Copy Number Variants / 13q12.11-q12.12

13q12.11-q12.12

Type
Deletion-Duplication
Average Length
1836432
Range
20411535-25458647
Associated Human Genes
-
Associated Animal Models
-
Autism Reports
2
Populations
2 (2 case / 0 control)
Individuals
8 (8 case / 0 control)
Summary

CNVs within this region were found in seven cases from a study of 15,749 individuals from the International Standards for Cytogenomic Arrays (ISCA) consortium with unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome (Kaminsky et al., 2011), as well as in an ASD case (Prasad et al., 2012).

Reports related to 13q12.11-q12.12 (2 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 Minor A discovery resource of rare copy number variations in individuals with autism spectrum disorder. Prasad A , et al. (2013)
Show all Case Details Show all Cohort Details

13q12.11-q12.12

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: 383829

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

13q12.11-q12.12

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: 5047112

Deletion: 2
Duplication: 5

Total CNV: 7
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

prasad_12_ASD_discovery_cases-case69180

Clinical Profile:

Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study

Cognitive Profile:

-

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

Age: NA

Gender: M
Primary Disorder Inheritence: -

Family Profile: Multiplex
CNV Start: -
CNV End: -
CNV Size: 383829
Validation Description: -
Primary Disorder Inheritence: -
CNV Inheritance: Unknown
Family Profile: Multiplex
Genome Build: -
Gene Content: -

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002409

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: 22672788
CNV End: 23489498
CNV Size: 816710
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: FTH1P7, DDX39AP1, RPL7AP73, IPMKP1, RFESDP1, BASP1P1, NUS1P2, RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00621, HMGA1P6, LINC00327, SGCG, SACS

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002451

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: 22941375
CNV End: 24286142
CNV Size: 1344766
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: RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00352, MTCO3P2, PCOTH, C1QTNF9B, ANKRD20A19P, IPO7P2, MIR2276, SPATA13-AS1, HMGA1P6, LINC00327, SGCG, SACS, TNFRSF19, MIPEP, SPATA13

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003776

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: 19837395
CNV End: 24884509
CNV Size: 5047112
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: PPIAP28, LINC00556, GJB2, GJB6, MIR4499, SLC35E1P1, RNU2-7P, RANP8, PPIAP27, RPSAP54, LATS2-AS1, RNU4-9P, RPS12P23, IPPKP1, FAS-AS1, SAP18, MRPL57, LINC01046, GRK6P1, GAPDHP52, RNA5SP25, ZDHHC20-IT1, HIST1H2BPS3, FNTAP2, RNU6-59P, RPS7P10, LINC00424, NME1P1, MTND3P1, FTH1P7, DDX39AP1, RPL7AP73, IPMKP1, RFESDP1, BASP1P1, NUS1P2, RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00352, MTCO3P2, PCOTH, C1QTNF9B, ANKRD20A19P, IPO7P2, MIR2276, SPATA13-AS1, C1QTNF9-AS1, NUS1P3, LINC00566, CYCSP33, PSPC1P2, RNY1P7, RPL26P34, IRX1P1, ANKRD20A10P, ZMYM5, KRR1P1, LINC01072, GJA3, EEF1AKMT1, CNOT4P1, HNRNPA1P30, LATS2, SKA3, ESRRAP2, MIPEPP3, LINC00539, ZDHHC20, FGF9, RN7SL766P, LINC00621, HMGA1P6, LINC00327, C1QTNF9, ATP12A, ZMYM2, CRYL1, IFT88, IL17D, XPO4, MICU2, LINC00540, SGCG, SACS, TNFRSF19, MIPEP, SPATA13, TPTE2P6, PARP4, RNF17, CENPJ

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003920

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: 22992823
CNV End: 24336605
CNV Size: 1343781
Validation Description: FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00352, MTCO3P2, PCOTH, C1QTNF9B, ANKRD20A19P, IPO7P2, MIR2276, SPATA13-AS1, C1QTNF9-AS1, NUS1P3, LINC00566, HMGA1P6, LINC00327, C1QTNF9, SGCG, SACS, TNFRSF19, MIPEP, SPATA13

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004073

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: 22992623
CNV End: 24336746
CNV Size: 1344122
Validation Description: FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Primary Disorder Inheritence: -
CNV Inheritance: Maternal
Family Profile: Unknown
Genome Build: GRCh38
Gene Content: RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00352, MTCO3P2, PCOTH, C1QTNF9B, ANKRD20A19P, IPO7P2, MIR2276, SPATA13-AS1, C1QTNF9-AS1, NUS1P3, LINC00566, HMGA1P6, LINC00327, C1QTNF9, SGCG, SACS, TNFRSF19, MIPEP, SPATA13

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004088

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: 22992823
CNV End: 24336605
CNV Size: 1343781
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: RNY3P4, LINC00362, RNU6-58P, TATDN2P3, SDAD1P4, RPLP1P13, SACS-AS1, LINC00352, MTCO3P2, PCOTH, C1QTNF9B, ANKRD20A19P, IPO7P2, MIR2276, SPATA13-AS1, C1QTNF9-AS1, NUS1P3, LINC00566, HMGA1P6, LINC00327, C1QTNF9, SGCG, SACS, TNFRSF19, MIPEP, SPATA13

kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004814

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: 19837395
CNV End: 22904755
CNV Size: 3067359
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: PPIAP28, LINC00556, GJB2, GJB6, MIR4499, SLC35E1P1, RNU2-7P, RANP8, PPIAP27, RPSAP54, LATS2-AS1, RNU4-9P, RPS12P23, IPPKP1, FAS-AS1, SAP18, MRPL57, LINC01046, GRK6P1, GAPDHP52, RNA5SP25, ZDHHC20-IT1, HIST1H2BPS3, FNTAP2, RNU6-59P, RPS7P10, LINC00424, NME1P1, MTND3P1, FTH1P7, DDX39AP1, RPL7AP73, IPMKP1, RFESDP1, BASP1P1, ZMYM5, KRR1P1, LINC01072, GJA3, EEF1AKMT1, CNOT4P1, HNRNPA1P30, LATS2, SKA3, ESRRAP2, MIPEPP3, LINC00539, ZDHHC20, FGF9, RN7SL766P, LINC00621, ZMYM2, CRYL1, IFT88, IL17D, XPO4, MICU2, LINC00540
Show all Control Details Show all Cohort Details

13q12.11-q12.12

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: 383829

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

13q12.11-q12.12

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

No control individuals reported.

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