Copy Number Variants / 13q12.13

13q12.13

Case population data
Control population data
Type
Deletion
Average Length
40345
Range
26914040-26936107
Associated Human Genes
-
Associated Animal Models
-
Autism Reports
6
Populations
12 (6 case / 6 control)
Individuals
13 (9 case / 4 control)
Summary

Summary statement in development

Reports related to 13q12.13 (6 Reports)
# Type Title Author, Year
1 Minor Rare structural variation of synapse and neurotransmission genes in autism. Gai X , et al. (2011)
2 Minor Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Sanders SJ , et al. (2011)
3 Major An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili... Kaminsky EB , et al. (2011)
4 Minor Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies. Iourov IY , et al. (2013)
5 Minor A discovery resource of rare copy number variations in individuals with autism spectrum disorder. Prasad A , et al. (2013)
6 Minor Performance of case-control rare copy number variation annotation in classification of autism. Engchuan W , et al. (2015)
Show all Case Details Show all Cohort Details

13q12.13

Description:

Replication case samples derived from AGRE sets 1-3

Diagnosis:

Idiopathic autism; cases designated as 'spectrum' and 'not quite autism' excluded, as were cases with known genetic syndromes or other non-idiopathic causes

Gai X , et al. (2011)
Cohort Size: 593

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 21191

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

Platform: Illumina Infinium II HumanHap550 BeadChip
Software: BeadStudio 3.0
Algorithm: -
Geographical Ancestry: European

13q12.13

Description:

Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children in Toronto, Ontario; McMaster University, Hamilton, Ontario; Memorial University of Newfoundland, St. John's, Newfoundland); the majority of these cases had been previously genotyped by SNP arrays with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were exclu

Diagnosis:

Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS

Prasad A , et al. (2013)
Cohort Size: 676

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 9767

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: Agilent 1M
Software: DNA Analytics v4.0.85 (Agilent), DNAcopy
Algorithm: ADM-2, DNAcopy (R Bioconductor)
Geographical Ancestry: Canada

13q12.13

Description:

Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.

Diagnosis:

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)

Sanders SJ , et al. (2011)
Cohort Size: 1124

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 22067

Deletion: 4
Duplication: 0

Total CNV: 4
Discovery Method:

Solid phase hybridization

Validation Method:

-

Platform: Illumina 1M v1 (n=334) or Illumina 1M v3 (n=840)
Software: -
Algorithm: PennCNV, QuantiSNP, & GNOSIS
Geographical Ancestry: White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&

13q12.13

Description:

Samples from the Autism Genome Project (AGP)

Diagnosis:

Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)

Engchuan W , et al. (2015)
Cohort Size: 1892

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 53290

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

Platform: Illumina 1M
Software: -
Algorithm: -
Geographical Ancestry: Caucasian

13q12.13

Description:

Individuals selected from a total of 2426 patients whom had been evaluated cytogenetically and molecularly between November 2007 and May 2012

Diagnosis:

Intellectual disability (ID), autism/ASD, epilepsy (EP), and/or congenital anomalies

Iourov IY , et al. (2013)
Cohort Size: 54

Age Min: 58
Age Max: 58
Average: 58

Male: -
Female: 100
Unknown: -
CNV Size: 3993

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: BACs aCGH
Software: -
Algorithm: -
Geographical Ancestry: Russian

13q12.13

Description:

Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium

Diagnosis:

Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome

Kaminsky EB , et al. (2011)
Cohort Size: 15749

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 324300

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis

Platform: Agilent 44K or 105K
Software: Feature Extraction & DNA Analytics
Algorithm: -
Geographical Ancestry: NA
Show all Case Details Show all Cohort Details

gai_11_ASD_replication_cases-AU0914301

Clinical Profile:

-

Cognitive Profile:

-

Gai X , et al. (2011)
Primary Diagnosis: Autism

Age: -

Gender: -
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: -
CNV End: -
CNV Size: 21191
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Inherited
Family Profile: -
Genome Build: -
Gene Content: -

sanders_11_ASD_discovery_cases-11168.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 96; non-verbal IQ, 106; verbal IQ, 119

Sanders SJ , et al. (2011)
Primary Diagnosis: Autism

Age: 11.3

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad-proband matched)
CNV Start: 26018753
CNV End: 26022812
CNV Size: 4059
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad-proband matched)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_cases-11919.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 84; non-verbal IQ, 77; verbal IQ, 104

Sanders SJ , et al. (2011)
Primary Diagnosis: ASD

Age: 4.1

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad-proband matched)
CNV Start: 26168661
CNV End: 26177061
CNV Size: 8400
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad-proband matched)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_cases-12670.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 106; non-verbal IQ, 108; verbal IQ, 104

Sanders SJ , et al. (2011)
Primary Diagnosis: ASD

Age: 10.5

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (trio)
CNV Start: 26175401
CNV End: 26189665
CNV Size: 14264
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (trio)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_cases-13045.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 37; non-verbal IQ, 38; verbal IQ, 35

Sanders SJ , et al. (2011)
Primary Diagnosis: Autism

Age: 11.1

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (trio)
CNV Start: 26339903
CNV End: 26361970
CNV Size: 22067
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (trio)
Genome Build: GRCh38
Gene Content: -

prasad_12_ASD_discovery_cases-case59800L

Clinical Profile:

Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV

Cognitive Profile:

-

Prasad A , et al. (2013)
Primary Diagnosis: ASD

Age: NA

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex
CNV Start: -
CNV End: -
CNV Size: 9767
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex
Genome Build: -
Gene Content: -

iourov_12_ASD/ID/EP_discovery_cases-case49

Clinical Profile:

Facial dysmorphisms, clinodactyly, dentinogenesis imperfecta, enteroparesis. Karyotype: 9phqh, 17ps.

