Copy Number Variants / 13q32.2-q32.3

13q32.2-q32.3

Type
Deletion-Duplication
Average Length
6831178
Range
99150575-115085141
Associated Human Genes
-
Associated Animal Models
-
Autism Reports
4
Populations
4 (4 case / 0 control)
Individuals
5 (5 case / 0 control)
Summary

CNVs within this region were identified in cases from two recent reports (Kaminsky et al., 2011; Nguyen et al., 2013).

Reports related to 13q32.2-q32.3 (4 Reports)
# Type Title Author, Year
1 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)
2 Major Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders. Nguyen LS , et al. (2013)
3 Minor Global increases in both common and rare copy number load associated with autism. Girirajan S , et al. (2013)
4 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

13q32.2-q32.3

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: 100631

Deletion: 0
Duplication: 1

Total CNV: 1
Discovery Method:

Solid phase hybridization

Validation Method:

None

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

13q32.2-q32.3

Description:

Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)

Diagnosis:

Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol

Girirajan S , et al. (2013)
Cohort Size: 243

Age Min: -
Age Max: -
Average: -

Male: -
Female: -
Unknown: 100
CNV Size: 369913

Deletion: 1
Duplication: 0

Total CNV: 1
Discovery Method:

aCGH

Validation Method:

None

Platform: Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
Software: -
Algorithm: DNA Copy Number v1.6
Geographical Ancestry: 133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American

13q32.2-q32.3

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: 1823969

Deletion: 0
Duplication: 1

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

13q32.2-q32.3

Description:

Patients from five databases: The Developmental Gene Anatomy Project at Harvard Medical School (DGAP, n=200); The Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP, n=120); The National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS, n=45); Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database (n=45,744); and DECIPHER

Diagnosis:

Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD

Nguyen LS , et al. (2013)
Cohort Size: 57365

Age Min: -
Age Max: -
Average: -

Male: 50
Female: 50
Unknown: -
CNV Size: 15934566

Deletion: 2
Duplication: 0

Total CNV: 2
Discovery Method:

aCGH (n=45,744 from Signature Genomic Labs)

Validation Method:

FISH

Platform: SignatureChip BACs aCGH or SignatureChip Oligo whole-genome microarray (n=45,744)
Software: -
Algorithm: -
Geographical Ancestry: N/A
Show all Case Details Show all Cohort Details

engchuan_15_ASD_discovery_cases-case3205_3

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: 98609074
CNV End: 98709705
CNV Size: 100631
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: -
Genome Build: GRCh38
Gene Content: NUS1P4, CYCSP35, CALM2P4, RN7SL60P, SLC15A1

girirajan_13b_ASD_discovery_cases-16708109743

Clinical Profile:

Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Caucasian

Cognitive Profile:

N/A

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

Age: N/A

Gender: N/A
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 98421241
CNV End: 98791154
CNV Size: 369913
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: FARP1-AS1, STK24-AS1, NUS1P4, CYCSP35, CALM2P4, RN7SL60P, FARP1, SLC15A1, STK24

nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC18255

Clinical Profile:

Database: Signature. Indication for study: 46,XY,del(13)(q31q3?2.3)

Cognitive Profile:

