4q21.21-q21.22CNV Type: Deletion
Largest CNV size: 2500000 bp
Statistics Box:
Number of Reports: 2
Number of Reports: 2
Summary Information
Deletions spanning this region were found to be statistically enriched in a cohort of 29,085 cases with intellectual disability, developmental delay, and/or ASD compared to controls (11 deletions in cases vs. 0 in controls; Window q value of 0.0324, simulated P value 0f 0.00025) (Coe et al., 2014).
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Minor Reports
Title
Author, Year
Report Class
CNV Type
Refining analyses of copy number variation identifies specific genes associated with developmental delay.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_cases
Primarily pediatric cases with intellectual disability, developmental delay, and/or ASD (cohort consists of 13,318 previously unpublished cases and 15,767 cases originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
29085
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
2500000
11
0
11
miyake_23_ASD_discovery_cases
Cohort of ASD probands consisting of 351 trios, 24 quads, and two quintets included in a multi-center cohort.
405
Cases were clinically diagnosed with ASD based on DSM-V.
NA
69.88% Male
3007311
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
coe_14_ASD/DD/ID_discovery_controls
Adult population controls (cohort consists of 11,255 new controls and 8329 controls originally published in Cooper et al., Nature Genetics 2011); annotated CNVs extracted from Table 1 ("New CNVs") and Supplementary Table 2 ("Newly Significant Genomic Disorders").
19584
Control
N/A
N/A
2500000
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
132102
0
1
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_cases
N/A
aCGH
N/A
None
miyake_23_ASD_discovery_cases
Japan
Exome sequencing
Illumina HiSeq 2000/2500
NA
XHMM
qPCR
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
coe_14_ASD/DD/ID_discovery_controls
N/A
aCGH, solid phase hybridization
Multiple platforms used (including HumanHap, Illumina, and Human610-Quad)
None
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
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
coe_14_ASD/DD/ID_discovery_cases-case684
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case685
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case686
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case687
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case688
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case689
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case690
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case691
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case692
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case693
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
coe_14_ASD/DD/ID_discovery_cases-case694
N/A
N/A
Intellectual disability, developmental delay, and/or ASD
N/A
N/A
79859822
82359823
2500002
GRCh38
Deletion
No
miyake_23_ASD_discovery_cases-case12035
NA
F
ASD
Case clinically diagnosed with ASD based on DSM-V criteria.
79977549
82984859
3007311
GRCh38
Deletion
Yes
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-controlHABC_901053_901053
N/A
N/A
Control
No previous psychiatric history
81452906
81585008
132103
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
coe_14_ASD/DD/ID_discovery_cases-case684
De novo
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case685
De novo
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case686
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case687
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case688
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case689
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case690
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case691
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case692
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case693
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
coe_14_ASD/DD/ID_discovery_cases-case694
Unknown
Unknown
Unknown
KPNA2P1,RPSAP39,RNU5A-2P,MTCYBP44,NPM1P41,HNRNPA3P13,RNU6-499P,BIN2P1,PCAT4,PRDM8,FGF5,BMP3,HNRNPD,ANTXR2,PRKG2,COX5BP1,VAMP9P,CFAP299,RASGEF1B
miyake_23_ASD_discovery_cases-case12035
qPCR
De novo
BMP3,FGF5,COX5BP1,ENOPH1,PRDM8,THAP9,SCD5,LIN54,ANTXR2,RASGEF1B,HNRNPD,CFAP299,BIN2P1,IGBP1P4,TMEM150C,LINC00575,HNRNPA3P13,KPNA2P1,MIR575,RPL7AP26,RPSAP39,THAP9-AS1,NPM1P41,RNU5A-2P,PRKG2,PRKG2-AS1,HNRNPD-DT,VAMP9P,PRDM8-AS1,RNU6-499P,MTCYBP44,HNRNPDL,SEC31A
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_901053_901053
Unknown
RASGEF1B
No Animal Model Data Available