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3q28-q29CNV Type: Duplication


Largest CNV size: 54000 bp

Statistics Box:
Number of Reports: 4



Summary Information

Summary statement in development

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

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
NA
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pediatric cases with intellectual disability, developmental delay, and/or ASD (cohort consists of 13,318 previously unpublished cases and 15,767 cases originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table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
  NA NA
 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

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

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
  NA NA
 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

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
 

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
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