-

Nguyen LS , et al. (2013)
Primary Diagnosis: DD/ID/MCA

Age: N/A

Gender: M
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 98498321
CNV End: 114319666
CNV Size: 15934566
Validation Description: FISH
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: STK24-AS1, NUS1P4, CYCSP35, CALM2P4, RN7SL60P, DOCK9-AS1, RPL7L1P12, RNU6-83P, DOCK9-AS2, RPS6P23, GAPDHP22, UBAC2-AS1, RN7SKP9, H2AFZP3, GPR18, MIR623, HMGB3P4, CCR12P, LINC01232, LINC01039, CFL1P8, MIR4306, CLYBL-AS2, CLYBL-AS1, ZIC5, ZIC2, LINC00554, NDUFA12P1, ASNSP3, RPL15P18, RPS26P47, COX5BP6, ARF4P3, RNU1-24P, HMGB3P7, MIR2681, LIPT1P1, RNY1P2, MIR4705, RPL39P29, FGF14-AS1, FGF14-AS2, LINC00555, METTL21C, TEX30, LINC01309, ATP6V1G1P7, RPL7P45, RNA5SP38, LINC00460, RPL35P9, ATP5G1P5, PPIAP24, SNORD31B, MIR1267, RNA5SP39, HCFC2P1, MYO16-AS2, LINC00370, LINC01067, LINC00399, LINC00676, RN7SKP10, LINC00396, RN7SL783P, MIR8073, COL4A2-AS1, RPL21P107, LINC00567, LINC00346, ANKRD10-IT1, PARP1P1, ARHGEF7-AS2, ARHGEF7-AS1, LINC00354, SNORD44, SOX1, LINC00404, LINC01043, F10-AS1, MIR8075, LDHBP1, RNU1-16P, LINC00552, GAS6-AS2, LINC00454, LINC00565, RASA3-IT1, MIR548AR, MIR4502, CLCP2, CHAMP1, GPR183, LINC00449, TM9SF2, PCCA-AS1, LINC00411, CCDC168, LINC00283, KDELC1, BIVM, BIVM-ERCC5, ERCC5, SLC10A2, DAOA-AS1, DAOA, LINC00343, EFNB2, LINC00551, LINC00443, FAM155A-IT1, LIG4, ABHD13, IRS2, COL4A2-AS2, RAB20, CARS2, ING1, LINC00431, LINC00368, ARHGEF7-IT1, TEX29, LINC02337, SPACA7, TUBGCP3, ATP11AUN, ATP11A-AS1, MCF2L-AS1, F10, KARSP2, PROZ, PCID2, LAMP1, GRTP1, GRTP1-AS1, ADPRHL1, DCUN1D2, DCUN1D2-AS, ATP4B, GRK1, GAS6-AS1, GAS6, CDC16, SLC15A1, DOCK9, UBAC2, PCCA, GGACT, NALCN-AS1, NALCN, FGF14-IT1, TPP2, METTL21EP, ARGLU1, FAM155A, TNFSF13B, MYO16-AS1, COL4A1, COL4A2, NAXD, ANKRD10, LINC01044, ATP11A, MCF2L, F7, TMCO3, TFDP1, TMEM255B, LINC00452, RASA3, STK24, CLYBL, ITGBL1, FGF14, ARHGEF7, LINC01070, CUL4A, UPF3A, TMTC4, MYO16

nguyen_13_DD/ID/MCA/ASD_discovery_cases-GC40227

Clinical Profile:

Database: Signature. Indication for study: Possible Trisomy 13 with 2 abnormal cell lines, mosaic r(13)

Cognitive Profile:

