4p16.3-p15.2CNV Type: Deletion-Duplication
Largest CNV size: 27614582 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
CNVs within this region were found in two 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).
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
The application of whole-exome sequencing in the early diagnosis of rare genetic diseases in children: a study from Southeastern China
Duplication
Minor Reports
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
27614582
1
1
2
lai_24_DD/ID_discovery_cases
Pediatric patients assessed at the Clinical Genetics Laboratory of the Ganzhou Maternal and Child Health Hospital who were recruited between January 2021 and December 2023.
144
Clinical manifestations observed in this cohort included global developmental delay (HP:0001263; n=46, 31.94%), intellectual disability (HP:0001249; n=44, 30.56%), seizures (HP:0001250, n = 24, 16.67%), and autistic behavior (HP:0000729; n=19, 13.19%).
Median age 4yrs. (range 0-17 yrs.)
59.03% Male
21795146
0
1
1
sherman_21_ASD_discovery_cases
ASD probands from the Simons Simplex Collection (n=2,594) and the SPARK cohort (n=9,483) screened for mosaic CNVs (mCNVs)
12077
Cohort diagnosis of ASD
Range, 3-40+ yrs.
NA
22859745
1
0
1
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
sherman_21_ASD_discovery_controls
Unaffected siblings of ASD probands from the Simons Simplex Collection (n=2,424) and the SPARK cohort (n=3,076) screened for mosaic CNVs (mCNVs)
5500
Control (unaffected siblings of ASD probands)
Range, 3-18 yrs.
NA
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
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
lai_24_DD/ID_discovery_cases
China
WES
Illumina NovaSeq 6000
PCR or Sanger
sherman_21_ASD_discovery_cases
NA
Solid phase hybridization
Illumina 1Mv1, Illumina 1Mv3, Illumina Omni2.5, Illumina Infinium Global Screening Array-24 v.1.0
MoChA
None
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
sherman_21_ASD_discovery_controls
NA
Solid phase hybridization
Illumina 1Mv1, Illumina 1Mv3, Illumina Omni2.5, Illumina Infinium Global Screening Array-24 v.1.0
MoChA
None
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001218
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
72555
28066309
27993755
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004401
