Copy Number Variants / 13q12.3

13q12.3

Case population data
Control population data
Type
Deletion-Duplication
Average Length
213063
Range
31096630-31127975
Associated Human Genes
ALOX5AP, FLT1, KATNAL1
Associated Animal Models
-
Autism Reports
6
Populations
12 (6 case / 6 control)
Individuals
14 (8 case / 6 control)
Summary

Summary statement in development

Reports related to 13q12.3 (6 Reports)
# Type Title Author, Year
1 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)
2 Minor Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE. Celestino-Soper PB , et al. (2011)
3 Minor A discovery resource of rare copy number variations in individuals with autism spectrum disorder. Prasad A , et al. (2013)
4 Minor Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Poultney CS , et al. (2013)
5 Minor The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population. Al-Qattan SM , et al. (2014)
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

13q12.3

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: 9725

Deletion: 1
Duplication: 0

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

13q12.3

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: 33
Female: 67
Unknown: -
CNV Size: 31345

Deletion: 2
Duplication: 1

Total CNV: 3
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&

13q12.3

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: 160197

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

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

13q12.3

Description:

ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)

Diagnosis:

Cases diagnosed with ASD

Poultney CS , et al. (2013)
Cohort Size: 299

Age Min: -
Age Max: -
Average: -

Male: -
Female: 100
Unknown: -
CNV Size: 132191

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

WES

Validation Method:

None

Platform: Agilent SureSelect Human All Exon v.2
Software: -
Algorithm: XHMM
Geographical Ancestry: European

13q12.3

Description:

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.

Diagnosis:

ASD

Celestino-Soper PB , et al. (2011)
Cohort Size: 99

Age Min: -
Age Max: -
Average: -

Male: 100
Female: -
Unknown: -
CNV Size: 275

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: Agilent 1M
Software: Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
Algorithm: ADM-2
Geographical Ancestry: -

13q12.3

Description:

Retrospective chart review of patients (n=584) with a neurocognitive phenotype (mainly referred from pediatric neurology clinics) seen by a single clinical geneticist from September 2007 to July 2013

Diagnosis:

Inclusion criteria: presence of a neurocognitive phenotype (i.e., syndromic and non-syndromic cases of developmental delay, autism, intellectual disability, and epilepsy) with a normal karyotype

Al-Qattan SM , et al. (2014)
Cohort Size: 584

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 2314000

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

Array SNP

Validation Method:

None

Platform: Affymetrix 6.0, Cyto-V2, or CytoScan HD
Software: Affymetrix GeneChip Command Console (version 1.2); Chromosome Analysis Suite version Cyto 2.0.0.195
Algorithm: HMM
Geographical Ancestry: Saudi Arabia
Show all Case Details Show all Cohort Details

prasad_12_ASD_discovery_cases-case47607

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: Unknown
CNV Start: -
CNV End: -
CNV Size: 9725
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: -
Gene Content: -

sanders_11_ASD_discovery_cases-12072.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 139; non-verbal IQ, 116; verbal IQ, 167

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

Age: 15.6

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad-proband unmatched)
CNV Start: 29505347
CNV End: 29517682
CNV Size: 12335
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (quad-proband unmatched)
Genome Build: GRCh38
Gene Content: SLC7A1, MTUS2

sanders_11_ASD_discovery_cases-12454.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 72; non-verbal IQ, 82; verbal IQ, 62

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

Age: 5.5

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (trio)
CNV Start: 30522493
CNV End: 30553838
CNV Size: 31345
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Paternal
Family Profile: Simplex (trio)
Genome Build: GRCh38
Gene Content: MFAP1P1, PTPN2P2, HMGB1, RBM22P2

sanders_11_ASD_discovery_cases-12524.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 146; non-verbal IQ, 130; verbal IQ, 166

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

Age: 6.4

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad-proband matched)
CNV Start: 30852074
CNV End: 30852299
CNV Size: 225
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Paternal
Family Profile: Simplex (quad-proband matched)
Genome Build: GRCh38
Gene Content: -

engchuan_15_ASD_discovery_cases-case2285_1

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: 31152516
CNV End: 31312713
CNV Size: 160197
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: ANKRD26P4, HSPH1, B3GLCT

celestino-soper_11_ASD_discovery_cases-11345

Clinical Profile:

NA

Cognitive Profile:

NA

Celestino-Soper PB , et al. (2011)
Primary Diagnosis: ASD

Age: NA

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex
CNV Start: 31138367
CNV End: 31138642
CNV Size: 275
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex
Genome Build: GRCh38
Gene Content: -

poultney_13_ASD_discovery_cases-case05HI4737A

Clinical Profile:

ASD case from AGRE (AGRE ID AU1482302; NDAR ID NDAR_INVEE937MZQ)

Cognitive Profile:

-

Poultney CS , et al. (2013)
Primary Diagnosis: ASD

Age: N/A

Gender: F
Primary Disorder Inheritence: -

Family Profile: Unknown (likely multiplex/AGRE)
CNV Start: 31154631
CNV End: 31286821
CNV Size: 132191
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown (likely multiplex/AGRE)
Genome Build: GRCh38
Gene Content: HSPH1, B3GLCT

al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case08DG00254

Clinical Profile:

Intellectual disability and speech delay, epilepsy, ADHD, microbrachycephaly, obesity, hypogonadism, exaggerated reflexes, in-toe gait. Non-consanguineous parents. Father has learning difficulties and psychological problems.

Cognitive Profile:

Intellectual disability

Al-Qattan SM , et al. (2014)
Primary Diagnosis: Intellectual disability, epilepsy, and ADHD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: Paternal

Family Profile: Multi-generational
CNV Start: 28652136
CNV End: 30966135
CNV Size: 2314000
Validation Description: -
Primary Disorder Inheritence: Paternal
CNV Inheritance: Paternal
Family Profile: Multi-generational
Genome Build: GRCh38
Gene Content: RNU6-53P, CYP51A1P2, POM121L13P, GAPDHP69, MTUS2-AS1, TIMM8BP1, LINC00572, LINC00365, LINC00384, LINC00385, RNU6-64P, PRDX2P1, LINC00427, LINC01058, MFAP1P1, PTPN2P2, LINC00398, LINC00545, POMP, MTUS2-AS2, SLC7A1, UBL3, LINC00544, LINC00426, UBE2L5P, USPL1, ALOX5AP, MEDAG, SLC46A3, LINC00297, KATNAL1, HMGB1, RBM22P2, TEX26-AS1, TEX26, MTUS2
Show all Control Details Show all Cohort Details

13q12.3

Description:

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

Diagnosis:

Controls (no history of psychiatric symptoms by self-report)

Nord AS , et al. (2011)
Cohort Size: 123

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 104061

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: NimbleGen HD2
Software: -
Algorithm: Sliding-window algorithm, ~10 kb minumum size threshold
Geographical Ancestry: -

13q12.3

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: 9725

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

13q12.3

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: 33
Female: 67
Unknown: -
CNV Size: 3874

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: -

13q12.3

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: 81192

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

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

13q12.3

Description:

Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)

Diagnosis:

Control

Poultney CS , et al. (2013)
Cohort Size: 260

Age Min: -
Age Max: -
Average: -

Male: -
Female: 100
Unknown: -
CNV Size: 132191

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

WES

Validation Method:

None

Platform: Agilent SureSelect Human All Exon v.2
Software: -
Algorithm: XHMM
Geographical Ancestry: European
Show all Control Details Show all Cohort Details

nord_11_ASD_discovery_controls-04C27213

Clinical Profile:

-

Cognitive Profile:

-

Nord AS , et al. (2011)
Primary Diagnosis: Control

Age: -

Gender: -
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: -
CNV End: -
CNV Size: 104061
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: -
Family Profile: -
Genome Build: -
Gene Content: -

sanders_11_ASD_discovery_controls-11446.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 11

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 30852074
CNV End: 30853122
CNV Size: 1048
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-12647.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 9.1

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 30852074
CNV End: 30852299
CNV Size: 225
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-12821.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 9

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 31550465
CNV End: 31554339
CNV Size: 3874
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

poultney_13_ASD_discovery_controls-control05C40631

Clinical Profile:

NIMH Control (NIMH ID 80004)

Cognitive Profile:

-

Poultney CS , et al. (2013)
Primary Diagnosis: Control

Age: N/A

Gender: F
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: 31154631
CNV End: 31286821
CNV Size: 132191
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: HSPH1, B3GLCT

engchuan_15_ASD_discovery_controls-controlB958271_1007843897

Clinical Profile:

No previous psychiatric history

Cognitive Profile:

-

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

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: -
CNV Start: 29217000
CNV End: 29298192
CNV Size: 81192
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: MTUS2-AS2, MTUS2
Genes associated with 13q12.3(0 Models)
ALOX5AP 1  /  4 Functional
Score
5
FLT1 2  /  4 Rare Single Gene Mutation, Functional
Score
5
KATNAL1 1  /  2 Rare Single Gene Mutation, Functional
Score
4
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