Cognitive Profile:

Developmental delay/intellectual disability

Iourov IY , et al. (2013)
Primary Diagnosis: Developmental delay/intellectual disability

Age: 4 yrs. 10 mos.

Gender: F
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 24233315
CNV End: 24237308
CNV Size: 3993
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: -

engchuan_15_ASD_discovery_cases-case14164_2680

Clinical Profile:

Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)

Cognitive Profile:

-

Engchuan W , et al. (2015)
Primary Diagnosis: ASD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: 24959693
CNV End: 25012983
CNV Size: 53290
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: RPL34P27, TPTE2P1

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004343

Clinical Profile:

Clinical profile NA

Cognitive Profile:

Cognitive profile NA

Kaminsky EB , et al. (2011)
Primary Diagnosis: Developmental delay/intellectual disability/ASD

Age: NA

Gender: NA
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 25779197
CNV End: 25998883
CNV Size: 324300
Validation Description: FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: RN7SL741P, RNY1P3, ATP8A2
Show all Control Details Show all Cohort Details

13q12.13

Description:

Unaffected siblings from quad families from the Simons Simplex Collection

Diagnosis:

Control

Krumm N , et al. (2015)
Cohort Size: 1786

Age Min: -
Age Max: -
Average: -

Male: -
Female: 100
Unknown: -
CNV Size: 47776

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

WES

Validation Method:

Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)

Platform: -
Software: -
Algorithm: CoNIFER, XHMM
Geographical Ancestry: N/A

13q12.13

Description:

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.

Diagnosis:

Control

Prasad A , et al. (2013)
Cohort Size: 5139

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 9767

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

aCGH (PDx controls)

Validation Method:

-

Platform: Agilent 1M (PDx controls)
Software: PDx controls: DNA Analytics v4.0.85 (Agilent), DNAcopy
Algorithm: PDx controls: ADM-2, DNAcopy (R Bioconductor)
Geographical Ancestry: NA

13q12.13

Description:

Matched siblings of autistic probands from the Simons Simplex Collection (SSC).

Diagnosis:

Controls

Sanders SJ , et al. (2011)
Cohort Size: 872

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 8400

Deletion: 3
Duplication: 0

Total CNV: 3
Discovery Method:

Solid phase hybridization

Validation Method:

-

Platform: Illumina 1M v1 or Illumina 1M v3
Software: -
Algorithm: PennCNV, QuantiSNP, & GNOSIS
Geographical Ancestry: -

13q12.13

Description:

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)

Diagnosis:

Controls; subjects had no previous psychiatric history

Engchuan W , et al. (2015)
Cohort Size: 2342

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 0

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

Solid phase hybridization

Validation Method:

None

Platform: Illumina 1M
Software: -
Algorithm: -
Geographical Ancestry: Caucasian

13q12.13

Description:

Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium

Diagnosis:

Controls

Kaminsky EB , et al. (2011)
Cohort Size: 10118

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: NA

Deletion: NA
Duplication: NA

Total CNV: NA
Discovery Method:

aCGH

Validation Method:

-

Platform: Agilent 44K or 105K
Software: Feature Extraction & DNA Analytics
Algorithm: -
Geographical Ancestry: NA
Show all Control Details Show all Cohort Details

sanders_11_ASD_discovery_controls-11178.s1

Clinical Profile:

NA

Cognitive Profile:

NA

Sanders SJ , et al. (2011)
Primary Diagnosis: Control (matched sibling)

Age: 5.1

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 27183768
CNV End: 27189086
CNV Size: 5318
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-11329.s1

Clinical Profile:

NA

Cognitive Profile:

NA

Sanders SJ , et al. (2011)
Primary Diagnosis: Control (matched sibling)

Age: 6.9

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 25105307
CNV End: 25106968
CNV Size: 1661
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Paternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-11919.s1

Clinical Profile:

NA

Cognitive Profile:

NA

Sanders SJ , et al. (2011)
Primary Diagnosis: Control (matched sibling)

Age: 6.7

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 26168661
CNV End: 26177061
CNV Size: 8400
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

krumm_15_ASD_discovery_controls-control13792.s1

Clinical Profile:

Unaffected sibling from the Simons Simplex Collection (SSC)

Cognitive Profile:

-

Krumm N , et al. (2015)
Primary Diagnosis: Control

Age: N/A

Gender: Female
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: 26337566
CNV End: 26385342
CNV Size: 47776
Validation Description: Omni2.5-4v1
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: -
Genome Build: GRCh38
Gene Content: -
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