9q33.3-q34.11CNV Type: Deletion
Largest CNV size: 6627 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
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...
Deletion
Novel 9q34.11 gene deletions encompassing combinations of four Mendelian disease genes: STXBP1, SPTAN1, ENG, and TOR1A.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
The combination of whole-exome sequencing and copy number variation sequencing enables the diagnosis of rare neurological disorders.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
campbell_12_ASD/EP/ID_discovery_cases
Unrelated children with variable clinical phenotypes found to have a 9q34.11 deletion as determined by aCGH.
10
All cases with intellectual disability (ranging from mild to profound), hypotonia, and speech impairment. 4 cases with epilepsy, 2 cases with ASD.
Range, 2-15 yrs.
60% Male
2649000
4
0
4
jiao_19_EP/DD/ID_discovery_cases
Consecutive pediatric patients with neurological disorders who visited Wuhan Children's Hospital between Jan 2017 and Dec 2018
220
Epilepsy/seizures were the most identified phenotype in this cohort (139/220, 63.2%), with developmental delay observed in 100 patients (45.45%), intellectual disability in 54 patients (24.5%), and autism/autistic behavior in 10 patients (4.5%).
Range, 1 mo.- 14 yrs.
60.45% Male
1270000
2
0
2
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
3688792
3
0
3
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
6627
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
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
campbell_12_ASD/EP/ID_discovery_cases
NA
aCGH
Agilent custom 9q34 60K arrays
Agilent Genomic Workbench, R Statistical Computing Package
FISH, long-range PCR
jiao_19_EP/DD/ID_discovery_cases
China
WGS
Low-coverage whole genome sequencing
Illumina BclToFastq
None
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
sanders_11_ASD_discovery_cases
White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
Solid phase hybridization
Illumina 1M v1, Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
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
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
campbell_12_ASD/EP/ID_discovery_cases-case10
6 yrs.
M
Intellectual disability
Age at onset of epilepsy: NA. Epilepsy type: none. EEG: NA. MRI/CT: normal. Neurological examination: ataxia, hypotonia. Ophthalmological abnormalities: none. Psychomotor regression: none. Speech impairment: severe. Other manifestations: mild dysmorphic features.
Moderate intellectual disability
127081229
127919677
838449
GRCh38
Deletion
Yes
campbell_12_ASD/EP/ID_discovery_cases-case2
3 yrs.
F
Epilepsy and intellectual disability
Age at onset of epilepsy: 3 months. Epilepsy type: infantile spasms and myoclonic epilepsy. EEG: hypsarrhythmia. MRI/CT: normal. Neurological examination: hypotonia and motor dyspraxia. Ophthalmological abnormalities: strabismus. Psychomotor regression: none. Speech impairment: severe. Other manifestations: nephrocalcinosis, gastroesophageal reflux, mild dysmorphic features, pulmonary arteriovenous malformation.
Severe intellectual disability
127519520
129446058
1926539
GRCh38
Deletion
Yes
campbell_12_ASD/EP/ID_discovery_cases-case3
6 yrs.
M
Epilepsy and intellectual disability
Age at onset of epilepsy: 6 years. Epilepsy type: tonic and localization related. EEG: right temporal spikes. MRI/CT: Chiari type I malformation. Neurological examination: hypotonia. Ophthalmological abnormalities: strabismus. Psychomotor regression: none. Speech impairment: severe. Other manifestations: microcephaly, plagiocephaly, recurrent infection, dysmorphic features.
Severe intellectual disability
126711435
128871020
2159586
GRCh38
Deletion
Yes
campbell_12_ASD/EP/ID_discovery_cases-case4
8 yrs.
M
ASD, epilepsy and ID
Age at onset of epilepsy: 5 weeks. Epilepsy type: partial seizures and nocturnal myoclonic-atonic in clusters. EEG: bifrontal temporal spikes. MRI/CT: Chiari type I malformation. Neurological examination: hypotonia, ataxia, tremulousness. Ophthalmological abnormalities: none. Psychomotor regression: none. Speech impairment: severe. Other manifestations: none.
Severe intellectual disability
127528996
127791882
262887
GRCh38
Deletion
Yes
jiao_19_EP/DD/ID_discovery_cases-case54926
2 mos.
Male
Epilepsy/seizures
Epilepsy/seizures: seizures (generalized tonic-clonic seizures). EEG: EEG abnormality
126841518
128111518
1270001
GRCh38
Deletion
No
jiao_19_EP/DD/ID_discovery_cases-caseDD18004877
3 yrs. 3 mos.
Female
DD, ID, and epilepsy/seizures
Developmental milestones: global developmental delay. Language and communication evaluation: loss of speech. Behavioral/psychiatric evaluation: dementia. Epilepsy/seizures: seizures. Additional medical history: tachycardia.
