Xp22.33-p22.11CNV Type: Deletion
Largest CNV size: 22841407 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
Rare singleton deletion within this region was found in a case from a study of 15,749 individuals from the International Standards for Cytogenomic Arrays (ISCA) consortium with unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome (Kaminsky et al., 2011).
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
Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
22841407
1
0
1
kushima_18_ASD_discovery_cases
Individuals predominantly recruited from the middle of Honshu Island (Japan)
1108
Cases were diagnosed with ASD according to DSM-5 criteria, with diagnostic and screening instruments (ADI-R, ADOS, ASQ, and SRS) used to evaluate ASD-related behaviors and symptoms in the majority of cases.
Median age, 19 years
78.0% Male
22464706
0
1
1
kushima_22_ASD_discovery_cases
Japanese ASD probands evaluated for copy number variation from an initial cohort of 1,236 probands before quality control.
1205
Cases diagnosed with autism spectrum disorder (ASD) according to DSM-5 criteria.
Median age, 19 yrs.
77.6% Male
22464706
0
1
1
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
21914669
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
kushima_18_ASD/SCZ_discovery_controls
Individuals selected from the general population and predominantly recruited from the middle of Honshu Island (Japan)
2095
Controls had no history of mental disorders based upon responses to questionnaires or self-reporting.
Median age, 37 years
52.0% Male
0
0
0
0
kushima_22_ASD/BPD/SCZ_discovery_controls
Psychiatrically normal control individuals selected from the general population evaluated for copy number variation from an initial cohort of 2,713 control individuals before quality control.
2671
Controls were psychiatrically normal and had no history of mental disorders based on responses to questionnaires or self-reporting.
Median age, 36 yrs.
47.8% Male
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
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
kushima_18_ASD_discovery_cases
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD_discovery_cases
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
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
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
kushima_18_ASD/SCZ_discovery_controls
Japanese
aCGH
NimbleGen 720K, Agilent 400K
FASST2
Nexus Copy Number v.9.0
N/A
kushima_22_ASD/BPD/SCZ_discovery_controls
Japan
aCGH
NimbleGen 720K Whole-Genome Tiling, Agilent SurePrint G3 Human CGH 400K
Fast Adaptive States Segmentation Technique 2
BioDiscovery Nexus Copy Number v.9.0
qRT-PCR
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001947
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
253129
23023165
22770037
GRCh38
Deletion
Yes
