13q12.13CNV Type: Deletion
Largest CNV size: 22067 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
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
Minor Reports
Title
Author, Year
Report Class
CNV Type
Rare structural variation of synapse and neurotransmission genes in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies.
Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
53290
0
1
1
feliciano_19_ASD_discovery_cases
ASD probands from 457 families (418 simplex, 39 multiplex) from the SPARK cohort
465
All cases diagnosed with ASD
Range of age at enrollment, 1.544.6 years
80.86% Male
16415
0
1
1
gai_11_ASD_replication_cases
Replication case samples derived from AGRE sets 1-3
593
Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes
21191
1
0
1
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
3993
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
324300
1
0
1
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
979000
1
0
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
9767
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
22067
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
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_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
47776
0
1
1
prasad_12_ASD_discovery_controls
PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
5139
Control
NA
NA (PDx controls 50.2% male)
9767
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.
8400
3
0
3
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
feliciano_19_ASD_discovery_cases
N/A
WES
Illumina HumanCoreExome 550K
CoNIFER, XHMM
None
gai_11_ASD_replication_cases
European
Solid phase hybridization
Illumina Infinium II HumanHap550 BeadChip
BeadStudio 3.0
None
iourov_12_ASD/ID/EP_discovery_cases
Russian
aCGH
BACs aCGH
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
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
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
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
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
engchuan_15_ASD_discovery_cases-case14164_2680
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
24959693
25012983
53291
GRCh38
Duplication
No
feliciano_19_ASD_discovery_cases-caseSP0020384
N/A
M
ASD
Family history: both parents are negative for ASD and have no reported mental health diagnoses.
26385211
26401625
16415
GRCh38
Duplication
No
gai_11_ASD_replication_cases-AU0914301
Autism
25144328
25165518
21191
Unknown
Deletion
No
iourov_12_ASD/ID/EP_discovery_cases-case49
4 yrs. 10 mos.
F
Developmental delay/intellectual disability
Facial dysmorphisms, clinodactyly, dentinogenesis imperfecta, enteroparesis. Karyotype: 9phqh, 17ps.
Developmental delay/intellectual disability
24233315
24237308
3994
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004343
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
25779197
25998883
219687
GRCh38
Deletion
Yes
maini_18_ASD/DD/ID_discovery_cases-case_unknown25
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)
25452399
26431541
979143
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case59800L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
25695049
25704815
9767
Unknown
Duplication
No
sanders_11_ASD_discovery_cases-11168.p1
11.3
M
Autism
NA
Full-scale IQ, 96; non-verbal IQ, 106; verbal IQ, 119
26018753
26022812
4060
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11919.p1
4.1
M
ASD
NA
Full-scale IQ, 84; non-verbal IQ, 77; verbal IQ, 104
26168661
26177061
8401
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12670.p1
10.5
M
ASD
NA
Full-scale IQ, 106; non-verbal IQ, 108; verbal IQ, 104
26175401
26189665
14265
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13045.p1
11.1
M
Autism
NA
Full-scale IQ, 37; non-verbal IQ, 38; verbal IQ, 35
26339903
26361970
22068
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
krumm_15_ASD_discovery_controls-control13792.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
26337566
26385342
47777
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_controls-11178.s1
5.1
M
Control (matched sibling)
NA
NA
27183768
27189086
5319
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11329.s1
6.9
M
Control (matched sibling)
NA
NA
25105307
25106968
1662
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11919.s1
6.7
M
Control (matched sibling)
NA
NA
26168661
26177061
8401
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case14164_2680
Unknown
RPL34P27,TPTE2P1
feliciano_19_ASD_discovery_cases-caseSP0020384
Maternal
Simplex
CDK8
null
gai_11_ASD_replication_cases-AU0914301
Inherited
ATP8A2 (intronic)
iourov_12_ASD/ID/EP_discovery_cases-case49
Unknown
Unknown
Unknown
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004343
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SL741P,RNY1P3,ATP8A2
maini_18_ASD/DD/ID_discovery_cases-case_unknown25
Maternal
Unknown
Unknown
RNU6-78P,RN7SL741P,RNY1P3,LINC00415,PRUNEP1,THAP12P6,SHISA2,ATP8A2P3,ATP8A2,CDK8,RNF6
prasad_12_ASD_discovery_cases-case59800L
Unknown
Simplex
Unknown
0 genes
sanders_11_ASD_discovery_cases-11168.p1
Maternal
Simplex (quad-proband matched)
Segregated
ATP8A2
sanders_11_ASD_discovery_cases-11919.p1
Maternal
Simplex (quad-proband matched)
Not segregated
RNF6
sanders_11_ASD_discovery_cases-12670.p1
Maternal
Simplex (trio)
NA
RNF6
sanders_11_ASD_discovery_cases-13045.p1
Maternal
Simplex (trio)
NA
CDK8
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_15_ASD_discovery_controls-control13792.s1
Omni2.5-4v1
Maternal
CDK8
sanders_11_ASD_discovery_controls-11178.s1
Maternal
Simplex (quad)
NA
LINC02340
sanders_11_ASD_discovery_controls-11329.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11919.s1
Maternal
Simplex (quad)
NA
RNF6
No Animal Model Data Available