16p13.3-p13.13CNV Type: Deletion-Duplication
Largest CNV size: 11346017 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
CNVs within this region were identified in four cases from two recent studies (Kaminsky et al., 2011; Nguyen et al., 2013).
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
akkus_24_ASD/DD/ID_discovery_cases
Patients with developmental delay/intellectual disability, autism spectrum disorder, and/or multiple congenital anomalies consulted by the Department of Medical Genetics at the Health Sciences University Kocaeli Derince Training and Research Hospital between January 1, 2017 and March 30, 2021.
1227
Patients presented with developmental delay/intellectual disability, autism spectrum disorder, and/or multiple congenital anomalies.
57.13% Male
5180433
1
0
1
kaminsky_11_DD/ID/ASD_discovery_cases
Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium
15749
Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome
NA
NA
11284912
1
1
2
nguyen_13_DD/ID/MCA/ASD_discovery_cases
Patients from the Developmental Gene Anatomy Project at Harvard Medical School (DGAP), the Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP), the National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS), the Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database, and DECIPHER
57365
Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD
N/A
N/A
11346017
0
2
2
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
kaminsky_11_DD/ID/ASD_discovery_controls
Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium
10118
Controls
NA
NA
NA
NA
NA
NA
nguyen_13_DD/ID/MCA/ASD_discovery_controls
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.
20474
Control
N/A
N/A
N/A
N/A
N/A
N/A
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
akkus_24_ASD/DD/ID_discovery_cases
Turkey
Array SNP
Affymetrix CytoScan Optima
ThermoFisher ChAS v.3.1.
kaminsky_11_DD/ID/ASD_discovery_cases
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
nguyen_13_DD/ID/MCA/ASD_discovery_cases
N/A
aCGH
SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
N/A
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
nguyen_13_DD/ID/MCA/ASD_discovery_controls
N/A
N/A
N/A
N/A
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
