3q28-q29CNV Type: Duplication
Largest CNV size: 54000 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
Summary statement in development
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...
Duplication
Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Refining analyses of copy number variation identifies specific genes associated with developmental delay.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_cases
Primarily pediatric cases with intellectual disability, developmental delay, and/or ASD (cohort consists of 13,318 previously unpublished cases and 15,767 cases originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
29085
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
1500000
13
0
13
digregorio_17_DD/ID_discovery_cases
Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
1015
Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
N/A
N/A
9000000
0
1
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
8855592
0
2
2
lesca_12_EP_discovery_cases
Epilepsy patients collected at four French hospitals from 2009: Strasbourg Univ. Hospital (n=40), Lyons Univ. Hospital (n=18), Henri Gastaut Hospital (St. Paul Centre) in Marseille (n=2), and Reims American Memorial Hospital (n=1).
61
Epilepsy/epileptic encephalopathy. 41 patients with continuous spike and wave during slow-wave sleep syndrome (CSWSS), 20 patients with Landau-Kleffner syndrome (LKS). 12 (out of 57) patients displayed autistic features; ADHD features (hyperactivity, attention deficit and/or aggressiveness) reported in 41/58 patients,
Mean age of diagnosis: 5.6 yrs. (range, 1-14 yrs.)
61% Male
54000
0
1
1
streata_22_ASD/DD/ID_discovery_cases
Patients evaluated for global developmental delay and/or intellectual disability in pediatric, child neurology, or medical genetics departments throughout Romania who were referred to the Regional Centre for Medical Genetics for genetic testing between 2015 and 2022.
371
All cases presented with global developmental delay (DD) and/or intellectual disability (ID); a subset of cases also presented with autism spectrum disorder (ASD).
Range, 6 mos.-40 yrs. (median age, 5.5 yrs.)
63.07% Male
7153050
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_controls
Adult population controls (cohort consists of 11,255 new controls and 8329 controls originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
19584
Control
N/A
N/A
1500000
1
0
1
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_cases
N/A
aCGH
N/A
None
digregorio_17_DD/ID_discovery_cases
Italian
aCGH
Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
ADM-2
Agilent CGH Analytics software ver. 4.0.81
qPCR
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
lesca_12_EP_discovery_cases
France
aCGH
Agilent SurePrint G3 Human CGH Microarray 4x180K
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent Genomic WORKBENCH v5.0.14
qPCR
streata_22_ASD/DD/ID_discovery_cases
Romania
aCGH
Agilent SurePrint G3 ISCA v.2 8x60K, Agilent 4x180K, OGT CytoSure ISCA v.2 8x60K
NA
Agilent CytoGenomics, OGT CytoSure Interpret
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_controls
N/A
aCGH, solid phase hybridization
Multiple platforms used (including HumanHap, Illumina, and Human610-Quad)
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
coe_14_ASD/DD/ID_discovery_cases-case619
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case620
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case621
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case622
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case623
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case624
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case625
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case626
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case627
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case628
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case629
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case630
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case631
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
digregorio_17_DD/ID_discovery_cases-DECIPHER_296352
N/A
M
Developmental delay/intellectual disability
189104977
198113468
9008492
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004699
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
189265371
198110178
8844808
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005350
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
190667663
198110178
7442516
GRCh38
Duplication
Yes
lesca_12_EP_discovery_cases-case7-1514
NA
M
Epilepsy
Phenotype: i-CSWSS. Seizure Characteristics: Mycoclonic, atonic. Autistic features: No. ADHD features: No. Other features: None.
Initial cognitive development: Normal. Cognitive regression: No.
192349731
192404442
54712
GRCh38
Duplication
Yes
streata_22_ASD/DD/ID_discovery_cases-case29
NA
F
Intellectual disability
Congenital anomalies, facial dysmorphism.