-

Nguyen LS , et al. (2013)
Primary Diagnosis: DD/ID/MCA

Age: N/A

Gender: F
Primary Disorder Inheritence: -

Family Profile: Unknown
CNV Start: 98498875
CNV End: 114312465
CNV Size: 15926811
Validation Description: FISH
Primary Disorder Inheritence: -
CNV Inheritance: De novo
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: STK24-AS1, NUS1P4, CYCSP35, CALM2P4, RN7SL60P, DOCK9-AS1, RPL7L1P12, RNU6-83P, DOCK9-AS2, RPS6P23, GAPDHP22, UBAC2-AS1, RN7SKP9, H2AFZP3, GPR18, MIR623, HMGB3P4, CCR12P, LINC01232, LINC01039, CFL1P8, MIR4306, CLYBL-AS2, CLYBL-AS1, ZIC5, ZIC2, LINC00554, NDUFA12P1, ASNSP3, RPL15P18, RPS26P47, COX5BP6, ARF4P3, RNU1-24P, HMGB3P7, MIR2681, LIPT1P1, RNY1P2, MIR4705, RPL39P29, FGF14-AS1, FGF14-AS2, LINC00555, METTL21C, TEX30, LINC01309, ATP6V1G1P7, RPL7P45, RNA5SP38, LINC00460, RPL35P9, ATP5G1P5, PPIAP24, SNORD31B, MIR1267, RNA5SP39, HCFC2P1, MYO16-AS2, LINC00370, LINC01067, LINC00399, LINC00676, RN7SKP10, LINC00396, RN7SL783P, MIR8073, COL4A2-AS1, RPL21P107, LINC00567, LINC00346, ANKRD10-IT1, PARP1P1, ARHGEF7-AS2, ARHGEF7-AS1, LINC00354, SNORD44, SOX1, LINC00404, LINC01043, F10-AS1, MIR8075, LDHBP1, RNU1-16P, LINC00552, GAS6-AS2, LINC00454, LINC00565, RASA3-IT1, MIR548AR, MIR4502, CLCP2, GPR183, LINC00449, TM9SF2, PCCA-AS1, LINC00411, CCDC168, LINC00283, KDELC1, BIVM, BIVM-ERCC5, ERCC5, SLC10A2, DAOA-AS1, DAOA, LINC00343, EFNB2, LINC00551, LINC00443, FAM155A-IT1, LIG4, ABHD13, IRS2, COL4A2-AS2, RAB20, CARS2, ING1, LINC00431, LINC00368, ARHGEF7-IT1, TEX29, LINC02337, SPACA7, TUBGCP3, ATP11AUN, ATP11A-AS1, MCF2L-AS1, F10, KARSP2, PROZ, PCID2, LAMP1, GRTP1, GRTP1-AS1, ADPRHL1, DCUN1D2, DCUN1D2-AS, ATP4B, GRK1, GAS6-AS1, GAS6, CDC16, SLC15A1, DOCK9, UBAC2, PCCA, GGACT, NALCN-AS1, NALCN, FGF14-IT1, TPP2, METTL21EP, ARGLU1, FAM155A, TNFSF13B, MYO16-AS1, COL4A1, COL4A2, NAXD, ANKRD10, LINC01044, ATP11A, MCF2L, F7, TMCO3, TFDP1, TMEM255B, LINC00452, RASA3, STK24, CLYBL, ITGBL1, FGF14, ARHGEF7, LINC01070, CUL4A, UPF3A, TMTC4, MYO16

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001747

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: 97674476
CNV End: 99498445
CNV Size: 1823969
Validation Description: FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Primary Disorder Inheritence: -
CNV Inheritance: Paternal
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: RPL7AP61, FTLP8, RNF113B, RN7SKP8, MIR3170, FARP1-AS1, STK24-AS1, NUS1P4, CYCSP35, CALM2P4, RN7SL60P, DOCK9-AS1, RPL7L1P12, RNU6-83P, DOCK9-AS2, RPS6P23, GAPDHP22, UBAC2-AS1, RN7SKP9, H2AFZP3, GPR18, MIR623, HMGB3P4, CCR12P, LINC01232, IPO5, GPR183, FARP1, SLC15A1, DOCK9, UBAC2, STK24
Show all Control Details Show all Cohort Details

13q32.2-q32.3

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: 0

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

Solid phase hybridization

Validation Method:

None

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

13q32.2-q32.3

Description:

Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)

Diagnosis:

Control

Girirajan S , et al. (2013)
Cohort Size: 223

Age Min: -
Age Max: -
Average: -

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

Deletion: 0
Duplication: 0

Total CNV: 0
Discovery Method:

aCGH

Validation Method:

-

Platform: Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
Software: -
Algorithm: DNA Copy Number v1.6
Geographical Ancestry: 116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American

13q32.2-q32.3

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

13q32.2-q32.3

Description:

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.

Diagnosis:

Control

Nguyen LS , et al. (2013)
Cohort Size: 20474

Age Min: -
Age Max: -
Average: -

Male: 50
Female: 50
Unknown: -
CNV Size: N/A

Deletion: N/A
Duplication: N/A

Total CNV: N/A
Discovery Method:

N/A

Validation Method:

N/A

Platform: N/A
Software: -
Algorithm: -
Geographical Ancestry: N/A
Show all Control Details Show all Cohort Details

No control individuals reported.

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