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
51519
26519788
26468270
GRCh38
Duplication
Yes
lai_24_DD/ID_discovery_cases-case46
2 mos.
M
Developmental delay and intellectual disability
Global developmental delay
Intellectual disability
10001
21805146
21795146
GRCh38
Duplication
Yes
sherman_21_ASD_discovery_cases-SSC_13674.p1
NA
M
ASD
ASD proband from the Simons Simplex Collection. SCQ summary score: 16. Mosaic cell fraction: 0.0831. CNV occurs on the maternal haplotype.
FSIQ 79, NVIQ 93
10000
22869744
22859745
GRCh38
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001218
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR571,ZNF519P4,TMEM271,ATP5ME,MYL5,NKX1-1,SCARNA22,MIR943,C4orf48,COX6B1P5,MIR4800,RN7SL589P,RNU6-204P,HGFAC,LINC02171,LINC02600,OR7E163P,OR7E162P,ALG1L7P,ENPP7P9,OR4D12P,OR7E99P,OR7E43P,STX18-IT1,RPS7P15,MSX1,LDHAP1,RN7SKP113,CYTL1,RN7SKP275,LINC01587,MIR378D1,MRFAP1,LINC002481,S100P,MRFAP1L1,RN7SKP292,CCDC96,LINC02447,RN7SKP36,MIR4798,PSAPL1,MIR4274,MIR95,GMPSP1,RNA5SP152,SNRPCP16,ALG1L14P,USP17L10,USP17L11,USP17L12,USP17L13,USP17L14P,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L23,USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P,DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,MIR572,RNPS1P1,RNA5SP156,RNU6-578P,ECM1P2,NKX3-2,LINC01096,MIR5091,MTND2P31,RN7SKP170,HPRT1P1,FGFBP1,FGFBP2,RPS21P4,MTND5P4,LINC02493,SNORA75B,RPS7P6,CLRN2,NACAP5,KRT18P63,RNA5SP157,SLIT2-IT1,MIR218-1,MIR7978,KCNIP4-IT1,RNU6-420P,CDC42P6,RFPL4AP3,MIR573,RN7SL16P,ATP5MGP3,LINC02473,HNRNPA1P65,SOD3,RNU7-126P,RPS29P11,MTND4P9,MTND4LP22,MTND3P5,MTCO3P44,CCKAR,IGBP1P5,ZNF595,ZNF876P,ZNF732,ZNF141,ABCA11P,ZNF721,SLC49A3,PCGF3,TMEM175,DGKQ,SLC26A1,IDUA,FGFRL1,RNF212,TMED11P,CTBP1-AS,CTBP1,CTBP1-DT,UVSSA,FAM53A,TMEM129,TACC3,FGFR3,NELFA,NAT8L,MXD4,CFAP99,SH3BP2,MFSD10,NOP14-AS1,NOP14,HTT-AS,MSANTD1,DOK7,LRPAP1,LINC00955,ADRA2C,FAM86EP,UNC93B4,TMEM128,LYAR,ZBTB49,NSG1,LINC02495,MAN2B2,LINC02482,BLOC1S4,TADA2B,GRPEL1,AFAP1-AS1,SH3TC1,HTRA3,LINC02517,TRMT44,GPR78,CPZ,HMX1,UNC93B8,ENPP7P10,FAM86KP,USP17L16P,OR7E84P,RAF1P1,ZNF518B,LINC02360,LINC02270,HSP90AB2P,LINC01097,BOD1L1,LINC01085,CPEB2,C1QTNF7,FBXL5,FAM200B,CD38,TAPT1,QDPR,LAP3,MED28,DCAF16,DHX15,LGI2,SEPSECS,PI4K2B,ZCCHC4,ANAPC4,SLC34A2,SMIM20,ZNF718,PIGG,PDE6B,CPLX1,GAK,SPON2,MAEA,SLBP,LETM1,NSD2,HAUS3,ZFYVE28,RNF4,FAM193A,TNIP2,ADD1,GRK4,RGS12,STX18,STX18