6q22.1CNV Type: Deletion-Duplication
Largest CNV size: 146941 bp
Statistics Box:
Number of Reports: 6
Number of Reports: 6
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
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures.
Deletion
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
166540
0
2
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
634084
0
2
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
8974
0
1
1
lionel_13_ASD/SCZ/EP_discovery_cases
Patient cohort composed of 1158 Canadian ASD patients, 72 Austrian ASD patients, 450 Canadian schizophrenia patients, and a clinical dataset of 3704 individuals with primary diagnosis of ASD and/or seizure disorder referred for clinical microarray testing at the Mayo Clinic cytogenetics laboratory.
5384
ASD (n=1230), schizophrenia (n=450), and ASD and/or seizure disorder (n=3704). Canadian and Austrian ASD patients met criteria for ASD diagnosis based on ADI-R and/or ADOS.
NA
NA
246804
1
0
1
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
75303
0
1
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
146941
5
1
6
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
0
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
23051
1
0
1
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
152236
4
2
6
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
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
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
lionel_13_ASD/SCZ/EP_discovery_cases
NA
aCGH, array SNP
Agilent ISCA 44K, Agilent 180K, Affymetrix 6.0
Agilent DNA Analytics, Birdsuite, iPattern, Affymetrix Genotyping Console
None
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
None (not tested or failure to confirm by qPCR)
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
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)
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
engchuan_15_ASD_discovery_cases-case14410_5190
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
115015594
115089977
74384
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5037_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
114920867
115087407
166541
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001894
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
115890731
116427566
536836
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004029
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
115532759
116166844
634086
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12641.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
117409562
117418536
8975
GRCh38
Duplication
Yes
lionel_13_ASD/SCZ/EP_discovery_cases-proband3
15 yrs.
M
ASD and ID
Diagnosis of ASD (pervasive developmental disorder/PDD) at age of 4 years by child psychologist on basis of behavioral assessments. Birth/neonatal history: uncomplicated pregnancy; natural delivery. Developmental milestones: crawling at 7 months, walking at 15 months; developmental delay noticed by parents at age two, two months after serious encephalitic illness that required hospitalization; speech and language delay (did not talk until approximately 4 years of age). Behavioral/psychiatric evaluation: continued behavioral issues including anxiety, OCD, tics, and impulsive, sometimes aggressive behaviors; frequently talks to himself, trouble concentrating and sitting still. Epilepsy/seizures: cyclical seizures began at time of encephalitic illness and recurred until age of 6 years; subsequently seizure-free without anti-convulsant treatment. Other features: clinical metabolic testing for molybdenum cofactor (MoCo) deficiency performed (negative results) after detection of de novo 14q23.3/GPHN deletion. Dysmorphic features: N/A. Family history: N/A.
Intellectual disability
114944571
115191374
246804
GRCh38
Deletion
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1250-0
N/A
N/A
ACC
Diagnosis of agenesis of the corpus callosum (ACC). ASD: no. Seizures: no.
Developmental delay: yes. Intellectual disability: no.
114160605
114235907
75303
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11446.p1
8.3
M
Autism
NA
Full-scale IQ, 68; non-verbal IQ, 76; verbal IQ, 63
113989649
114010406
20758
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11610.p1
7.3
M
Autism
NA
Full-scale IQ, 127; non-verbal IQ, 138; verbal IQ, 99
113989649
114005626
15978
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12044.p1
5.6
M
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 75; verbal IQ, 76
114920867
115067808
146942
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-12201.p1
13.3
M
Autism
NA
Full-scale IQ, 130; non-verbal IQ, 131; verbal IQ, 116
114653534
114675117
21584
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12355.p1
4.6
M
Autism
NA
Full-scale IQ, 59; non-verbal IQ, 63; verbal IQ, 55
115955576
115959193
3618
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12701.p1
6.7
M
Autism
NA
Full-scale IQ, 73; non-verbal IQ, 77; verbal IQ, 74
115385540
115396178
10639
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
krumm_15_ASD_discovery_controls-control14306.s1
N/A
Male
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
117265753
117288804
23052
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_controls-11041.s1
15.7
M
Control (matched sibling)
NA
NA
115385540
115401536
15997
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11895.s1
4
M
Control (matched sibling)
NA
NA
116447754
116458529
10776
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12044.s1
8.8
M
Control (matched sibling)
NA
NA
114920867
115073103
152237
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12595.s1
10.4
M
Control (matched sibling)
NA
NA
115955576
115959193
3618
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12701.s1
10.4
M
Control (matched sibling)
NA
NA
116139657
116144140
4484
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-13070.s1
11.6
M
Control (matched sibling)
NA
NA
113989649
114005626
15978
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_cases-case14410_5190
Unknown
engchuan_15_ASD_discovery_cases-case5037_3
Unknown
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001894
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
TPI1P3,NIP7P3,TSPYL4,TSPYL1,FRK,NT5DC1,COL10A1,DSE
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004029
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
LINC02534,TPI1P3,NIP7P3,FRK,NT5DC1,COL10A1
krumm_15_ASD_discovery_cases-case12641.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
ROS1
lionel_13_ASD/SCZ/EP_discovery_cases-proband3
Unknown
Simplex
Unknown
sajan_13_ACC/CBLH/PMG_discovery_cases-case1250-0
qPCR (CNV not detected)
Biparental/Diploid copy number
Unknown
Unknown
RNA5SP213,HDAC2-AS2,HS3ST5
sanders_11_ASD_discovery_cases-11446.p1
Unknown
Simplex (quad-proband matched)
Segregated
HDAC2,HDAC2-AS2
sanders_11_ASD_discovery_cases-11610.p1
Unknown
Simplex (quad-proband matched)
Not segregated
HDAC2,HDAC2-AS2
sanders_11_ASD_discovery_cases-12044.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12201.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12355.p1
Paternal
Simplex (trio)
NA
FRK
sanders_11_ASD_discovery_cases-12701.p1
Paternal
Simplex (quad-proband matched)
Not segregated
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
krumm_15_ASD_discovery_controls-control14306.s1
Omni2.5-4v1
Paternal
VGLL2,ROS1
sanders_11_ASD_discovery_controls-11041.s1
Maternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-11895.s1
Paternal
Simplex (quad)
NA
CBX3P9,KRT18P22
sanders_11_ASD_discovery_controls-12044.s1
Paternal
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12595.s1
Paternal
Simplex (quad)
NA
FRK
sanders_11_ASD_discovery_controls-12701.s1
Paternal
Simplex (quad)
NA
NT5DC1,COL10A1
sanders_11_ASD_discovery_controls-13070.s1
Unknown
Simplex (quad)
NA
HDAC2,HDAC2-AS2
No Animal Model Data Available