Copy Number Variants / 13q13.1

13q13.1

Case population data
Control population data
Type
Deletion
Average Length
207238
Range
33521094-33541005
Associated Human Genes
BRCA2
Associated Animal Models
-
Autism Reports
4
Populations
10 (4 case / 6 control)
Individuals
12 (6 case / 6 control)
Summary

Summary statement in development

Reports related to 13q13.1 (4 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 Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. Girirajan S , et al. (2013)
Show all Case Details Show all Cohort Details

13q13.1

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: 86649

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

13q13.1

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: 19911

Deletion: 3
Duplication: 0

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&

13q13.1

Description:

1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.

Diagnosis:

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

Girirajan S , et al. (2013)
Cohort Size: 2588

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 1773000

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
Software: Agilent Genomic Workbench
Algorithm: ADM-2
Geographical Ancestry: NA

13q13.1

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: 371524

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-AU015805

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: 86649
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Inherited
Family Profile: -
Genome Build: -
Gene Content: -

sanders_11_ASD_discovery_cases-12102.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 45; non-verbal IQ, 52; verbal IQ, 38

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

Age: 5.1

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (trio)
CNV Start: 32956017
CNV End: 32957890
CNV Size: 1873
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (trio)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_cases-12170.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 80; non-verbal IQ, 85; verbal IQ, 77

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

Age: 7.8

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad-proband matched)
CNV Start: 31954821
CNV End: 31961859
CNV Size: 7038
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Both parents
Family Profile: Simplex (quad-proband matched)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_cases-12757.p1

Clinical Profile:

NA

Cognitive Profile:

Full-scale IQ, 57; non-verbal IQ, 62; verbal IQ, 55

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

Age: 5.3

Gender: M
Primary Disorder Inheritence: -

Family Profile: Simplex (trio)
CNV Start: 32946956
CNV End: 32966867
CNV Size: 19911
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (trio)
Genome Build: GRCh38
Gene Content: -

girirajan_13a_ASD_discovery_cases-13590.p1

Clinical Profile:

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

Cognitive Profile:

N/A

Girirajan S , et al. (2013)
Primary Diagnosis: ASD

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: Simplex
CNV Start: 32717863
CNV End: 34487863
CNV Size: 1773000
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex
Genome Build: GRCh38
Gene Content: RNY1P4, TOMM22P3, LINC02344, RNU5A-4P, VDAC1P12, STARD13-AS, PDS5B, LINC00423, KL, STARD13, STARD13-IT1, RFC3, LINC02343, LINC00457

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005049

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: 33018055
CNV End: 33389580
CNV Size: 371524
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: LINC02344, STARD13-AS, KL, STARD13, STARD13-IT1
Show all Control Details Show all Cohort Details

13q13.1

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: 15818

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: -

13q13.1

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: 87901

Deletion: 2
Duplication: 1

Total CNV: 3
Discovery Method:

Solid phase hybridization

Validation Method:

None

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

13q13.1

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-11088.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 14.5

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 32325251
CNV End: 32341069
CNV Size: 15818
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-11715.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 6.6

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 31954821
CNV End: 31961859
CNV Size: 7038
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Paternal
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

sanders_11_ASD_discovery_controls-13083.s1

Clinical Profile:

NA

Cognitive Profile:

NA

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

Age: 9.8

Gender: F
Primary Disorder Inheritence: -

Family Profile: Simplex (quad)
CNV Start: 33027446
CNV End: 33032891
CNV Size: 5444
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Simplex (quad)
Genome Build: GRCh38
Gene Content: -

engchuan_15_ASD_discovery_controls-controlB495422_1007852884

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: 32332309
CNV End: 32363866
CNV Size: 31557
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: -

engchuan_15_ASD_discovery_controls-controlB944304_1007853858

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: 32319134
CNV End: 32398243
CNV Size: 79109
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: IFIT1P1, BRCA2

engchuan_15_ASD_discovery_controls-controlHABC_900046_900046

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: 32757748
CNV End: 32845649
CNV Size: 87901
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: RNY1P4, PDS5B
Genes associated with 13q13.1(0 Models)
BRCA2 2  /  3 Rare Single Gene Mutation
Score
4
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