kushima_18_ASD_discovery_cases-caseASD0407
17 yrs.
M
ASD, ID, epilepsy/seizures
Developmental milestones: language delay, motor delay. Behavioral/psychiatric evaluation: self-mutilation. Epilepsy/seizures: positive for epileptic seizures/epilepsy. Family history: negative.
Intellectual disability (IQ < 70)
10000
22474705
22464706
GRCh38
Duplication
N/A
kushima_22_ASD_discovery_cases-caseASD0407
NA
NA
ASD
Diagnosis of ASD according to DSM-5 criteria.
10000
22474705
22464706
GRCh38
Duplication
Yes
miyake_23_ASD_discovery_cases-case11153
NA
M
ASD
Case clinically diagnosed with ASD based on DSM-V criteria.
359761
22274429
21914669
GRCh38
Duplication
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001947
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,DRAXINP1,RNA5SP499,EIF5P1,HMGN1P33,CLDN34,RNU6-800P,HCCS,AMELX,MIR548AX,FRMPD4-AS1,RPL17P49,RN7SKP290,PSMA6P2,TLR8-AS1,GS1-600G8.3,GPX1P1,RPL30P15,MIR6086,RN7SKP20,NPM1P9,TPT1P14,INE2,RNU5F-7P,SETP15,RPL6P30,RN7SL658P,MIR548AM,S100G,RNU7-56P,RPL12P49,RNU4-6P,CBX1P2,CBX1P4,MIR4768,NHS-AS1,TMSB10P2,GJA6P,PPEF1-AS1,HAUS1P2,RN7SL48P,MIR23C,EIF1AX-AS1,RN7SKP183,RNU6-133P,RARRES2P3,KLHL34,CBLL2,METTL15P3,RNU6-266P,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,FAM9A,GPR143,WWC3-AS1,MSL3,PRPS2,TLR7,TLR8,FAM9C,LINC02154,ATXN3L,TCEANC,RAB9A,TRAPPC2,FANCB,MOSPD2,ASB9,ASB11,VEGFD,GS1-594A7.3,CLTRN,CA5BP1,ZRSR2,AP1S2,GRPR,MAGEB17,SYAP1,TXLNG,RBBP7,SCML1,RS1,PHKA2-AS1,PHKA2,PDHA1,EIF5P2,EIF1AX,MBTPS2,YY2,SMS,PHEX-AS1,DDX53,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,ANOS1,FAM9B,TBL1X,SHROOM2,WWC3,CLCN4,MRPL35P4,TMSB4X,LINC01203,OFD1,GPM6B,GEMIN8,PIGA,PIR,BMX,ACE2,CTPS2,REPS2,NHS,LINC01456,BEND2,SCML2,CDKL5,PPEF1,ADGRG2,MAP3K15,SH3KBP1,MAP7D2,RPS6KA3,CNKSR2,SMPX,PHEX,STS,MID1,ARHGAP6,FRMPD4,EGFL6,GLRA2,CA5B,RAI2,BCLAF3,PTCHD1-AS
kushima_18_ASD_discovery_cases-caseASD0407
While a subset of CNVs were reported to have been validated by qPCR in the report, precisely which CNVs were validated was not reported
De novo
Simplex
Segregated
LINC00685,FABP5P13,KRT18P53,RPL14P5,MIR3690,RNA5SP498,LINC00106,AKAP17A,DHRSX-IT1,MIR6089,LINC00102,GYG2-AS1,ARSD-AS1,RN7SL578P,ASS1P4,SNORA48B,RNU6-114P,RNU6-146P,PRKX-AS1,MTND6P12,MTCYBP12,MIR4770,VCX3A,RPS27AP17,MIR4767,VCX,MIR651,VCX2,VCX3B,DRAXINP1,RNA5SP499,EIF5P1,HMGN1P33,CLDN34,RNU6-800P,HCCS,AMELX,MIR548AX,FRMPD4-AS1,RPL17P49,RN7SKP290,PSMA6P2,TLR8-AS1,GS1-600G8.3,GPX1P1,RPL30P15,MIR6086,RN7SKP20,NPM1P9,TPT1P14,INE2,RNU5F-7P,SETP15,RPL6P30,RN7SL658P,MIR548AM,S100G,RNU7-56P,RPL12P49,RNU4-6P,CBX1P2,CBX1P4,MIR4768,NHS-AS1,TMSB10P2,GJA6P,PPEF1-AS1,HAUS1P2,RN7SL48P,MIR23C,EIF1AX-AS1,RN7SKP183,RNU6-133P,RARRES2P3,KLHL34,CBLL2,METTL15P3,PLCXD1,GTPBP6,PPP2R3B,CRLF2,CSF2RA,IL3RA,SLC25A6,ASMTL-AS1,P2RY8,ASMT,CD99,GYG2,ARSD,ARSE,ARSF,MXRA5,PNPLA4,FAM9A,GPR143,WWC3-AS1,MSL3,PRPS2,TLR7,TLR8,FAM9C,LINC02154,ATXN3L,