3q27.3-q29CNV Type: Deletion
Largest CNV size: 7584438 bp
Statistics Box:
Number of Reports: 6
Number of Reports: 6
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
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
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
Deletion
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
11004248
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
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
mahjani_21_ASD_discovery_cases
Study participants in the PAGES cohort, a large ongoing population-based cohort study in Sweden that started in 2012 with the overall aim to identify possible genetic and environmental risk factors for ASD.
996
Cases diagnosed with ASD according to ICD-9 and ICD-10 criteria.
Average age at diagnosis, 8.2 yrs.
70% Male
8989157
1
0
1
mazzonetto_24_ASD/DD/ID_discovery_cases
Patients from a total of 15 non-profit organizations and university centers located in different states of Brazil who were enrolled between July 2021 and June 2022 and referred with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorder (ASD), and/or multiple congenital anomalies.
1363
"95% of individuals in this cohort reported with the HPO phenotype ""Abnormality of the nervous system"" (HP:0000707); the HPO phenotypes ""Intellectual disability"" (HP:0001249; 36%), ""Global developmental delay"" (HP:0001263; 32%), and ""Autism"" (HP:0000717; 28%) were the most frequently reported phenotype subcategories within this subset of individuals."
63.17% Male
11710135
0
3
3
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
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
kushima_18_SCZ_discovery_cases
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
mahjani_21_ASD_discovery_cases
Sweden
WES
Infinium OmniExpress Exome
PennCNV
NA
None
mazzonetto_24_ASD/DD/ID_discovery_cases
Brazil
Low-pass WGS
Illumina NovaSeq 6000
SNP-FASST2 (HMM)
BioDiscovery NxClinical
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
akkus_24_ASD/DD/ID_discovery_cases-case3A
5 yrs.
F
Developmental delay/intellectual disability
Developmental delay/intellectual disability
Developmental delay/intellectual disability
187120868
198125115
11004248
GRCh38
Duplication
No
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
mahjani_21_ASD_discovery_cases-case209
NA
M
ASD
Diagnosis of ASD according to ICD-9 and ICD-10 criteria.
187722717
196711873
8989157
GRCh38
Deletion
No
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530471
F
MCA
Abnormal facial shape (HP:0001999), orofacial cleft (HP:0000202)
186585425
198295559
11710135
GRCh38
Triplication
No
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530472
M
MCA
Orofacial cleft (HP:0000202)
186635425
198295559
11660135
GRCh38
