12q24.32-q24.33CNV Type: Duplication
Largest CNV size: 7100000 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...
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization.
Duplication
Dysfunction of SHANK2 and CHRNA7 in a patient with intellectual disability and language impairment supports genetic epistasis of the two loci.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chilian_13_DD/ID_discovery_cases
Patient, born to healthy non-consanguineous parents with no family history of ID, referred at 18 months of age for marked psychomotor and developmental delay; patient carries balanced de novo triple translocation t(11;17;19)(q13.3;q25.1;q13.42)dn with breakpoint disrupting the SHANK2 gene.
1
Severe DD/ID, language impairment, behavioral abnormalities
5 yrs.
Male
285622
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
6799468
0
2
2
larson_17_ASD_discovery_cases
Participants with a dual diagnosis of ASD and psychosis that were recruited from clinical services in the public and independent sectors in the United Kingdom, as well as from charities and an Asperger's syndrome social networking website (study took place from January 2011 and April 2014)
116
All cases with a dual diagnosis of ASD and psychosis (affective, schizophrenic, and atypical)
N/A
N/A
2629266
0
1
1
tzetis_12_DD/ID_discovery_cases
Patients referred for aCGH analysis from 2008-present
334
Cases presented with at least one of the following clinical indications: developmental delay (DD), intellectual disability (ID), dysmorphic features, unique or multiple congenital anomalies (MCA), growth disorder, behavior disorder, and/or autism (ASD)
Range, 1 month-38 years (median age of 4 years)
7100000
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_controls
Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)
2342
Controls; subjects had no previous psychiatric history
N/A
46.67% Male
678829
0
1
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
larson_17_ASD_discovery_controls
Entries listed in the Database of Genomic Variants (up to October 2017)
N/A
Control
N/A
N/A
2629266
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chilian_13_DD/ID_discovery_cases
Germany
aCGH
Agilent Human Genome CGH Microarray 244A
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
larson_17_ASD_discovery_cases
United Kingdom
Array SNP
Affymetrix CytoScan HD 2.8M, Affymetrix Cytogenetics
SNP-FASST2 Segmentation
Nexus Copy Number 7 (BioDiscovery), Affymetrix ChAS
None
tzetis_12_DD/ID_discovery_cases
Greece
aCGH
Agilent 244K, Agilent 4x180K
ADM-1
Agilent Feature Extraction V9.1, Agilent CGH Analytics V4.0, Illumina GenomeStudio V2011.1
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
larson_17_ASD_discovery_controls
N/A
N/A
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
chilian_13_DD/ID_discovery_cases-case1
5 yrs.
M
Developmental delay/intellectual disability
Patient referred at 18 months for marked psychomotor and developmental delay. Karyotype: 46, XY, t(11;17;19)(q13.3;q25.1;q13.42)dn; translocation with breakpoints within the SHANK2 and UBE2O genes. Birth/neonatal history: duing pregnancy mother had cervical cancer (treated after birth), born at 39 weeks gestation by C-section; birth weight -0.23 SD, length -0.83 SD, OFC +0.7 SD; uneventful perinatal adaption; ventricular septal defect diagnosed at 2 months. Developmental milestones: psychomotor retardation noted at 1.5 years; sat independently at 8 months, began to walk with support at 2.5 years, independent walking at 3.5 years, not toilet trained at 5 years of age. Language and communication evaluation: no spoken language. Motor and musculoskeletal evaluation: ataxia, able to stand with support. Behavioral/psychiatric evaluation: anxious, exhibited habit disorder with stereotypic movements, decreased sensitivity to pain, often caused self-injury. EEG: increased irregular activity. Brain imaging: normal by ultrasound. Visual and auditory evaluation: normal. Sleep disturbances: serious sleeping disturbances. Other features: elevated alkaline phosphatase, lactate dehydrogenase, and serum magnesium levels. Dysmorphic features: coarse face with facial dysmorphism, broad thorax, clinodactyly of 2nd and 3rd toes. Growth parameters: weight of 19.3 kg (+0.1 SD), length of 105 cm (-1.0 SD) and OFC of 51 cm (0 SD) at 5 years of age. Family history: second child of healthy non-consanguineous parents; no family history of miscarriages, ID, or alcohol exposure in utero.
Severe DD/ID. Evaluation at age of 1.5 years: Brunet-Lezine development test showed delay in movements, coordination, communication, and social skills; psychomotor development corresponded to 9 months, development quotient of 48; Bayley Scales of Infant Development gave Developmental Index score of 84.
