3p21.1CNV Type: Deletion
Largest CNV size: 90755 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
Paternally inherited cis-regulatory structural variants are associated with autism.
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
Relative burden of large CNVs on a range of neurodevelopmental phenotypes.
Duplication
Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
1100
1
0
1
digregorio_17_DD/ID_discovery_cases
Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
1015
Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
N/A
N/A
1100000
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
287033
3
1
4
girirajan_11_ASD_discovery_cases
ASD cases with sporadic autism from the Simons Simplex Collection (SSC)
336
Diagnosis of ASD based on meeting criteria on ADOS, ADI-R, and expert clinical judgment. 246 cases with no intellectual disability, 90 cases with intellectual disability. Exclusion criteria: significant hearing, vision, or motor problems; significant birth complications; a diagnosis of ASD-related disorders, such as Fragile X; or having a relative (up to 3rd degree) with ASD or sibling showing ASD-related symptoms.
470979
0
1
1
leblond_12_ASD_replication_cases
Dataset featuring ASD patients from the Autism Genome Project carrying de novo SHANK2 deletions previously identified by Pinto et al. 2010. CNV validation information taken from Pinto report.
2
1 patient diagnosed with autism, 1 patient diagnosed with PDD-NOS.
NA
100% Male
26745
2
0
2
mazzonetto_24_ASD/DD/ID_discovery_cases
Patients from a total of 15 non-profit organizations and university centers located in different states of Brazil who were enrolled between July 2021 and June 2022 and referred with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorder (ASD), and/or multiple congenital anomalies.
1363
"95% of individuals in this cohort reported with the HPO phenotype ""Abnormality of the nervous system"" (HP:0000707); the HPO phenotypes ""Intellectual disability"" (HP:0001249; 36%), ""Global developmental delay"" (HP:0001263; 32%), and ""Autism"" (HP:0000717; 28%) were the most frequently reported phenotype subcategories within this subset of individuals."
63.17% Male
700000
0
3
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
90755
5
0
5
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
84725
2
0
2
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
142051
5
1
6
girirajan_11_ASD_discovery_controls
Control individuals ascertained by NIMH Genetics Initiative. DNA samples from these individuals were obtained from the Rutgers Univ. Cell & DNA Repository.
337
Control. Individuals screened specifically for eight mental health disorders.
470979
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.
100631
2
1
3
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
84725
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
digregorio_17_DD/ID_discovery_cases
Italian
aCGH
Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
ADM-2
Agilent CGH Analytics software ver. 4.0.81
qPCR
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
girirajan_11_ASD_discovery_cases
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
None
leblond_12_ASD_replication_cases
1 Canadian, 1 French
Solid phase hybridization
Illumina 1M SNP array
QuantiSNP, PennCNV
None
mazzonetto_24_ASD/DD/ID_discovery_cases
Brazil
Low-pass WGS
Illumina NovaSeq 6000
SNP-FASST2 (HMM)
BioDiscovery NxClinical
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
yin_16_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix 6.0
Affymetrix Genotyping Console v.4.1
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
girirajan_11_ASD_discovery_controls
aCGH
Custom microarray targeting 107 genomic hotspot regions (Roche NimbleGen Hotspot v1.0 array; 12 x 135K)
HMM
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
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
brandler_18_ASD_discovery_cases-caseMT_26.3
N/A
M
PDD-NOS
Case from REACH cohort
53489686
53490786
1101
GRCh38
Deletion
Yes
digregorio_17_DD/ID_discovery_cases-DECIPHER_296509
N/A
M
Developmental delay
Global developmental delay (CNV locus reported as 3p21.1-p14.3 in the report)
53228280
54324330
1096051
GRCh38
Duplication
Yes
engchuan_15_ASD_discovery_cases-case14222_3560
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
52993967
53026621
32655
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case20187_1464001
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
53858526
54145559
287034
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case4219_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
52993967
53026621
32655
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4330_100
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
52993967
53026621
32655
GRCh38
Deletion
No
girirajan_11_ASD_discovery_cases-Si109
8
M
Autism
ADOS score: 6. Vineland composite score: 62.
Mild mental retardation/intellectual disability. Full-scale IQ, 65; Verbal IQ, 79; Non-verbal IQ, 64.
52058589
52529568
470980
GRCh38
Duplication
No
leblond_12_ASD_replication_cases-Pintocase6319_3
NA
M
PDD-NOS
ADI-R domain scores: social, 14; communication, 8; behaviors, 2; age at first symptoms <36 months. Developmental milestones: delayed langauge (1st words at 24 months, 1st sentences at 48 months); no history of regression. Language and communication evaluation: delayed but functional language. Epilepsy/seizures: no history of epilepsy. Neurological examination: normal. Dysmorphic features: large and prominent ears, flat feet. Other comorbid medical conditions: hypermetropia.
Mild intellectual disability (ID). WISC-III IQ scores: full-scale IQ, 60; performance IQ, 60; verbal IQ, 67.
52993967
53020711
26745
GRCh38
Homozygous deletion
No
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530913
M
Intellectual disability
Intellectual disability (HP:0001249).
53660005
54360004
700000
GRCh38
Duplication
No
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530919
M
Intellectual disability and autistic behavior
Atypical behavior (HP:0000708), autistic behavior (HP:0000729), poor speech (HP:0002465)
Intellectual disability (HP:0001249).