Duplication
No
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
akkus_24_ASD/DD/ID_discovery_cases-case3A
De novo
APOD,BDH1,BCL6,DLG1,CPN2,FGF12,PIGX,P3H2,LSG1,PLAAT1,RTP4,ATP13A3,IQCG,PIGZ,FYTTD1,ATP13A4,LMLN,LRCH3,CEP19,TMEM44,RPL39L,ZDHHC19,TMEM207,TM4SF19,RTP1,FAM43A,LRRC15,CCDC50,MB21D2,PYDC2,XXYLT1,NCBP2AS2,RNF168,SENP5,SLC51A,MUC20,FBXO45,HES1,GP5,IL1RAP,SMCO1,SDHAP1,DYNLT2B,UTS2B,LPP-AS2,TPRG1,RTP2,LINC02028,ATP13A5,OSTN,WDR53,ANKRD18DP,NRROS,LINC00885,NMNAT1P3,MIR28,RPS29P3,GMNC,VEZF1P1,LINC02026,SDHAP2,MIR570,MUC20P1,DPPA2P3,MIR922,MIR944,TNK2-AS1,CCT6P4,FRG2FP,LINC02012,PAK2,OPA1,MUC4,LPP,MELTF,LINC00887,RNU7-18P,RPL23AP93,RNU6-42P,MTAPP2,GCNT1P3,KIF3AP1,LINC02036,MIR3137,DLG1-AS1,TM4SF19-DYNLT2B,LINC01968,MELTF-AS1,MIR4797,TMEM44-AS1,FGF12-AS3,TM4SF19-AS1,OPA1-AS1,TPRG1-AS2,TPRG1-AS1,NCBP2-AS1,RNU1-20P,UBXN7-AS1,FGF12-AS2,LMLN-AS1,XXYLT1-AS1,ACAP2-IT1,FGF12-AS1,ATP13A5-AS1,LPP-AS1,RPSAP69,XXYLT1-AS2,RPL35A,PPP1R2,PCYT1A,MASP1,P3H2-AS1,LINC01063,ATP13A4-AS1,LINC01983,LINC02037,MIR6829,TUBB8P8,LINC02048,LINC01972,LINC01991,LINC02038,LINC02013,LINC02041,RN7SL447P,RN7SL36P,RN7SL73P,RN7SKP222,TFRC,SST,RNU6-858P,RNU6-1109P,RNU6ATAC24P,RNU6-1101P,RN7SL434P,RN7SL215P,RNU6-646P,RNU4-89P,OSTN-AS1,RNU6-25P,RNU6-1279P,RN7SL738P,RNU6-821P,RNU2-11P,RNU6-621P,RN7SKP296,RNU6-910P,SMBD1P,MUC20-OT1,TP63,TNK2,RUBCN,CLDN1,CLDN16,NCBP2,UBXN7,ACAP2
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
mahjani_21_ASD_discovery_cases-case209
Unknown
APOD,BCL6,FGF12,CPN2,P3H2,LSG1,PIGX,PLAAT1,ATP13A3,ATP13A4,TMEM44,CEP19,TMEM207,ZDHHC19,LRRC15,TM4SF19,FAM43A,MB21D2,XXYLT1,PYDC2,CCDC50,SLC51A,MUC20,FBXO45,RNF168,HES1,GP5,IL1RAP,SDHAP1,SMCO1,UTS2B,DYNLT2B,ATP13A5,LPP-AS2,LINC02028,OSTN,TPRG1,WDR53,NRROS,NMNAT1P3,LINC00885,FLJ42393,MIR28,RPS29P3,LINC02026,VEZF1P1,GMNC,MIR570,SDHAP2,MUC20P1,DPPA2P3,MIR944,TNK2-AS1,CCT6P4,LPP,MUC4,OPA1,LINC00887,RNU7-18P,RPL23AP93,GCNT1P3,KIF3AP1,MTAPP2,MIR3137,LINC02036,TM4SF19-DYNLT2B,LINC01968,TMEM44-AS1,XXYLT1-AS1,ACAP2-IT1,ATP13A5-AS1,FGF12-AS1,LPP-AS1,UBXN7-AS1,FGF12-AS2,TPRG1-AS2,OPA1-AS1,TPRG1-AS1,RNU1-20P,FGF12-AS3,TM4SF19-AS1,XXYLT1-AS2,PCYT1A,PPP1R2,P3H2-AS1,LINC02037,ATP13A4-AS1,LINC01063,LINC01983,MIR6829,LINC01991,LINC02038,LINC02013,LINC02048,LINC01972,RN7SL447P,RN7SL36P,RN7SL73P,RN7SKP222,TFRC,RNU6-1101P,RNU6ATAC24P,RNU6-1109P,RNU6-646P,RN7SL215P,RN7SL434P,RNU6-25P,RN7SL738P,RNU6-1279P,OSTN-AS1,RNU2-11P,RN7SKP296,RNU6-910P,SMBD1P,MUC20-OT1,TP63,TNK2,CLDN1,CLDN16,UBXN7,ACAP2
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530471
Unknown
