17q23.2CNV Type: Deletion
Largest CNV size: 8418 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
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
Phenotypic heterogeneity of genomic disorders and rare copy-number variants.
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Novel copy number variants in children with autism and additional developmental anomalies.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Novel candidate genes and regions for childhood apraxia of speech identified by array comparative genomic hybridization.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Functional analysis of TLK2 variants and their proximal interactomes implicates impaired kinase activity and chromatin maintenance defects in their pathogenesis
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
davis_09_ASD_discovery_cases
Autistic cases from Autism Genetic Research Exchange (AGRE)
36
ASD: diagnosis confirmed through ADI and in some cases ADOS-G. 17 cases with syndromic autism (autism and less than common craniofacial dysmorphology, limb or digit abnormality, or ocular abnormality), 19 cases selected at random with autism and no associated syndromic features
NA
NA
12603
2
0
2
engchuan_15_ASD_discovery_cases
Samples from the Autism Genome Project (AGP)
1892
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
N/A
85.78% Male
99104
0
1
1
girirajan_12_ASD/DD/ID_discovery_cases
Samples from affected children submitted to Signature Genomic Laboratories from 2008-2010.
32587
Developmental delay with or without congenital malformations
2020000
6
1
7
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
1461167
1
0
1
laffin_12_CAS_discovery_cases
Participants recruited and consented for a study of pediatric motor speech disorders
24
Diagnosis of childhood apraxia of speech (CAS) assessed by Madison Speech Assessment Protocol.
Mean, 8.3 3.7 yrs.
66% Male
53144
1
0
1
pavinato_20_DD/ID_discovery_cases
Patients from three families with TLK2 variants identified by screening of an in-house cohort of 736 patients with ASD and/or ID, a publically available cohort from the ASC (11,986 ASD cases), and the DECIPHER database
6
Affected individuals frequently presented with developmental delay and/or intellectual disability.
Range, 3-47 yrs.
50.0% Male
38938
1
0
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
9832
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
8418
3
0
3
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
92036
1
1
2
girirajan_12_ASD/DD/ID_discovery_controls
Persons found to have no overt neurological disorders during screening for other studies
8329
Control
2020000
0
0
0
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
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
110337
0
1
1
prasad_12_ASD_discovery_controls
PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
5139
Control
NA
NA (PDx controls 50.2% male)
9832
0
0
0
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
10193
1
0
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
davis_09_ASD_discovery_cases
NA
Array SNP
Affymetrix 250K Nsp, Affymetrix 250K Syt
HMM
CNAG v2.0
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_12_ASD/DD/ID_discovery_cases
aCGH
BACs aCGH, SignatureChipOS
FISH, aCGH, or confirmation by inheritance
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
laffin_12_CAS_discovery_cases
NA
aCGH
Customized 385K NimbleGen array with increased coverage of genes & regions previously associated with CAS
OGT CytoSure Interpret v.3.4.3
None
pavinato_20_DD/ID_discovery_cases
Caucasian
aCGH
Agilent 60K
None
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
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
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_12_ASD/DD/ID_discovery_controls
aCGH
BACs ACGH (SignatureChipoWG) or oligoarray (SignatureChipOS)
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
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
davis_09_ASD_discovery_cases-AU038703
NA
NA
Non-syndromic ASD
Diagnosis: broad spectrum autism. Non-syndromic autism (no craniofacial dysmorphology, limb or digit malformation, or ocular abnormality).
51510249
51520028
9779
Unknown
Deletion
No
davis_09_ASD_discovery_cases-AU057905
NA
NA
Non-syndromic ASD
Diagnosis: broad spectrum autism. Non-syndromic autism (no craniofacial dysmorphology, limb or digit malformation, or ocular abnormality).
51510249
51522852
12603
Unknown
Deletion
No
engchuan_15_ASD_discovery_cases-case3481_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
60352936
60452040
99105
GRCh38
Duplication
No
girirajan_12_ASD/DD/ID_discovery_cases-case1534
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1535
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1536
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1537
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1538
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1539
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Deletion
NA
girirajan_12_ASD/DD/ID_discovery_cases-case1540
NA
NA
Developmental delay
NA
NA
60207857
62227857
2020001
GRCh38
Duplication
NA
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001145
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
60857298
62318465
1461168
GRCh38
Deletion
Yes
laffin_12_CAS_discovery_cases-case12
10-15 yrs.
NA
CAS
Years of apraxia treatment: 10. Familial status: positive (one or more nuclear family members with a verbal trait disorder including speech disorder, language disorder, reading disorder, cognitive disability, or learning disability). Language impairment: none. Motor impairment: none.