akkus_24_ASD/DD/ID_discovery_cases-case73A
1 yr.
F
Hypotonia
Hypotonia
6547420
11727852
5180433
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002440
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
23141
11296695
11273555
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004717
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
4536131
10852466
6316336
GRCh38
Deletion
Yes
nguyen_13_DD/ID/MCA/ASD_discovery_cases-251553
N/A
F
MCA
Database: DECIPHER. Indication for study: Atrial septum defect, cleft palate, feeding problems in infants, hyptonia (non-myopathic), low birthweight (<3rd centile), low-set ears, microcephaly, single palmar crease.
10001
11312161
11302161
GRCh38
Duplication
N/A
nguyen_13_DD/ID/MCA/ASD_discovery_cases-256897
N/A
M
DD/ID/MCA
Database: DECIPHER. Indication for study: NF (nothing found/no phenotypic information available)
22798
10655138
10632341
GRCh38
Duplication
N/A
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
akkus_24_ASD/DD/ID_discovery_cases-case73A
Unknown
ABAT,EMP2,C16orf72,TXNDC11,DEXI,RBFOX1,PRM3,METTL22,ATF7IP2,RMI2,TEKT5,GRIN2A,TMEM114,RPL7P46,IMPDH1P11,RPL21P119,TVP23A,NUBP1,CIITA,RNU7-63P,MIR548H2,HNRNPCP4,RNA5SP404,LINC02177,PRM2,PMM2,PRM1,LITAFD,LINC01177,LINC01195,USP7-AS1,LINC02152,RN7SL493P,LINC01290,RNA5SP403,TNP2,RNU6-457P,RN7SL743P,RNU6-328P,RNU7-99P,RNU6-633P,MTND3P13,MTATP6P24,MTND4LP24,MTCO3P24,MTND5P33,MTND6P33,MTND4P34,MTCYBP33,SOCS1,SNN,USP7,CARHSP1-DT,LITAF,CARHSP1,CLEC16A,TMEM186
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002440
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
WASIR2,SNRNP25,HBZ,HBA2,HBA1,HBQ1,RGS11,PDIA2,MRPL28,LINC00235,MIR5587,MIR3176,PRR35,NHLRC4,WFIKKN1,METTL26,RHBDL1,STUB1,JMJD8,METRN,CCDC78,HAGHL,MSLN,MIR662,CHTF18,GNG13,SSTR5,C1QTNF8,TPSG1,TPSAB1,TPSD1,TPSP2,RPS20P2,TSR3,C16orf91,RPS3AP2,PTX4,MIR3177,NME3,MRPS34,EME2,IGFALS,LINC02124,MSRB1,NDUFB10,RPS2,SNORA10,SNORA64,SNHG9,SNORA78,RNF151,GFER,SYNGR3,RN7SL219P,NTHL1,MIR1225,MIR6511B1,MIR4516,MIR3180-5,SNHG19,SNORD60,MLST8,PGP,DNASE1L2,MIR3677,MIR940,MIR4717,MIR6767,TEDC2,MIR6768,ATP6V0C,CEMP1,MIR3178,ELOB,SNORA3C,EIF1P4,PRSS30P,PRSS22,RPL23AP86,PKMYT1,PAQR4,LINC00514,CLDN9,CLDN6,TNFRSF12A,HCFC1R1