matched)
Segregated
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900060_900060
Unknown
RNU7-40P,APONP,STAT2,APOF
krumm_15_ASD_discovery_controls-control11121.s1
Illumina 1M
Maternal
MMP19
poultney_13_ASD_discovery_controls-control05C44621
Unknown
ERBB3
poultney_13_ASD_discovery_controls-control05C44621
Unknown
DGKA,RAB5B,SUOX,PMEL,CDK2
sanders_11_ASD_discovery_controls-11905.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12201.s1
Paternal
Simplex (quad)
NA
No Animal Model Data Available