-AS1,LINC01396,EVC2,EVC,CRMP1,C4orf50,JAKMIP1,PPP2R2C,KIAA0232,TBC1D14,AFAP1,ABLIM2,FAM90A26,FAM86MP,SLC2A9,WDR1,CLNK,LINC02498,HS3ST1,RAB28,LINC01182,CPEB2-DT,CC2D2A,PROM1,TAPT1-AS1,ZEB2P1,FAM184B,LCORL,LINC02438,SLIT2,PACRGL,ADGRA3,GBA3,ERVH-1,PPARGC1A,CCDC149,SEL1L3,LINC02357,TBC1D19,STIM2,POLN,HTT,OTOP1,STK32B,WFS1,SORCS2,LINC00504,BST1,NCAPG,KCNIP4,RBPJ,LINC02261,ACOX3,LDB2,SEPSECS-AS1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004401
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR571,ZNF519P4,TMEM271,ATP5ME,MYL5,NKX1-1,SCARNA22,MIR943,C4orf48,COX6B1P5,MIR4800,RN7SL589P,RNU6-204P,HGFAC,LINC02171,LINC02600,OR7E163P,OR7E162P,ALG1L7P,ENPP7P9,OR4D12P,OR7E99P,OR7E43P,STX18-IT1,RPS7P15,MSX1,LDHAP1,RN7SKP113,CYTL1,RN7SKP275,LINC01587,MIR378D1,MRFAP1,LINC002481,S100P,MRFAP1L1,RN7SKP292,CCDC96,LINC02447,RN7SKP36,MIR4798,PSAPL1,MIR4274,MIR95,GMPSP1,RNA5SP152,SNRPCP16,ALG1L14P,USP17L10,USP17L11,USP17L12,USP17L13,USP17L14P,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L23,USP17L24,USP17L25,USP17L26,USP17L5,USP17L27,USP17L28,USP17L29,USP17L9P,USP17L30,USP17L6P,DEFB108F,RNA5SP153,DEFB130D,DEFB131A,OR7E86P,OR7E85P,UNC93B7,OR7E83P,MIR548I2,SNRPCP13,ENPP7P11,ALG1L3P,OR7E35P,DRD5,RNA5SP154,MIR3138,RNA5SP155,MIR572,RNPS1P1,RNA5SP156,RNU6-578P,ECM1P2,NKX3-2,LINC01096,MIR5091,MTND2P31,RN7SKP170,HPRT1P1,FGFBP1,FGFBP2,RPS21P4,MTND5P4,LINC02493,SNORA75B,RPS7P6,CLRN2,NACAP5,KRT18P63,RNA5SP157,SLIT2-IT1,MIR218-1,MIR7978,KCNIP4-IT1,RNU6-420P,CDC42P6,RFPL4AP3,MIR573,RN7SL16P,ATP5MGP3,LINC02473,HNRNPA1P65,SOD3,RNU7-126P,RPS29P11,MTND4P9,MTND4LP22,MTND3P5,MTCO3P44,CCKAR,ZNF595,ZNF876P,ZNF732,ZNF141,ABCA11P,ZNF721,SLC49A3,PCGF3,TMEM175,DGKQ,SLC26A1,IDUA,FGFRL1,RNF212,TMED11P,CTBP1-AS,CTBP1,CTBP1-DT,UVSSA,FAM53A,TMEM129,TACC3,FGFR3,NELFA,NAT8L,MXD4,CFAP99,SH3BP2,MFSD10,NOP14-AS1,NOP14,HTT-AS,MSANTD1,DOK7,LRPAP1,LINC00955,ADRA2C,FAM86EP,UNC93B4,TMEM128,LYAR,ZBTB49,NSG1,LINC02495,MAN2B2,LINC02482,BLOC1S4,TADA2B,GRPEL1,AFAP1-AS1,SH3TC1,HTRA3,LINC02517,TRMT44,GPR78,CPZ,HMX1,UNC93B8,ENPP7P10,FAM86KP,USP17L16P,OR7E84P,RAF1P1,ZNF518B,LINC02360,LINC02270,HSP90AB2P,LINC01097,BOD1L1,LINC01085,CPEB2,C1QTNF7,FBXL5,FAM200B,CD38,TAPT1,QDPR,LAP3,MED28,DCAF16,DHX15,LGI2,SEPSECS,PI4K2B,ZCCHC4,ANAPC4,SLC34A2,SMIM20,ZNF718,PIGG,PDE6B,CPLX1,GAK,SPON2,MAEA,SLBP,LETM1,NSD2,HAUS3,ZFYVE28,RNF4,FAM193A,TNIP2,ADD1,GRK4,RGS12,STX18,STX18