,THOC6,RNU1-125P,RNU1-22P,ZNF213,OR1F1,OR1F2P,LINC00921,TIGD7,OR2C1,MTCO1P28,MTND1P8,MTRNR2L4,MIR6126,C16orf90,LINC01569,SUB1P3,UBALD1,RN7SL850P,MIR6769A,NUDT16L1,SMIM22,LINC02164,SNRPCP20,MIR8065,RNU7-99P,RNU6-457P,RNU6-328P,LINC02152,RNU7-63P,RPL21P119,LINC01177,RNA5SP403,RNA5SP404,IMPDH1P11,RN7SL493P,RNU6-633P,MTCYBP33,MTND6P33,MTND5P33,MTND4P34,MTND4LP24,MTND3P13,MTCO3P24,MTATP6P24,DEXI,RPL7P46,HNRNPCP4,TNP2,PRM3,PRM2,PRM1,IL9RP3,POLR3K,RHBDF1,MPG,HBM,HBZP1,LUC7L,ARHGDIG,AXIN1,TMEM8A,NME4,DECR2,RAB11FIP3,CAPN15,PIGQ,RAB40C,MCRIP2,RHOT2,WDR24,FBXL16,FAM173A,CIAO3,MSLNL,LMF1-AS1,SOX8,SSTR5-AS1,TPSB2,PRSS29P,BAIAP3,GNPTG,UNKL,CLCN7,TELO2,TMEM204,CRAMP1,JPT2,MAPK8IP3,SPSB3,NUBP2,HAGH,LINC00254,HS3ST6,RPL3L,TBL3,NOXO1,ZNF598,NPW,SLC9A3R2,TSC2,RAB26,TRAF7,CASKIN1,BRICD5,ECI1,RNPS1,ABCA3,CCNF,NTN3,AMDHD2,PDPK1,ERVK13-1,KCTD5,PRSS27,PRSS33,PRSS41,PRSS21,ZG16B,FLYWCH1,KREMEN2,BICDL2,MMP25-AS1,MMP25,IL32,ZSCAN10,ZNF213-AS1,ZNF205,ZNF200,MEFV,ZNF75A,ZSCAN32,ZNF597,NAA60,NLRC3,SLX4,TFAP4,PAM16,CORO7-PAM16,CORO7,VASN,NMRAL1,HMOX2,CDIP1,MGRN1,C16orf71,ZNF500,SEPT12,ROGDI,GLYR1,PPL,NAGPA-AS1,NAGPA,ALG1,C16orf89,EEF2KMT,LINC01570,TMEM114,METTL22,RN7SL743P,PMM2,CARHSP1,C16orf72,LINC02177,LINC01195,LINC01290,EMP2,TEKT5,TVP23A,SOCS1,NPRL3,FAM234A,WDR90,RPUSD1,LMF1,CACNA1H,UBE2I,CCDC154,IFT140,FAHD1,MEIOB,E4F1,ABCA17P,TBC1D24,PDPK2P,SRRM2-AS1,SRRM2,FLYWCH2,ZNF263,ZNF174,CLUAP1,DNASE1,TRAP1,CREBBP,ADCY9,GLIS2,GLIS2-AS1,DNAJA3,C16orf96,ANKS3,UBN1,SEC14L5,ENPP7P14,ABAT,TMEM186,USP7,GRIN2A,ATF7IP2,NUBP1,CIITA,CLEC16A,RMI2,PKD1,CASP16P,SRL,RBFOX1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004717
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SUB1P3,UBALD1,RN7SL850P,MIR6769A,NUDT16L1,SMIM22,LINC02164,SNRPCP20,MIR8065,RNU7-99P,RNU6-457P,RNU6-328P,LINC02152,RNU7-63P,RPL21P119,LINC01177,RNA5SP403,RNA5SP404,IMPDH1P11,RN7SL493P,RNU6-633P,MTCYBP33,MTND6P33,MTND5P33,MTND4P34,MTND4LP24,MTND3P13,MTCO3P24,MTATP6P24,CDIP1,MGRN1,C16orf71,ZNF500,SEPT12,ROGDI,GLYR1,PPL,NAGPA-AS1,NAGPA,ALG1,C16orf89,EEF2KMT,LINC01570,TMEM114,METTL22,RN7SL743P,PMM2,CARHSP1,C16orf72,LINC02177,LINC01195,LINC01290,EMP2,TEKT5,TVP23A,C16orf96,ANKS3,UBN1,SEC14L5,ENPP7P14,ABAT,TMEM186,USP7,GRIN2A,ATF7IP2,NUBP1,RBFOX1