APOD,BDH1,BCL6,AHSG,EIF4A2,DLG1,CPN2,FGF12,FETUB,DNAJB11,PIGX,P3H2,LSG1,PLAAT1,RTP4,ATP13A3,IQCG,PIGZ,FYTTD1,ATP13A4,LMLN,LRCH3,CEP19,TMEM44,RPL39L,ZDHHC19,TMEM207,TM4SF19,RTP1,FAM43A,LRRC15,CCDC50,MB21D2,PYDC2,XXYLT1,NCBP2AS2,RNF168,SENP5,SLC51A,MUC20,FBXO45,HRG,HES1,GP5,IL1RAP,SMCO1,SDHAP1,DYNLT2B,UTS2B,PSMD10P2,LPP-AS2,TPRG1,RTP2,LINC02028,ATP13A5,OSTN,WDR53,ANKRD18DP,NRROS,LINC00885,NMNAT1P3,RPS20P14,MIR28,SNORA4,RPS29P3,SNORD2,GMNC,VEZF1P1,LINC02026,SDHAP2,MIR570,MUC20P1,SNORA81,FAM157A,DPPA2P3,MIR922,MIR944,TNK2-AS1,CCT6P4,FRG2FP,LINC02012,PAK2,OPA1,MUC4,KNG1,LPP,MELTF,LINC00887,GPS2P2,RNU7-18P,RPL23AP93,MIR1248,RNU6-42P,MTAPP2,GCNT1P3,KIF3AP1,LINC02036,MIR3137,DLG1-AS1,TM4SF19-DYNLT2B,CICP6,LINC01968,MELTF-AS1,MIR4797,TMEM44-AS1,FGF12-AS3,TM4SF19-AS1,OPA1-AS1,TPRG1-AS2,TPRG1-AS1,NCBP2-AS1,RNU1-20P,UBXN7-AS1,FGF12-AS2,LMLN-AS1,ADIPOQ-AS1,XXYLT1-AS1,ACAP2-IT1,FGF12-AS1,ATP13A5-AS1,LPP-AS1,RPSAP69,XXYLT1-AS2,RPL35A,PPP1R2,PCYT1A,RFC4,MASP1,P3H2-AS1,LINC01063,ATP13A4-AS1,LINC01983,LINC02037,MIR6829,TUBB8P8,LINC02043,LINC02048,LINC01972,LINC01991,LINC02038,LINC02013,LINC02041,RN7SL447P,RN7SL36P,RN7SL73P,RN7SKP222,TFRC,SST,ST6GAL1,RNU6-858P,RNU6-1105P,RNU6-1109P,RNU6ATAC24P,RNU6-1101P,RNU6-860P,RN7SL434P,RN7SL215P,RNU6-646P,RNU4-89P,OSTN-AS1,RNU6-25P,RNU6-1279P,RN7SL738P,RNU6-821P,RNU2-11P,RNU6-621P,RN7SKP296,RNU6-910P,SEPTIN14P3,SNORA63B,SMBD1P,MUC20-OT1,TP63,TNK2,RUBCN,CLDN1,ADIPOQ,CLDN16,NCBP2,UBXN7,ACAP2
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530472
Unknown
APOD,BDH1,BCL6,EIF4A2,DLG1,CPN2,FGF12,FETUB,PIGX,P3H2,LSG1,PLAAT1,RTP4,ATP13A3,IQCG,PIGZ,FYTTD1,ATP13A4,LMLN,LRCH3,CEP19,TMEM44,RPL39L,ZDHHC19,TMEM207,TM4SF19,RTP1,FAM43A,LRRC15,CCDC50,MB21D2,PYDC2,XXYLT1,NCBP2AS2,RNF168,SENP5,SLC51A,MUC20,FBXO45,HRG,HES1,GP5,IL1RAP,SMCO1,SDHAP1,DYNLT2B,UTS2B,PSMD10P2,LPP-AS2,TPRG1,RTP2,LINC02028,ATP13A5,OSTN,WDR53,ANKRD18DP,NRROS,LINC00885,NMNAT1P3,RPS20P14,MIR28,SNORA4,RPS29P3,SNORD2,GMNC,VEZF1P1,LINC02026,SDHAP2,MIR570,MUC20P1,SNORA81,FAM157A,DPPA2P3,MIR922,MIR944,TNK2-AS1,CCT6P4,FRG2FP,LINC02012,PAK2,OPA1,MUC4,KNG1,LPP,MELTF,LINC00887,GPS2P2,RNU7-18P,RPL23AP93,MIR1248,RNU6-42P,MTAPP2,GCNT1P3,KIF3AP1,LINC02036,MIR3137,DLG1-AS1,TM4SF19-DYNLT2B,CICP6,LINC01968,MELTF-AS1,MIR4797,TMEM44-AS1,FGF12-AS3,TM4SF19-AS1,OPA1-AS1,TPRG1-AS2,TPRG1-AS1,NCBP2-AS1,RNU1-20P,UBXN7-AS1,FGF12-AS2,LMLN-AS1,ADIPOQ-AS1,XXYLT1-AS1,ACAP2-IT1,FGF12-AS1,ATP13A5-AS1,LPP-AS1,RPSAP69,XXYLT1-AS2,RPL35A,PPP1R2,PCYT1A,RFC4,MASP1,P3H2-AS1,LINC01063,ATP13A4-AS1,LINC01983,LINC02037,MIR6829,TUBB8P8,LINC02043,LINC02048,LINC01972,LINC01991,LINC02038,LINC02013,LINC02041,RN7SL447P,RN7SL36P,RN7SL73P,RN7SKP222,TFRC,SST,ST6GAL1,RNU6-858P,RNU6-1105P,RNU6-1109P,RNU6ATAC24P,RNU6-1101P,RNU6-860P,RN7SL434P,RN7SL215P,RNU6-646P,RNU4-89P,OSTN-AS1,RNU6-25P,RNU6-1279P,RN7SL738P,RNU6-821P,RNU2-11P,RNU6-621P,RN7SKP296,RNU6-910P,SEPTIN14P3,SNORA63B,SMBD1P,MUC20-OT1,TP63,TNK2,RUBCN,CLDN1,ADIPOQ,CLDN16,NCBP2,UBXN7,ACAP2
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