53660005
54360004
700000
GRCh38
Duplication
No
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530920
M
Autism and developmental delay
Global developmental delay (HP:0001263), atypical behavior (HP:0000708), autism (HP:0000717), poor speech (HP:0002465)
53660005
54360004
700000
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11350.p1
9.1
M
Autism
NA
Full-scale IQ, 80; non-verbal IQ, 92; verbal IQ, 93
52082698
52110166
27469
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11676.p1
7.1
F
Autism
NA
Full-scale IQ, 78; non-verbal IQ, 79; verbal IQ, 83
52082698
52110166
27469
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12558.p1
10.5
M
Autism
NA
Full-scale IQ, 81; non-verbal IQ, 95; verbal IQ, 51
51702328
51715522
13195
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12710.p1
4
M
Autism
NA
Full-scale IQ, 88; non-verbal IQ, 81; verbal IQ, 105
51701459
51715522
14064
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-13097.p1
9.9
M
Autism
NA
Full-scale IQ, 34; non-verbal IQ, 37; verbal IQ, 27
54191973
54282728
90756
GRCh38
Deletion
No
yin_16_ASD_discovery_cases-case101
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
52562382
52647106
84725
GRCh38
Deletion
No
yin_16_ASD_discovery_cases-case102
N/A
N/A
ASD
Cases diagnosed with autistic disorder according to DSM-IV and confirmed by using the Chinese version of ADI-R.
52916375
52988839
72465
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-controlB137135_1007853656
N/A
N/A
Control
No previous psychiatric history
52988392
53026621
38230
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB476509_1007853948
N/A
N/A
Control
No previous psychiatric history
52993967
53026621
32655
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB667434_1007854745
N/A
N/A
Control
No previous psychiatric history
52993967
53026621
32655
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB772297_1007873646
N/A
N/A
Control
No previous psychiatric history
53928107
54070158
142052
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB782997_1007853703
N/A
N/A
Control
No previous psychiatric history
52993967
53026621
32655
GRCh38
Deletion
No
engchuan_15_ASD_discovery_controls-controlB916764_1007873302
N/A
N/A
Control
No previous psychiatric history
52993967
53026621
32655
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11798.s1
7.2
F
Control (matched sibling)
NA
NA
53447270
53455063
7794
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11869.s1
5.5
F
Control (matched sibling)
NA
NA
51881397
51928065
46669
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-13097.s1
12.4
F
Control (matched sibling)
NA
NA
54191973
54292604
100632
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseMT_26.3
PCR or SNP data validation
Maternal
CACNA1D
digregorio_17_DD/ID_discovery_cases-DECIPHER_296509
qPCR
De novo
CABYRP1,TKT,CHDH,IL17RB,SELENOK,DCP1A,ACTR8,CACNA1D,CACNA2D3
engchuan_15_ASD_discovery_cases-case14222_3560
Unknown
SFMBT1
engchuan_15_ASD_discovery_cases-case20187_1464001
Unknown
CABYRP1,IL17RB,SELENOK,ACTR8,CACNA2D3
engchuan_15_ASD_discovery_cases-case4219_1
Unknown
SFMBT1
engchuan_15_ASD_discovery_cases-case4330_100
Unknown
SFMBT1
girirajan_11_ASD_discovery_cases-Si109
Unknown
Simplex
ALDOAP1,TLR9,MIRLET7G,GLYCTK,MIR135A1,BAP1,SEMA3G,TNNC1,POC1A,ALAS1,TWF2,PPM1M,WDR82,DNAH1,PHF7,NISCH,STAB1,NT5DC2,GLYCTK-AS1
leblond_12_ASD_replication_cases-Pintocase6319_3
Both parents
SFMBT1
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530913
Unknown
CACNA1D,IL17RB,CHDH,SELENOK,CACNA2D3,ACTR8,CABYRP1
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530919
Unknown
CACNA1D,IL17RB,CHDH,SELENOK,CACNA2D3,ACTR8,CABYRP1
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530920
Unknown
CACNA1D,IL17RB,CHDH,SELENOK,CACNA2D3,ACTR8,CABYRP1
sanders_11_ASD_discovery_cases-11350.p1
Unknown
Simplex (quad-proband matched)
Segregated
POC1A
sanders_11_ASD_discovery_cases-11676.p1
Unknown
Simplex (quad-proband matched)
Not segregated
POC1A
sanders_11_ASD_discovery_cases-12558.p1
Maternal
Simplex (trio)
NA
TEX264,GRM2
sanders_11_ASD_discovery_cases-12710.p1
Maternal
Simplex (trio)
NA
TEX264,GRM2
sanders_11_ASD_discovery_cases-13097.p1
Paternal
Simplex (quad-proband matched)
Not segregated
CACNA2D3
yin_16_ASD_discovery_cases-case101
Unknown
Unknown
Unknown
SMIM4,PBRM1
yin_16_ASD_discovery_cases-case102
Unknown
Unknown
Unknown
SFMBT1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB137135_1007853656
Unknown
SFMBT1
engchuan_15_ASD_discovery_controls-controlB476509_1007853948
Unknown
SFMBT1
engchuan_15_ASD_discovery_controls-controlB667434_1007854745
Unknown
SFMBT1
engchuan_15_ASD_discovery_controls-controlB772297_1007873646
Unknown
CABYRP1
engchuan_15_ASD_discovery_controls-controlB782997_1007853703
Unknown
SFMBT1
engchuan_15_ASD_discovery_controls-controlB916764_1007873302
Unknown
SFMBT1
sanders_11_ASD_discovery_controls-11798.s1
Both parents
Simplex (quad)
NA
CACNA1D
sanders_11_ASD_discovery_controls-11869.s1
Maternal
Simplex (quad)
NA
IQCF1
sanders_11_ASD_discovery_controls-13097.s1
Paternal
Simplex (quad)
NA
CACNA2D3
No Animal Model Data Available