nguyen_13_DD/ID/MCA/ASD_discovery_cases-251553
Unknown
Unknown
Unknown
DDX11L10,MIR6859-4,WASIR2,SNRNP25,HBZ,HBA2,HBA1,HBQ1,RGS11,PDIA2,MRPL28,LINC00235,MIR5587,MIR3176,PRR35,NHLRC4,WFIKKN1,METTL26,RHBDL1,STUB1,JMJD8,METRN,CCDC78,HAGHL,MSLN,MIR662,CHTF18,GNG13,SSTR5,C1QTNF8,TPSG1,TPSAB1,TPSD1,TPSP2,RPS20P2,TSR3,C16orf91,RPS3AP2,PTX4,MIR3177,NME3,MRPS34,EME2,IGFALS,LINC02124,MSRB1,NDUFB10,RPS2,SNORA10,SNORA64,SNHG9,SNORA78,RNF151,GFER,SYNGR3,RN7SL219P,NTHL1,MIR1225,MIR6511B1,MIR4516,MIR3180-5,SNHG19,SNORD60,MLST8,PGP,DNASE1L2,MIR3677,MIR940,MIR4717,MIR6767,TEDC2,MIR6768,ATP6V0C,CEMP1,MIR3178,ELOB,SNORA3C,EIF1P4,PRSS30P,PRSS22,RPL23AP86,PKMYT1,PAQR4,LINC00514,CLDN9,CLDN6,TNFRSF12A,HCFC1R1,THOC6,RNU1-125P,RNU1-22P,ZNF213,OR1F1,OR1F2P,LINC00921,TIGD7,OR2C1,MTCO1P28,MTND1P8,MTRNR2L4,MIR6126,C16orf90,LINC01569,SUB1P3,UBALD1,RN7SL850P,MIR6769A,NUDT16L1,SMIM22,LINC02164,SNRPCP20,MIR8065,RNU7-99P,RNU6-457P,RNU6-328P,LINC02152,RNU7-63P,RPL21P119,LINC01177,RNA5SP403,RNA5SP404,IMPDH1P11,RN7SL493P,RNU6-633P,MTCYBP33,MTND6P33,MTND5P33,MTND4P34,MTND4LP24,MTND3P13,MTCO3P24,MTATP6P24,DEXI,RPL7P46,HNRNPCP4,TNP2,PRM3,PRM2,PRM1,MIR548H2,WASH4P,IL9RP3,POLR3K,RHBDF1,MPG,HBM,HBZP1,LUC7L,ARHGDIG,AXIN1,TMEM8A,NME4,DECR2,RAB11FIP3,CAPN15,PIGQ,RAB40C,MCRIP2,RHOT2,WDR24,FBXL16,FAM173A,CIAO3,MSLNL,LMF1-AS1,SOX8,SSTR5-AS1,TPSB2,PRSS29P,BAIAP3,GNPTG,UNKL,CLCN7,TELO2,TMEM204,CRAMP1,JPT2,MAPK8IP3,SPSB3,NUBP2,HAGH,LINC00254,HS3ST6,RPL3L,TBL3,NOXO1,ZNF598,NPW,SLC9A3R2,TSC2,RAB26,TRAF7,CASKIN1,BRICD5,ECI1,RNPS1,ABCA3,CCNF,NTN3,AMDHD2,PDPK1,ERVK13-1,KCTD5,PRSS27,PRSS33,PRSS41,PRSS21,ZG16B,FLYWCH1,KREMEN2,BICDL2,MMP25-AS1,MMP25,IL32,ZSCAN10,ZNF213-AS1,ZNF205,ZNF200,MEFV,ZNF75A,ZSCAN32,ZNF597,NAA60,NLRC3,SLX4,TFAP4,PAM16,CORO7-PAM16,CORO7,VASN,NMRAL1,HMOX2,CDIP1,MGRN1,C16orf71,ZNF500,SEPT12,ROGDI,GLYR1,PPL,NAGPA-AS1,NAGPA,ALG1,C16orf89,EEF2KMT,LINC01570,TMEM114,METTL22,RN7SL743P,PMM2,CARHSP1,C16orf72,LINC02177,LINC01195,LINC01290,EMP2,TEKT5,TVP23A,SOCS1,NPRL3,FAM234A,WDR90,RPUSD1,LMF1,CACNA1H,UBE2I,CCDC154,IFT140,FAHD1,MEIOB,E4F1,ABCA17P,TBC1D24,PDPK2P,SRRM2-AS1,SRRM2,FLYWCH2,ZNF263,ZNF174,CLUAP1,DNASE1,TRAP1,CREBBP,ADCY9,GLIS2,GLIS2-AS1,DNAJA3,C16orf96,ANKS3,UBN1,SEC14L5,ENPP7P14,ABAT,TMEM186,USP7,GRIN2A,ATF7IP2,NUBP1,CIITA,CLEC16A,RMI2,PKD1,CASP16P,SRL,RBFOX1