-AS1,LINC01396,EVC2,EVC,CRMP1,C4orf50,JAKMIP1,PPP2R2C,KIAA0232,TBC1D14,AFAP1,ABLIM2,FAM90A26,FAM86MP,SLC2A9,WDR1,CLNK,LINC02498,HS3ST1,RAB28,LINC01182,CPEB2-DT,CC2D2A,PROM1,TAPT1-AS1,ZEB2P1,FAM184B,LCORL,LINC02438,SLIT2,PACRGL,ADGRA3,GBA3,ERVH-1,PPARGC1A,CCDC149,SEL1L3,LINC02357,POLN,HTT,OTOP1,STK32B,WFS1,SORCS2,LINC00504,BST1,NCAPG,KCNIP4,RBPJ,ACOX3,LDB2,SEPSECS-AS1
lai_24_DD/ID_discovery_cases-case46
PCR or Sanger
Unknown
BST1,NKX3-2,ADD1,CD38,ADRA2C,ATP5ME,EVC,DGKQ,DRD5,FGFR3,CTBP1,CRMP1,OR7E43P,GPR78,NSG1,FAM184B,LAP3,STX18,DCAF16,LYAR,FGFRL1,CYTL1,NKX1-1,STK32B,SH3TC1,PIGG,BLOC1S4,TBC1D14,UVSSA,CC2D2A,ZFYVE28,SLC2A9,AFAP1,SORCS2,HAUS3,TNIP2,NCAPG,KCNIP4,FGFBP2,ABLIM2,OR7E99P,MED28,ABCA11P,SLC49A3,GRPEL1,TMEM175,TMEM129,TMEM128,AFAP1-AS1,HTRA3,CTBP1-DT,MRFAP1,ZNF518B,TADA2B,MRFAP1L1,C1QTNF7,CLNK,FAM53A,PACRGL,EVC2,OTOP1,TRMT44,CPEB2,ZNF595,LINC01085,JAKMIP1,TAPT1,ZNF721,TAPT1-AS1,LINC00504,ZBTB49,HGFAC,HTT,GRK4,IDUA,GAK,HMX1,OR7E103P,ZNF718,CCDC96,LCORL,BOD1L1,LINC01097,DOK7,FAM200B,NAT8L,CTBP1-AS,LINC01096,LINC00955,LINC02481,NOP14-AS1,JAKMIP1-DT,RNF212,MSANTD1,RAF1P1,C4orf50,FAM86EP,POLN,OR7E83P,C4orf48,OR7E35P,USP17L9P,OR7E84P,HSP90AB2P,USP17L6P,CPEB2-DT,MIR218-1,CFAP99,MIR95,OR7E86P,OR7E85P,OR7E162P,ZNF876P,NACAP5,DEFB131A,UNC93B4,FAM86MP,CLRN2,RNPS1P1,USP17L27,MIR572,RPS3AP19,RPS7P15,USP17L30,USP17L25,USP17L28,MIR571,OR7E85BP,GMPSP1,ALG1L7P,ZNF732,USP17L29,USP17L5,USP17L26,RPS3AP16,USP17L24,SCARNA22,PSAPL1,LINC02447,MIR943,RPL32P12,RPS21P4,HPRT1P1,LRPAP1,MYL5,MSX1,LDHAP1,LETM1,DEFB108F,LINC02171,ALG1L3P,OR7E163P,RPS7P6,USP17L15,USP17L10,USP17L20,OR7E111FP,USP17L11,USP17L21,USP17L12,USP17L22,USP17L16P,USP17L14P,FAM90A26,USP17L19,FAM86KP,USP17L17,USP17L18,USP17L13,KRT18P63,TMED11P,MIR548I2,COX6B1P5,ENPP7P9,ENPP7P10,ZEB2P1,ENPP7P11,MIR4274,SLIT2-IT1,MIR3138,MIR4800,STX18-AS1,MIR378D1,RNA5SP152,RNA5SP156,MIR5091,RNA5SP155,HTT-AS,MTND5P4,RNA5SP153,MIR4798,RNA5SP157,RNA5SP154,MTND2P31,UNC93B8,ALG1L14P,UNC93B7,USP17L23,BNIP3P41,SNORA63,RNF4,RGS12,QDPR,PDE6B,S100P,PPP2R2C,LINC01182,PDE6B-AS1,C1QTNF7-AS1,LINC02270,LINC02493,MIR7978,LINC02498,LINC01396,STX18-IT1,SLC2A9-AS1,LINC02360,LINC02517,LINC02482,RN7SKP170,RN7SKP292,NSD2,NELFA,WFS1,SH3BP2,SNRPCP16,RN7SL589P,RN7SKP275,RNU6-204P,RN7SKP36,RN7SKP113,SNRPCP13,ZNF519P4,ECM1P2,RNU6-578P,LINC02438,LINC02600,SNORA75B,DEFB130D,TMEM271,FAM193A,ACOX3,NOP14,SLBP,PROM1,ZNF141,CPZ,MED28-DT,FGFBP1,HS3ST1,MFSD10,RAB28,SLIT2,KIAA0232,WDR1,LDB2,LINC01587,CPLX1,PCGF3,MAEA,TACC3,MXD4,SPON2,SLC26A1,MAN2B2,FBXL5
