7q22.3CNV Type: Deletion
Largest CNV size: 110252 bp
Statistics Box:
Number of Reports: 13
Number of Reports: 13
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
High resolution analysis of rare copy number variants in patients with autism spectrum disorder from Taiwan.
Duplication
O'Donnell-Luria-Rodan syndrome: description of a second multinational cohort and refinement of the phenotypic spectrum
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
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
RYR2, PTDSS1 and AREG genes are implicated in a Lebanese population-based study of copy number variation in autism.
Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Duplication
De Novo Mutations of CCNK Cause a Syndromic Neurodevelopmental Disorder with Distinctive Facial Dysmorphism.
Deletion
Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chen_17_ASD_discovery_cases
Patients recruited from the Children's Mental Health Center, National Taiwan University Hospital, Taipei, Taiwan and Department of Psychiatry, Chang-Gung Memorial Hospital, Kuei-Shan, Taiwan.
335
All cases met the clinical diagnosis of autistic disorder as defined by DSM-IV; diagnosis was confirmed by interviewing parents using the Chinese version of ADI-R, and all cases received further clincial evaluation according to DSM-5 diagnostic criteria for ASD. Intelligence was measured using the Wechsler Primary and Preschool Scale of Intelligence-Revised (WPPSI-R), the Wechsler Intelligence Scale for Children-3rd Edition (WISC-III), or the Wechsler Adult Intelligence Scale (WAIS). Autistic-like social deficits were assessed using the Social Responsiveness Scale (SRS); symptoms of inattention, hyperactivity, and oppositional behavior were assessed using the Swanson, Nolan and Pelham Quest
Mean age, 9.4 4.0 years
89.25% Male
423000
0
1
1
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
170300
0
1
1
fan_18_DD/ID_discovery_cases
Individuals from unrelated families presenting with de novo 14q32.2 deletions affecting the CCNK gene
3
All three cases presented with severe to extremely severe developmental delay/intellectual disability (DD/ID) with profounds delays in language and social communication; two cases also presented with autistic behaviors
Range, 4-9 yrs.
33.33% Male
90636
1
0
1
krumm_13_ASD_discovery_cases
Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
81.265% Male
7854
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
78850
1
0
1
o'donnell-luria_19_ASD/DD/ID/EP_discovery_cases
Individuals with de novo microdeletions encompassing the KMT2E gene (one individual had been previously reported in Uliana et al., European Journal of Human Genetics 2010)
4
All four cases present with developmental delay and intellectual disability; three cases also present with epilepsy, while one case was diagnosed with ASD
Range,7-22 years
50% Male
52000
1
0
1
poultney_13_ASD_discovery_cases
ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
299
Cases diagnosed with ASD
N/A
79.86% Male (before filtering)
6003
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
18391
1
0
1
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
110252
2
0
2
soueid_16_ASD_discovery_cases
Autistic children; 37/41 from 35 fully analyzed families (33 simplex, 2 multiplex)
41
All cases fulfilled DSM-V criteria for autism
Range, 3-18 yrs.
92.68% Male
174000
0
1
1
velmans_21_DD/ID/EP_discovery_cases
Individuals with de novo 7q22.3 deletions affecting the KMT2E gene presenting with ODonnell-Luria-Rodan syndrome.
2
Both individuals presented with developmental delay; one case also presented with intellectual disability and pervasive developmental disorder, while the other also presented with seizures.
Range, 5-10 yrs.
50% Male
710945
2
0
2
yin_16_ASD_discovery_cases
Discovery cohort of ASD cases recruited from the Department of Psychiatry of National Taiwan University Hospital (NTUH), Chang Gung Memorial Hospital (CGMH), Taoyuan, and Taoyuan Mental Hospital (TMH), Taiwan.
335
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R. Cases' autistic behaviors assessed by Social Responsiveness Scale (SRS), and cognitive functions assessed by the Weschler Intelligence Scale for Children-Third Edition (WISC-III) and the Wisconsin Card Sorting Test (WCST).
Mean, 9.39 4.04 yrs.
89.3% Male
422822
0
1
1
yuan_23_ASD_discovery_cases
ASD probands from 353 pedigrees (338 simplex trios, 15 multiplex families) recruited from the Department of Child and Adolescent Psychiatry, Shanghai Mental Health Center (Shanghai, China).
369
Cases diagnosed with ASD using DSM-IV.
NA
NA
748259
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chen_17_ASD_discovery_controls1
Control subjects chosen from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
1093
Subjects received physical check-up and questionnaire screening to ensure that they did not have any abnormal physical condition and mental illness
Mean age, 68.1 10.1 years
48.03% Male
0
0
0
0
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
108985
0
1
1
krumm_13_ASD_discovery_controls
Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
46.47% Male
7854
1
0
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
poultney_13_ASD_discovery_controls
Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
260
Control
N/A
47.49% Male (before filtering)
0
0
0
0
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)
18391
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.