nguyen_13_DD/ID/MCA/ASD_discovery_cases-256897
Imbalance arising from a balanced parental rearrangement
Unknown
Unknown
WASIR2,SNRNP25,HBZ,HBA2,HBA1,HBQ1,RGS11,PDIA2,MRPL28,LINC00235,MIR5587,MIR3176,PRR35,NHLRC4,WFIKKN1,METTL26,RHBDL1,STUB1,JMJD8,METRN,CCDC78,HAGHL,MSLN,MIR662,CHTF18,GNG13,SSTR5,C1QTNF8,TPSG1,TPSAB1,TPSD1,TPSP2,RPS20P2,TSR3,C16orf91,RPS3AP2,PTX4,MIR3177,NME3,MRPS34,EME2,IGFALS,LINC02124,MSRB1,NDUFB10,RPS2,SNORA10,SNORA64,SNHG9,SNORA78,RNF151,GFER,SYNGR3,RN7SL219P,NTHL1,MIR1225,MIR6511B1,MIR4516,MIR3180-5,SNHG19,SNORD60,MLST8,PGP,DNASE1L2,MIR3677,MIR940,MIR4717,MIR6767,TEDC2,MIR6768,ATP6V0C,CEMP1,MIR3178,ELOB,SNORA3C,EIF1P4,PRSS30P,PRSS22,RPL23AP86,PKMYT1,PAQR4,LINC00514,CLDN9,CLDN6,TNFRSF12A,HCFC1R1,THOC6,RNU1-125P,RNU1-22P,ZNF213,OR1F1,OR1F2P,LINC00921,TIGD7,OR2C1,MTCO1P28,MTND1P8,MTRNR2L4,MIR6126,C16orf90,LINC01569,SUB1P3,UBALD1,RN7SL850P,MIR6769A,NUDT16L1,SMIM22,LINC02164,SNRPCP20,MIR8065,RNU7-99P,RNU6-457P,RNU6-328P,LINC02152,RNU7-63P,RPL21P119,LINC01177,RNA5SP403,RNA5SP404,IMPDH1P11,RN7SL493P,RNU6-633P,IL9RP3,POLR3K,RHBDF1,MPG,HBM,HBZP1,LUC7L,ARHGDIG,AXIN1,TMEM8A,NME4,DECR2,RAB11FIP3,CAPN15,PIGQ,RAB40C,MCRIP2,RHOT2,WDR24,FBXL16,FAM173A,CIAO3,MSLNL,LMF1-AS1,SOX8,SSTR5-AS1,TPSB2,PRSS29P,BAIAP3,GNPTG,UNKL,CLCN7,TELO2,TMEM204,CRAMP1,JPT2,MAPK8IP3,SPSB3,NUBP2,HAGH,LINC00254,HS3ST6,RPL3L,TBL3,NOXO1,ZNF598,NPW,SLC9A3R2,TSC2,RAB26,TRAF7,CASKIN1,BRICD5,ECI1,RNPS1,ABCA3,CCNF,NTN3,AMDHD2,PDPK1,ERVK13-1,KCTD5,PRSS27,PRSS33,PRSS41,PRSS21,ZG16B,FLYWCH1,KREMEN2,BICDL2,MMP25-AS1,MMP25,IL32,ZSCAN10,ZNF213-AS1,ZNF205,ZNF200,MEFV,ZNF75A,ZSCAN32,ZNF597,NAA60,NLRC3,SLX4,TFAP4,PAM16,CORO7-PAM16,CORO7,VASN,NMRAL1,HMOX2,CDIP1,MGRN1,C16orf71,ZNF500,SEPT12,ROGDI,GLYR1,PPL,NAGPA-AS1,NAGPA,ALG1,C16orf89,EEF2KMT,LINC01570,TMEM114,METTL22,RN7SL743P,PMM2,CARHSP1,C16orf72,LINC02177,LINC01195,LINC01290,EMP2,TEKT5,NPRL3,FAM234A,WDR90,RPUSD1,LMF1,CACNA1H,UBE2I,CCDC154,IFT140,FAHD1,MEIOB,E4F1,ABCA17P,TBC1D24,PDPK2P,SRRM2-AS1,SRRM2,FLYWCH2,ZNF263,ZNF174,CLUAP1,DNASE1,TRAP1,CREBBP,ADCY9,GLIS2,GLIS2-AS1,DNAJA3,C16orf96,ANKS3,UBN1,SEC14L5,ENPP7P14,ABAT,TMEM186,USP7,GRIN2A,ATF7IP2,PKD1,CASP16P,SRL,RBFOX1
Controls
No Control Data Available
No Animal Model Data Available