Mild/moderate intellectual disability
190957129
198110178
7153050
GRCh38
Duplication
No
Controls
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
coe_14_ASD/DD/ID_discovery_controls-control69
N/A
N/A
Control
N/A
N/A
191799517
193299517
1500001
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
coe_14_ASD/DD/ID_discovery_cases-case619
Inherited
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case620
Inherited
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case621
Inherited
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case622
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case623
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case624
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case625
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case626
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case627
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case628
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case629
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case630
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
coe_14_ASD/DD/ID_discovery_cases-case631
Unknown
Unknown
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
digregorio_17_DD/ID_discovery_cases-DECIPHER_296352
qPCR
Unknown
TPRG1-AS2,MIR944,MTAPP2,RNU6-1109P,NMNAT1P3,GCNT1P3,RN7SKP296,LINC02013,CCT6P4,PYDC2,RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,ATP13A5-AS1,ATP13A4-AS1,RN7SL447P,LINC02038,DPPA2P3,HES1,RN7SL215P,RNU6-1101P,RPL23AP93,TMEM44-AS1,FAM43A,LINC01972,XXYLT1-AS1,MIR3137,RN7SL36P,RNU6-25P,RNU6ATAC24P,RN7SL73P,MUC20P1,MIR570,KIF3AP1,MIR6829,TNK2-AS1,RNU2-11P,RNU7-18P,TM4SF19-AS1,RNU6-910P,RNU6-1279P,RN7SL434P,RN7SL738P,UBXN7-AS1,RPS29P3,LINC01063,RNU6-646P,RNU4-89P,RNU6-42P,NCBP2-AS1,NCBP2-AS2,MIR4797,DLG1-AS1,LINC02012,MIR922,RNU6-858P,RNU6-621P,LMLN-AS1,RNU6-821P,FRG2FP,P3H2-AS1,CLDN16,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,CPN2,LRRC15,GP5,ATP13A3,TMEM44,XXYLT1-AS2,ACAP2-IT1,PPP1R2,APOD,SDHAP2,SMBD1P,MUC20,MUC4,LINC01983,TNK2,SDHAP1,TFRC,LINC00885,ZDHHC19,TCTEX1D2,TM4SF19-TCTEX1D2,TM4SF19,UBXN7,SMCO1,WDR53,FBXO45,NRROS,PIGX,CEP19,PAK2,NCBP2,PIGZ,RPSAP69,RUBCN,FYTTD1,LRCH3,RPL35A,LMLN,ANKRD18DP,TPRG1,P3H2,CLDN1,TMEM207,IL1RAP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LINC00884,LSG1,LINC01968,XXYLT1,ACAP2,MUC20-OT1,SLC51A,PCYT1A,RNF168,SENP5,MELTF,MELTF-AS1,BDH1,IQCG,TP63,LINC02026,DLG1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004699
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR944,MTAPP2,RNU6-1109P,NMNAT1P3,GCNT1P3,RN7SKP296,LINC02013,CCT6P4,PYDC2,RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,ATP13A5-AS1,ATP13A4-AS1,RN7SL447P,LINC02038,DPPA2P3,HES1,RN7SL215P,RNU6-1101P,RPL23AP93,TMEM44-AS1,FAM43A,LINC01972,XXYLT1-AS1,MIR3137,RN7SL36P,RNU6-25P,RNU6ATAC24P,RN7SL73P,MUC20P1,MIR570,KIF3AP1,MIR6829,TNK2-AS1,RNU2-11P,RNU7-18P,TM4SF19-AS1,RNU6-910P,RNU6-1279P,RN7SL434P,RN7SL738P,UBXN7-AS1,RPS29P3,LINC01063,RNU6-646P,RNU4-89P,RNU6-42P,NCBP2-AS1,NCBP2-AS2,MIR4797,DLG1-AS1,LINC02012,MIR922,RNU6-858P,RNU6-621P,LMLN-AS1,RNU6-821P,FRG2FP,P3H2-AS1,CLDN16,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,CPN2,LRRC15,GP5,ATP13A3,TMEM44,XXYLT1-AS2,ACAP2-IT1,PPP1R2,APOD,SDHAP2,SMBD1P,MUC20,MUC4,LINC01983,TNK2,SDHAP1,TFRC,LINC00885,ZDHHC19,TCTEX1D2,TM4SF19-TCTEX1D2,TM4SF19,UBXN7,SMCO1,WDR53,FBXO45,NRROS,PIGX,CEP19,PAK2,NCBP2,PIGZ,RPSAP69,RUBCN,FYTTD1,LRCH3,RPL35A,LMLN,ANKRD18DP,TPRG1,P3H2,CLDN1,TMEM207,IL1RAP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LINC00884,LSG1,LINC01968,XXYLT1,ACAP2,MUC20-OT1,SLC51A,PCYT1A,RNF168,SENP5,MELTF,MELTF-AS1,BDH1,IQCG,TP63,LINC02026,DLG1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005350
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
LINC02013,CCT6P4,PYDC2,RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,ATP13A5-AS1,ATP13A4-AS1,RN7SL447P,LINC02038,DPPA2P3,HES1,RN7SL215P,RNU6-1101P,RPL23AP93,TMEM44-AS1,FAM43A,LINC01972,XXYLT1-AS1,MIR3137,RN7SL36P,RNU6-25P,RNU6ATAC24P,RN7SL73P,MUC20P1,MIR570,KIF3AP1,MIR6829,TNK2-AS1,RNU2-11P,RNU7-18P,TM4SF19-AS1,RNU6-910P,RNU6-1279P,RN7SL434P,RN7SL738P,UBXN7-AS1,RPS29P3,LINC01063,RNU6-646P,RNU4-89P,RNU6-42P,NCBP2-AS1,NCBP2-AS2,MIR4797,DLG1-AS1,LINC02012,MIR922,RNU6-858P,RNU6-621P,LMLN-AS1,RNU6-821P,FRG2FP,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,CPN2,LRRC15,GP5,ATP13A3,TMEM44,XXYLT1-AS2,ACAP2-IT1,PPP1R2,APOD,SDHAP2,SMBD1P,MUC20,MUC4,LINC01983,TNK2,SDHAP1,TFRC,LINC00885,ZDHHC19,TCTEX1D2,TM4SF19-TCTEX1D2,TM4SF19,UBXN7,SMCO1,WDR53,FBXO45,NRROS,PIGX,CEP19,PAK2,NCBP2,PIGZ,RPSAP69,RUBCN,FYTTD1,LRCH3,RPL35A,LMLN,ANKRD18DP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LINC00884,LSG1,LINC01968,XXYLT1,ACAP2,MUC20-OT1,SLC51A,PCYT1A,RNF168,SENP5,MELTF,MELTF-AS1,BDH1,IQCG,LINC02026,DLG1
lesca_12_EP_discovery_cases-case7-1514
qPCR
Maternal
Unknown
Unknown
FGF12
streata_22_ASD/DD/ID_discovery_cases-case29
Unknown
APOD,BDH1,DLG1,CPN2,FGF12,PIGX,LSG1,PLAAT1,ATP13A3,IQCG,PIGZ,FYTTD1,ATP13A4,LMLN,LRCH3,CEP19,TMEM44,ZDHHC19,TM4SF19,FAM43A,LRRC15,CCDC50,MB21D2,PYDC2,XXYLT1,NCBP2AS2,RNF168,SENP5,SLC51A,MUC20,FBXO45,HES1,GP5,SMCO1,SDHAP1,DYNLT2B,UTS2B,LINC02028,ATP13A5,OSTN,WDR53,ANKRD18DP,NRROS,LINC00885,RPS29P3,VEZF1P1,LINC02026,SDHAP2,MIR570,MUC20P1,DPPA2P3,MIR922,TNK2-AS1,FRG2FP,LINC02012,PAK2,OPA1,MUC4,MELTF,LINC00887,RNU7-18P,RPL23AP93,RNU6-42P,KIF3AP1,LINC02036,MIR3137,DLG1-AS1,TM4SF19-DYNLT2B,LINC01968,MELTF-AS1,MIR4797,TMEM44-AS1,FGF12-AS3,TM4SF19-AS1,OPA1-AS1,NCBP2-AS1,RNU1-20P,UBXN7-AS1,FGF12-AS2,LMLN-AS1,XXYLT1-AS1,ACAP2-IT1,FGF12-AS1,ATP13A5-AS1,RPSAP69,XXYLT1-AS2,RPL35A,PPP1R2,PCYT1A,LINC01063,ATP13A4-AS1,LINC01983,LINC02037,MIR6829,LINC02048,LINC01972,LINC02038,RN7SL447P,RN7SL36P,RN7SL73P,RN7SKP222,TFRC,RNU6-858P,RNU6ATAC24P,RNU6-1101P,RN7SL434P,RN7SL215P,RNU6-646P,RNU4-89P,OSTN-AS1,RNU6-25P,RNU6-1279P,RN7SL738P,RNU6-821P,RNU2-11P,RNU6-621P,RNU6-910P,SMBD1P,MUC20-OT1,TNK2,RUBCN,NCBP2,UBXN7,ACAP2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
coe_14_ASD/DD/ID_discovery_controls-control69
Unknown
RN7SKP222,FGF12-AS2,FGF12-AS3,RNU1-20P,VEZF1P1,HRASLS,FGF12,FGF12-AS1,MB21D2,ATP13A5
No Animal Model Data Available