128584255
128869877
285623
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001083
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
129325762
129943507
617746
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002268
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
126403612
133166920
6763309
GRCh38
Duplication
Yes
larson_17_ASD_discovery_cases-case16
N/A
F
ASD and psychosis
Female, normal range IQ, psychosis onset early teens, diagnosis of psychosis NOS, FDR affected by psychosis and mood problems (depression). CNV not reported in DGV.
IQ with normal range
127897104
130526370
2629267
GRCh38
Duplication
No
tzetis_12_DD/ID_discovery_cases-case33
M
DD/ID
Cleft palate, cryptorchid testes, short stature
126162882
133202490
7039609
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
engchuan_15_ASD_discovery_controls-controlB266791_1007871681
N/A
N/A
Control
No previous psychiatric history
129319609
129998438
678830
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chilian_13_DD/ID_discovery_cases-case1
Unknown
Possibly simplex (no info on 1st child)
Unknown
SLC15A4,TMEM132C,GLT1D1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001083
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
TMEM132D
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002268
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
NDUFA5P6,LINC02372,HSPE1P20,LINC02376,RNU1-104P,LINC02368,MIR3612,NLRP9P1,TMEM132D-AS1,TMEM132D-AS2,FZD10,RNU6-1077P,ADGRD1-AS1,RPS6P20,LINC02415,RNA5SP376,LINC02414,RNA5SP377,RPS6P21,RNA5SP378,RNU6-1017P,SNORA49,NOC4L,LINC02361,MIR6763,LRCOL1,P2RX2,PGAM5,RNA5SP379,RPS11P5,RNU6-327P,RNU4ATAC12P,PTP4A1P2,RPL23AP67,LINC02347,LINC00943,LINC02375,LINC02411,LINC02393,LINC00508,LINC02441,LINC02369,SLC15A4,LINC02418,LINC02419,PIWIL1,RAN,LINC02370,MMP17,ULK1,PUS1,DDX51,PXMP2,ANKLE2,ZNF605,NANOGNBP2,ZNF26,ZNF140,ZNF891,ZNF10,LINC00944,LINC02405,TMEM132C,TMEM132D,RIMBP2,STX2,LINC01257,SFSWAP,EP400,GALNT9,FBRSL1,POLE,GOLGA3,CHFR,ZNF84,LINC00507,GLT1D1,ADGRD1,EP400P1
larson_17_ASD_discovery_cases-case16
Unknown
Unknown
LINC02368,MIR3612,NLRP9P1,TMEM132D-AS1,TMEM132D-AS2,FZD10,LINC02393,LINC00508,LINC02441,LINC02369,SLC15A4,LINC02418,LINC02419,PIWIL1,TMEM132C,TMEM132D,RIMBP2,LINC00507,GLT1D1
tzetis_12_DD/ID_discovery_cases-case33
Unknown
Unknown
NDUFA5P6,LINC02372,HSPE1P20,LINC02376,RNU1-104P,LINC02368,MIR3612,NLRP9P1,TMEM132D-AS1,TMEM132D-AS2,FZD10,RNU6-1077P,ADGRD1-AS1,RPS6P20,LINC02415,RNA5SP376,LINC02414,RNA5SP377,RPS6P21,RNA5SP378,RNU6-1017P,SNORA49,NOC4L,LINC02361,MIR6763,LRCOL1,P2RX2,PGAM5,RNA5SP379,RPS11P5,RNU6-327P,RNU4ATAC12P,PTP4A1P2,RPL23AP67,LINC02359,LINC02347,LINC00943,LINC02375,LINC02411,LINC02393,LINC00508,LINC02441,LINC02369,SLC15A4,LINC02418,LINC02419,PIWIL1,RAN,LINC02370,MMP17,ULK1,PUS1,DDX51,PXMP2,ANKLE2,ZNF605,NANOGNBP2,ZNF26,ZNF140,ZNF891,ZNF10,ZNF268,LINC00944,LINC02405,TMEM132C,TMEM132D,RIMBP2,STX2,LINC01257,SFSWAP,EP400,GALNT9,FBRSL1,POLE,GOLGA3,CHFR,ZNF84,LINC00507,GLT1D1,ADGRD1,EP400P1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB266791_1007871681
Unknown
TMEM132D
No Animal Model Data Available