Intellectual disability
126841518
128091518
1250001
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000863
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
126081595
127781685
1700091
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001806
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
125993583
129682375
3688793
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001815
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
125993583
129682375
3688793
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_cases-12180.p1
16.3
M
Autism
NA
Full-scale IQ, 88; non-verbal IQ, 92; verbal IQ, 86
127497339
127503966
6628
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
campbell_12_ASD/EP/ID_discovery_cases-case10
FISH, long-range PCR
Unknown
Unknown
Unknown
SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,RALGPS1,GARNL3,SLC2A8,FAM129B,STXBP1,FPGS
campbell_12_ASD/EP/ID_discovery_cases-case2
FISH
Unknown
Unknown
Unknown
MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,SLC25A25-AS1,PTGES2-AS1,LCN2,C9orf16,MIR199B,MIR3154,COQ4,TMSB4XP4,MIR219A2,MIR219B,ODF2-AS1,RNU7-171P,VTI1BP4,RN7SL560P,ZDHHC12,ENDOG,DOLK,IER5L,C9orf106,RN7SL159P,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,PTGES2,DNM1,GOLGA2,SWI5,SLC27A4,URM1,CERCAM,ODF2,GLE1,WDR34,HMGA1P4,SET,ZER1,TBC1D13,SPOUT1,LRRC8A,PHYHD1,SH3GLB2,MIGA2,DOLPP1,PTPA,LINC01503,FAM129B,STXBP1,FPGS,CIZ1,TRUB2,SPTAN1,PKN3,KYAT1,CRAT,PIP5KL1,NUP188
campbell_12_ASD/EP/ID_discovery_cases-case3
FISH
Unknown
Unknown
Unknown
SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,SLC25A25-AS1,PTGES2-AS1,LCN2,C9orf16,MIR199B,MIR3154,COQ4,TMSB4XP4,MIR219A2,MIR219B,ODF2-AS1,RNU7-171P,VTI1BP4,RN7SL560P,ZDHHC12,ENDOG,ZBTB43,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,PTGES2,DNM1,GOLGA2,SWI5,SLC27A4,URM1,CERCAM,ODF2,GLE1,WDR34,HMGA1P4,SET,ZER1,TBC1D13,SPOUT1,RALGPS1,GARNL3,SLC2A8,FAM129B,STXBP1,FPGS,CIZ1,TRUB2,SPTAN1,PKN3,KYAT1,ZBTB34,PIP5KL1
campbell_12_ASD/EP/ID_discovery_cases-case4
FISH, long-range PCR
Unknown
Unknown
Unknown
MIR3911,TOR2A,CDK9,MIR3960,MIR2861,PTRH1,CFAP157,TTC16,SH2D3C,FAM129B,STXBP1
jiao_19_EP/DD/ID_discovery_cases-case54926
Unknown
Unknown
Unknown
SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,SLC25A25-AS1,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,RALGPS1,GARNL3,SLC2A8,STXBP1,FPGS,ZBTB34,PIP5KL1
jiao_19_EP/DD/ID_discovery_cases-caseDD18004877
De novo
Simplex
Segregated
SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,RALGPS1,GARNL3,SLC2A8,STXBP1,FPGS,ZBTB34,PIP5KL1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000863
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
NRON,SNORA65,MIR3911,TOR2A,ZBTB43,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,MVB12B,LMX1B,RALGPS1,GARNL3,SLC2A8,FAM129B,STXBP1,ZBTB34
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001806
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
NRON,SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,SLC25A25-AS1,PTGES2-AS1,LCN2,C9orf16,MIR199B,MIR3154,COQ4,TMSB4XP4,MIR219A2,MIR219B,ODF2-AS1,RNU7-171P,VTI1BP4,RN7SL560P,ZDHHC12,ENDOG,DOLK,IER5L,C9orf106,RN7SL159P,ASB6,ZBTB43,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,PTGES2,DNM1,GOLGA2,SWI5,SLC27A4,URM1,CERCAM,ODF2,GLE1,WDR34,HMGA1P4,SET,ZER1,TBC1D13,SPOUT1,LRRC8A,PHYHD1,SH3GLB2,MIGA2,DOLPP1,PTPA,LINC01503,C9orf50,PRRX2,MVB12B,LMX1B,RALGPS1,GARNL3,SLC2A8,FAM129B,STXBP1,FPGS,CIZ1,TRUB2,SPTAN1,PKN3,KYAT1,CRAT,LINC00963,NTMT1,ZBTB34,PIP5KL1,NUP188
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001815
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
NRON,SNORA65,MIR3911,TOR2A,CDK9,MIR3960,MIR2861,RNA5SP296,MIR4672,DPM2,NAIF1,SLC25A25-AS1,PTGES2-AS1,LCN2,C9orf16,MIR199B,MIR3154,COQ4,TMSB4XP4,MIR219A2,MIR219B,ODF2-AS1,RNU7-171P,VTI1BP4,RN7SL560P,ZDHHC12,ENDOG,DOLK,IER5L,C9orf106,RN7SL159P,ASB6,ZBTB43,ANGPTL2,ZNF79,RPL12,LRSAM1,PTRH1,CFAP157,TTC16,SH2D3C,ENG,AK1,ST6GALNAC6,ST6GALNAC4,FAM102A,SLC25A25,PTGES2,DNM1,GOLGA2,SWI5,SLC27A4,URM1,CERCAM,ODF2,GLE1,WDR34,HMGA1P4,SET,ZER1,TBC1D13,SPOUT1,LRRC8A,PHYHD1,SH3GLB2,MIGA2,DOLPP1,PTPA,LINC01503,C9orf50,PRRX2,MVB12B,LMX1B,RALGPS1,GARNL3,SLC2A8,FAM129B,STXBP1,FPGS,CIZ1,TRUB2,SPTAN1,PKN3,KYAT1,CRAT,LINC00963,NTMT1,ZBTB34,PIP5KL1,NUP188
sanders_11_ASD_discovery_cases-12180.p1
Paternal
Simplex (quad-proband matched)
Segregated
LRSAM1
Controls
No Control Data Available
No Animal Model Data Available