114930
1
0
1
soueid_16_ASD_discovery_controls
Control cohort of normal participants
37
Control
N/A
51.35% Male
0
0
0
0
yin_16_ASD_discovery_controls
Individuals from the Han Chinese Cell and Genome Bank (HCCGB) in Taiwan
1093
Controls
Mean, 68.07 10.12 yrs.
48.0% Male
422822
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chen_17_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
RT-qPCR
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
fan_18_DD/ID_discovery_cases
Chinese
Array SNP, solid phase hybridization
Affymetrix CytoScan HD, Illumina HumanCytoSNP-12
None
krumm_13_ASD_discovery_cases
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
o'donnell-luria_19_ASD/DD/ID/EP_discovery_cases
European
N/A
N/A
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
soueid_16_ASD_discovery_cases
Lebanon
Array SNP
Affymetrix 2.7M, Affymetrix CytoScan
Affymetrix ChAS
None
velmans_21_DD/ID/EP_discovery_cases
N/A
CMA
BlueGnome 44K
N/A
Illumina BlueFuse MULTI v.4.1, Agilent Cartagenia
FISH
yin_16_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
None
yuan_23_ASD_discovery_cases
China
WES
Illumina HiSeq
NA
GATK v.4.2.0.0.
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chen_17_ASD_discovery_controls1
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_13_ASD_discovery_controls
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
soueid_16_ASD_discovery_controls
Lebanon
Array SNP
Affymetrix 2.7M, Affymetrix CytoScan
Affymetrix ChAS
None
yin_16_ASD_discovery_controls
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
None
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
chen_17_ASD_discovery_cases-caseU-890
N/A
M
ASD
Case met the clinical diagnosis of autistic disorder as defined by DSM-IV, which was confirmed by interviewing parents using the Chinese version of ADI-R; case also received further clincial evaluation according to DSM-5 diagnostic criteria for ASD. ADI-R evaluation results: Qualitative abnormalities in reciprocal social interaction, current score 17 (past score 18); Qualitative abnormalities in verbal and nonverbal communication, current score 22 (past score 22); Qualitative abnormalities in nonverbal communication, current score 14 (past score 14); Restricted, repetitive, and stereotyped patterns of behaviour, current score 5 (past score 9); Abnormality of development evident at or before 36 months, past score 4. Behavioral/psychiatric evaluation: Social Responsiveness Scale (SRS) score 78; Swanson, Nolan and Pelham Questionnaire (SNAP-IV) score n/a. Epilepsy: no history of epilepsy.
Performance IQ n/a, Verbal IQ n/a, Full-scale IQ n/a
105036075
105458896
422822
GRCh38
Duplication
Yes
engchuan_15_ASD_discovery_cases-case4387_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
107234955
107405255
170301
GRCh38
Duplication
No
fan_18_DD/ID_discovery_cases-subject1
4 yrs.
M
Developmental delay/intellectual disability and autistic features
Developmental milestones: moderately delayed gross motor skill development, severely delayed fine motor skill development, extremely severe delays in language development and social communication development, severe delays in adaptivity. Language and communication evaluation: absent speech (language ability equivalent to 6 months). Behavioral/psychiatric evaluation: autistic behaviors. Dysmorphic features: hypertelorism, thin eyebrows, dysmorphic ears, high anterior hairline, palpebral fissures, broad nasal bridge and tip, thick nasal alae, long philtrum, thin upper lip vermillion, narrow jaw. Growth parameters: height normal, weight 90th-97th %ile, head circumference +1 SD ~ +2 SD.
Severe intellectual disability
106266864
106357500
90637
GRCh38
Deletion
No
krumm_13_ASD_discovery_cases-case13346.p1
N/A
F
ASD
ASD proband from SSC quad family 13346. SRS score of 84.
Full-scale IQ (FSIQ) score of 59.
107621330
107629184
7855
GRCh38
Deletion
No (not tested)
krumm_15_ASD_discovery_cases-case13023.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
107283570
107362420
78851
GRCh38
Deletion
Yes
o'donnell-luria_19_ASD/DD/ID/EP_discovery_cases-case30
18 yrs.
F
DD, ID, and epilepsy
Developmental milestones: developmental delay (walking at 420 months, first words at 36 months); developmental regression. Language and communication evaluation: absence of fluent speech. Motor and musculoskeletal evaluation: hypotonia. Epilepsy/seizures: seizures. Brain imaging: suspicion of cortical dysplasia. Additional medical history: cerebral vision impairment, hearing impairment. Dysmorphic features: bushy eyebrows, short middle face, full lips, broad mouth, small ears, large tongue. Growth parameters: head circumference N/A, weight - 0.4 SD, height - 0.6 SD.