sherman_21_ASD_discovery_cases-SSC_13674.p1
Simplex
ATP5ME,NKX3-2,ADD1,ADRA2C,BST1,CD38,CTBP1,EVC,DGKQ,FGFR3,CRMP1,DRD5,NSG1,OR7E43P,FAM184B,GPR78,LAP3,STX18,NKX1-1,LYAR,STK32B,DCAF16,BLOC1S4,FGFRL1,CYTL1,SH3TC1,PIGG,UVSSA,GBA3,SLC2A9,TBC1D14,CC2D2A,ZFYVE28,AFAP1,SORCS2,HAUS3,NCAPG,TNIP2,GRPEL1,SLC49A3,TMEM175,KCNIP4,FGFBP2,ABCA11P,MED28,OR7E99P,TADA2B,TMEM129,HTRA3,AFAP1-AS1,TMEM128,CTBP1-DT,MRFAP1,ABLIM2,ZNF518B,CLNK,MRFAP1L1,C1QTNF7,CPEB2,EVC2,LINC01085,OTOP1,PACRGL,ZNF595,FAM53A,TRMT44,JAKMIP1,TAPT1-AS1,ZBTB49,ZNF721,ADGRA3,TAPT1,LINC00504,HTT,IDUA,HMX1,GRK4,GAK,HGFAC,LCORL,BOD1L1,ZNF718,CCDC96,OR7E103P,LINC01097,LINC02495,FAM200B,DOK7,LINC02481,LINC00955,NOP14-AS1,LINC01096,RNF212,CTBP1-AS,MSANTD1,NAT8L,RAF1P1,KCNIP4-IT1,C4orf50,POLN,FAM86EP,C4orf48,HSP90AB2P,OR7E35P,OR7E83P,USP17L6P,OR7E84P,USP17L9P,MIR95,CFAP99,MIR218-1,CPEB2-DT,OR7E162P,OR7E85P,OR7E86P,ZNF876P,UNC93B4,CLRN2,RNPS1P1,CDC42P6,NACAP5,DEFB131A,FAM86MP,RPS7P15,MIR571,OR7E85BP,USP17L26,USP17L25,RPS3AP16,ZNF732,USP17L30,USP17L29,SCARNA22,USP17L5,USP17L27,MIR572,GMPSP1,USP17L24,RPS3AP19,ALG1L7P,USP17L28,LINC02447,MIR943,RPL32P12,PSAPL1,RPS21P4,HPRT1P1,LRPAP1,LETM1,LDHAP1,MSX1,MYL5,LINC02171,OR7E163P,ALG1L3P,DEFB108F,RPS7P6,USP17L18,FAM86KP,USP17L17,KRT18P63,USP17L11,USP17L12,OR7E111FP,USP17L16P,USP17L15,USP17L21,USP17L14P,USP17L19,USP17L13,USP17L10,USP17L20,USP17L22,FAM90A26,COX6B1P5,TMED11P,MIR548I2,ENPP7P10,ENPP7P9,ENPP7P11,ZEB2P1,MIR4274,SLIT2-IT1,MIR3138,STX18-AS1,MIR378D1,MIR4800,HTT-AS,RNA5SP153,RNA5SP152,RNA5SP154,RNA5SP155,MTND5P4,RNA5SP157,MTND2P31,MIR5091,MIR4798,RNA5SP156,UNC93B8,UNC93B7,ALG1L14P,USP17L23,BNIP3P41,QDPR,PDE6B,S100P,RGS12,PPP2R2C,RNF4,LINC01182,C1QTNF7-AS1,LINC02270,PDE6B-AS1,LINC02493,MIR7978,LINC02498,LINC01396,STX18-IT1,LINC02482,LINC02360,SLC2A9-AS1,LINC02517,RN7SKP292,RN7SKP170,NSD2,SH3BP2,NELFA,WFS1,RN7SL589P,SNRPCP16,RN7SKP36,RN7SKP113,RN7SKP275,RNU6-204P,ZNF519P4,SNRPCP13,ECM1P2,RNU6-578P,RNU6-420P,LINC02438,LINC02600,SNORA75B,DEFB130D,TMEM271,CPZ,FAM193A,NOP14,ACOX3,ZNF141,PROM1,SLBP,SLBP-DT,LINC01587,KIAA0232,RAB28,WDR1,HS3ST1,FGFBP1,LDB2,SLIT2,MFSD10,MAEA,CPLX1,SPON2,MXD4,TACC3,SLC26A1,PCGF3,FBXL5,MAN2B2
Controls
No Control Data Available
No Animal Model Data Available