No cognitive impairment
57315787
57368931
53145
GRCh38
Deletion
No
pavinato_20_DD/ID_discovery_cases-caseFam3-p6
16 yrs.
F
Developmental delay
Birth/neonatal history: premature birth (35 weeks), small for gestational age (birth weight -2.10 SD), birth length less than 3rd percentile (height 1st %ile). Developmental milestones: delayed motor development. Motor and musculoskeletal evaluation: skeletal anomalies of the hands (absence of flexure fold of the thumbs, short hands with inability to bend thumbs, short and brittle nails). Additional medical history: persistent arterial canal, feeding difficulties. Dysmorphic features: slightly short forehead, hypertelorism, large nasal root, epicanthus, bifid nasal tip, absent earlobes, narrow and upslanted palpebral fissures. Growth parameters: underweight (BMI 17.9 at 17 years).
Difficulties in memory and transcription
62606100
62645037
38938
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case63582-L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
56212732
56222563
9832
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case83553L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
56212732
56222563
9832
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case91617
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
56212732
56222563
9832
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11121.p1
10.3
M
Autism
NA
Full-scale IQ, 102; non-verbal IQ, 103; verbal IQ, 99
62916947
62925365
8419
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12252.p1
7.2
M
Autism
NA
Full-scale IQ, 87; non-verbal IQ, 79; verbal IQ, 106
61042000
61047056
5057
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13367.p1
9.7
F
Autism
NA
Full-scale IQ, 53; non-verbal IQ, 57; verbal IQ, 46
61330689
61333241
2553
GRCh38
Deletion
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-controlB531891_1007854698
N/A
N/A
Control
No previous psychiatric history
61467355
61502720
35366
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlHABC_901248_901248
N/A
N/A
Control
No previous psychiatric history
61738555
61830591
92037
GRCh38
Duplication
No
krumm_15_ASD_discovery_controls-control14008.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
61952964
62063301
110338
GRCh38
Duplication
Yes
sanders_11_ASD_discovery_controls-11135.s1
12.9
F
Control (matched sibling)
NA
NA
62915172
62925365
10194
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
davis_09_ASD_discovery_cases-AU038703
Unknown
Unknown
Unknown
0 genes
davis_09_ASD_discovery_cases-AU057905
Unknown
Unknown
Unknown
0 genes
engchuan_15_ASD_discovery_cases-case3481_3
Unknown
RPL12P38,APPBP2,USP32,C17orf64
girirajan_12_ASD/DD/ID_discovery_cases-case1534
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1535
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1536
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1537
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1538
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1539
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
girirajan_12_ASD/DD/ID_discovery_cases-case1540
NA
Unknown
Unknown
Unknown
SCARNA20,RPL12P38,RPSAP66,RNU6-623P,RN7SL606P,KRT18P61,HMGN1P28,RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,APPBP2,LINC01999,PPM1D,TBX2-AS1,TBX2,USP32,C17orf64,TBX4,BRIP1,MED13,BCAS3,INTS2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001145
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SL448P,RPL23AP74,C17orf82,NACA2,RN7SL800P,POLRMTP1,TBX2-AS1,TBX2,TBC1D3P2,TBX4,BRIP1,MED13,BCAS3,INTS2
laffin_12_CAS_discovery_cases-case12
Unknown
Multiplex
Unknown
MSI2
pavinato_20_DD/ID_discovery_cases-caseFam3-p6
De novo
Simplex
MRC2,TLK2
Patient fibroblasts showed approximately 50% reduction in TLK2 mRNA expression.
prasad_12_ASD_discovery_cases-case63582-L
Unknown
Unknown
Unknown
BCAS3
prasad_12_ASD_discovery_cases-case83553L
Unknown
Unknown
Unknown
BCAS3
prasad_12_ASD_discovery_cases-case91617
Unknown
Simplex
Segregated
BCAS3
sanders_11_ASD_discovery_cases-11121.p1
Unknown
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12252.p1
Maternal
Simplex (quad-proband matched)
Segregated
BCAS3
sanders_11_ASD_discovery_cases-13367.p1
Paternal
Simplex (trio)
NA
BCAS3
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB531891_1007854698
Unknown
TBX4
engchuan_15_ASD_discovery_controls-controlHABC_901248_901248
Unknown
BRIP1
krumm_15_ASD_discovery_controls-control14008.s1
Omni2.5-4v1
Paternal
RN7SL800P,MED13
sanders_11_ASD_discovery_controls-11135.s1
Unknown
Simplex (quad)
NA
No Animal Model Data Available