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3q27.3-q29CNV Type: Deletion


Largest CNV size: 7584438 bp

Statistics Box:
Number of Reports: 3



Summary Information

Rare singleton deletion within this region was found in a case 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

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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

Minor Reports

Title
Author, Year
Report Class
CNV Type
Routine Chromosomal Microarray Analysis is Necessary in Korean Patients With Unexplained Developmental Delay/Mental Retardation/Autism Spectrum Dis...
Deletion
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Deletion

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
 7584438
 1
 0
 1
 kushima_18_SCZ_discovery_cases
 Individuals predominantly recruited from the middle of Honshu Island (Japan)
 2458
 Cases were diagnosed with schizophrenia (SCZ) according to DSM-5 criteria.
 Median age, 44 years
 55.0% Male
 7089844
 1
 0
 1
 shin_15_ASD/DD/ID_discovery_cases
 Patients with normal karyotype referred for further genetic testing from March 2012-April 2014
 96
 34 cases with ASD, 54 cases with DD/ID, 8 cases with ASD and DD/ID
 N/A
 69.8% Male
 8120000
 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
 kushima_18_ASD/SCZ_discovery_controls
 Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
 2095
 Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
 Median age, 37 years
 52.0% Male
 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
 kushima_18_SCZ_discovery_cases
  Japanese
 aCGH
  NimbleGen 720K, Agilent 400K
 FASST2
 Nexus Copy Number v.9.0
 N/A
 shin_15_ASD/DD/ID_discovery_cases
  Korean
 Array SNP
  Affymetrix CytoScan 750K
 
 Affymetrix ChAS v.2.1, Nexus Copy Number v.7.5 (BioDiscovery)
 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
 
  kushima_18_ASD/SCZ_discovery_controls
  Japanese
  aCGH
  NimbleGen 720K, Agilent 400K
  FASST2
  Nexus Copy Number v.9.0
  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
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002068
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 187446231
 195029133
  7582903
 GRCh38
 Deletion
 Yes
  kushima_18_SCZ_discovery_cases-caseSCZ1729
 44 yrs.
 M
 Schizophrenia
 No additional clinical information reported for this individual. Family history: unknown.
 
 187222939
 194312782
  7089844
 GRCh38
 Deletion
 N/A
  shin_15_ASD/DD/ID_discovery_cases-case2
 5 yrs.
 M
 DD and seizures
 Developmental delay, seizures, short stature, microcephaly
 
 187156775
 195273886
  8117112
 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-ISCA00002068
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 SST,RTP2,FLJ42393,MIR28,TPRG1-AS1,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,LINC02041,BCL6,LINC01991,LPP-AS2,LPP-AS1,P3H2-AS1,CLDN16,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,CPN2,LRRC15,GP5,ATP13A3,TMEM44,TPRG1,P3H2,CLDN1,TMEM207,IL1RAP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LINC00884,LSG1,LINC01968,LPP,TP63,LINC02026
 
 kushima_18_SCZ_discovery_cases-caseSCZ1729
 While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
 
 Unknown
 Unknown
 Unknown
 RTP4,SST,RTP2,FLJ42393,MIR28,TPRG1-AS1,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,MASP1,LINC02041,BCL6,LINC01991,LPP-AS2,LPP-AS1,P3H2-AS1,CLDN16,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,TPRG1,P3H2,CLDN1,TMEM207,IL1RAP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LPP,TP63,LINC02026
 
 shin_15_ASD/DD/ID_discovery_cases-case2
 
 
 Unknown
 
 Unknown
 RTP1,RTP4,SST,RTP2,FLJ42393,MIR28,TPRG1-AS1,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,MASP1,LINC02041,BCL6,LINC01991,LPP-AS2,LPP-AS1,P3H2-AS1,CLDN16,GMNC,UTS2B,HRASLS,OPA1-AS1,LINC02028,LINC02048,LINC00887,CPN2,LRRC15,GP5,ATP13A3,TMEM44,XXYLT1-AS2,RPL39L,TPRG1,P3H2,CLDN1,TMEM207,IL1RAP,OSTN,OSTN-AS1,CCDC50,FGF12,FGF12-AS1,MB21D2,ATP13A5,ATP13A4,OPA1,LINC02036,LINC02037,LINC00884,LSG1,LINC01968,XXYLT1,LPP,TP63,LINC02026
 

Controls

No Control Data Available
No Animal Model Data Available
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