Moderate intellectual disability
105038295
105090100
51806
GRCh38
Deletion
No
poultney_13_ASD_discovery_cases-case98HI0489B
N/A
M
ASD
ASD case from AGRE (AGRE ID AU014505; NDAR ID NDAR_INVHD431YKU)
107683200
107689202
6003
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case155486L
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
107049516
107067906
18391
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11982.p1
9.3
M
Autism
NA
Full-scale IQ, 79; non-verbal IQ, 78; verbal IQ, 86
107195797
107203223
7427
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13023.p1
4.3
F
Autism
NA
Full-scale IQ, 115; non-verbal IQ, 118; verbal IQ, 106
107287375
107397627
110253
GRCh38
Deletion
No
soueid_16_ASD_discovery_cases-caseLAS9
N/A
M
Autism
Case fulfilled DSM-V criteria for autism; no other information available
106249907
106424348
174442
GRCh38
Duplication
No
velmans_21_DD/ID/EP_discovery_cases-case17
10 yrs.
M
Developmental delay, intellectual disability, and pervasive developmental disorder
Birth/neonatal history: macrocephaly in infancy (OFC Z-score +1.8 SD). Developmental milestones: motor delay, speech delay. Behavioral/psychiatric evaluation: pervasive developmental disorder, sleep disturbance. Brain imaging: cerebral cysts. Dysmorphic features: large forehead, mildly deep-set eyes, full cheeks, everted lower lip, low-hanging columella.
Intellectual disability
105056238
105767182
710945
GRCh38
Deletion
Yes
velmans_21_DD/ID/EP_discovery_cases-case18
5 yrs.
F
Developmental delay and seizures
Developmental milestones: motor delay, delayed ability to walk (18 months), speech delay (expressive language delay with first words at 45 months). Motor and musculoskeletal evaluation: muscular hypotonia. Epilepsy/seizures: febrile seizures. Brain imaging: bilateral periventricular heterotopia, pachygyria. Dysmorphic features: large forehead, epicanthal folds. Growth parameters: macrocephaly.
105089852
105150661
60810
GRCh38
Deletion
No
yin_16_ASD_discovery_cases-case276
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
105036075
105458896
422822
GRCh38
Duplication
No
yuan_23_ASD_discovery_cases-qma01973s000
NA
NA
ASD
Case diagnosed with ASD according to DSM-IV criteria.
105040702
105788960
748259
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-controlB754625_1007874648
N/A
N/A
Control
No previous psychiatric history
106517924
106626909
108986
GRCh38
Duplication
No
krumm_13_ASD_discovery_controls-control13346.s1
N/A
F
Control
Unaffected sibling from SSC quad family 13346. SRS score of 60.
107621330
107629184
7855
GRCh38
Deletion
No (not tested)
sanders_11_ASD_discovery_controls-13023.s1
8.8
M
Control (matched sibling)
NA
NA
107287375
107402305
114931
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chen_17_ASD_discovery_cases-caseU-890
RT-qPCR
Paternal
RWDD4P1,RNU6-1322P,KMT2E,SRPK2,PUS7
engchuan_15_ASD_discovery_cases-case4387_1
Unknown
COG5
fan_18_DD/ID_discovery_cases-subject1
Unknown
Unknown
LARP1BP2,NAMPT
krumm_13_ASD_discovery_cases-case13346.p1
Maternal
Simplex
Not segregated
WBP1LP2,BCAP29
krumm_15_ASD_discovery_cases-case13023.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
COG5
o'donnell-luria_19_ASD/DD/ID/EP_discovery_cases-case30
CNV validation not reported
De novo
KMT2E
poultney_13_ASD_discovery_cases-case98HI0489B
Unknown
Unknown (likely multiplex/AGRE)
Unknown
SLC26A4
prasad_12_ASD_discovery_cases-case155486L
Unknown
Unknown
Unknown
BCAP29
sanders_11_ASD_discovery_cases-11982.p1
Paternal
Simplex (quad-proband matched)
Segregated
HBP1,COG5
sanders_11_ASD_discovery_cases-13023.p1
Paternal
Simplex (quad-proband matched)
Not segregated
COG5
soueid_16_ASD_discovery_cases-caseLAS9
Both parents
Simplex
LARP1BP2,NAMPT
velmans_21_DD/ID/EP_discovery_cases-case17
FISH
De novo
PUS7,KMT2E,RINT1,ATXN7L1,YBX1P2,EFCAB10,RWDD4P1,SRPK2,RNU6-1322P
velmans_21_DD/ID/EP_discovery_cases-case18
De novo
KMT2E,SRPK2
yin_16_ASD_discovery_cases-case276
Unknown
Unknown
Unknown
RWDD4P1,RNU6-1322P,KMT2E,SRPK2,PUS7
yuan_23_ASD_discovery_cases-qma01973s000
De novo
PUS7,RINT1,KMT2E,ATXN7L1,YBX1P2,EFCAB10,RWDD4P1,SRPK2,RNU6-1322P
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB754625_1007874648
Unknown
krumm_13_ASD_discovery_controls-control13346.s1
Maternal
Simplex
WBP1LP2,BCAP29
sanders_11_ASD_discovery_controls-13023.s1
Paternal
Simplex (quad)
NA
COG5
No Animal Model Data Available