TCEANC,RAB9A,TRAPPC2,FANCB,MOSPD2,ASB9,ASB11,VEGFD,GS1-594A7.3,CLTRN,CA5BP1,ZRSR2,AP1S2,GRPR,MAGEB17,SYAP1,TXLNG,RBBP7,SCML1,RS1,PHKA2-AS1,PHKA2,PDHA1,EIF5P2,EIF1AX,MBTPS2,YY2,SMS,PHEX-AS1,SHOX,ASMTL,DHRSX,ZBED1,CD99P1,XG,ARSH,LINC01546,PRKX,NLGN4X,PUDP,ANOS1,FAM9B,TBL1X,SHROOM2,WWC3,CLCN4,MRPL35P4,TMSB4X,LINC01203,OFD1,GPM6B,GEMIN8,PIGA,PIR,BMX,ACE2,CTPS2,REPS2,NHS,LINC01456,BEND2,SCML2,CDKL5,PPEF1,ADGRG2,MAP3K15,SH3KBP1,MAP7D2,RPS6KA3,CNKSR2,SMPX,PHEX,STS,MID1,ARHGAP6,FRMPD4,EGFL6,GLRA2,CA5B,RAI2,BCLAF3,PTCHD1-AS
kushima_22_ASD_discovery_cases-caseASD0407
qRT-PCR
De novo
ASMT,BMX,SHROOM2,AMELX,SLC25A6,ARSD,ASS1P4,ARSL,ARHGAP6,CLCN4,S100G,STS,ARSF,CSF2RA,EIF1AX,FANCB,VEGFD,VCX,PPP2R3B,RNU4-6P,VCX3A,SH3KBP1,VCX2,TLR8,MBTPS2,TLR7,PLCXD1,GEMIN8,CTPS2,CLTRN,ACE2,TXLNG,WWC3,NLGN4X,CRLF2,ASMTL-AS1,ATXN3L,SYAP1,LIMK2P1,RPL6P30,ASB9,BEND2,ASB11,TCEANC,FAM9A,FAM9B,CBLL2,MOSPD2,FAM9C,DHRSX,IL3RA,GPM6B,GLRA2,GRPR,HCCS,MAP7D2,BCLAF3,KLHL34,LINC00685,P2RY8,UBE2E4P,CA5BP1,MRPL35P4,ARSH,TLR8-AS1,RPS27AP17,NOLC1P1,NPM1P9,RPS5P8,MAP3K15,VCX3B,YY2,GPX1P1,CD99P1,HAUS1P2,RPL14P5,MAGEB17,MIR651,GJA6P,METTL15P3,PSMA6P2,LINC00106,DRAXINP1,RPL35AP37,BLOC1S6P1,ANAPC15P1,CBX1P4,SLC35C2P1,TPT1P14,RPS27AP20,LINC01546,RPL24P9,MID1,ANOS1,NHS,CD99,GPR143,PHKA2-AS1,CBX1P2,RNU7-56P,LINC01203,RPL30P15,RPL17P49,HADHBP1,CLDN34,BRK1P1,LINC00102,CYTH1P1,EIF5P2,EIF5P1,MIR23C,GOT2P7,MIR3690,MIR4770,MIR4768,ARSD-AS1,MDM4P1,SETP15,MIR548AX,MIR4767,MIR548AM,RNA5SP499,PTCHD1-AS,PPEF1-AS1,RNU5F-7P,GYG2-AS1,FRMPD4-AS1,PHEX-AS1,PRKX-AS1,WWC3-AS1,HMGN1P33,EIF1AX-AS1,NHS-AS1,TMSB10P2,RPS6KA3,RBBP7,PHKA2,PIGA,PDHA1,RS1,PRPS2,PRKX,PPEF1,PHEX,MIR6089,MIR6086,LINC01456,KRT18P53,DHRSX-IT1,RN7SKP20,TMSB4X,CDKL5,TBL1X,SMS,SCML1,TRAPPC2,SHOX,RN7SL578P,RN7SKP183,FABP5P13,RN7SL658P,RNA5SP498,RN7SKP290,RPL12P49,RNU6-146P,RNU6-114P,RN7SL48P,RNU6-800P,RNU6-133P,MTCYBP12,RARRES2P3,MTND6P12,FAM136GP,SNORA48B,LINC02154,PNPLA4,GYG2,ZRSR2,OFD1,GTPBP6,XG,INE2,AKAP17A,ASMTL,AP1S2,PUDP,PIR,RPS24P21,CHP1P3,REPS2,ADGRG2,ZBED1,FRMPD4,RAB9A,MSL3,CA5B,RAI2,SCML2,CNKSR2,EGFL6,SMPX,MXRA5
miyake_23_ASD_discovery_cases-case11153
qPCR
De novo
ASMT,BMX,SHROOM2,AMELX,SLC25A6,ARSD,ASS1P4,ARSL,ARHGAP6,CLCN4,S100G,STS,ARSF,CSF2RA,EIF1AX,FANCB,VEGFD,VCX,PPP2R3B,RNU4-6P,VCX3A,SH3KBP1,VCX2,TLR8,MBTPS2,TLR7,GEMIN8,CTPS2,CLTRN,ACE2,TXLNG,WWC3,NLGN4X,CRLF2,ASMTL-AS1,ATXN3L,SYAP1,LIMK2P1,RPL6P30,ASB9,BEND2,ASB11,TCEANC,FAM9A,FAM9B,CBLL2,MOSPD2,FAM9C,DHRSX,IL3RA,GPM6B,GLRA2,GRPR,HCCS,MAP7D2,BCLAF3,KLHL34,P2RY8,UBE2E4P,CA5BP1,MRPL35P4,ARSH,TLR8-AS1,RPS27AP17,NOLC1P1,NPM1P9,RPS5P8,MAP3K15,VCX3B,YY2,GPX1P1,CD99P1,HAUS1P2,RPL14P5,MAGEB17,MIR651,GJA6P,PSMA6P2,LINC00106,DRAXINP1,RPL35AP37,BLOC1S6P1,ANAPC15P1,CBX1P4,SLC35C2P1,TPT1P14,RPS27AP20,LINC01546,RPL24P9,MID1,ANOS1,NHS,CD99,GPR143,PHKA2-AS1,CBX1P2,RNU7-56P,LINC01203,RPL30P15,RPL17P49,HADHBP1,CLDN34,BRK1P1,LINC00102,CYTH1P1,EIF5P2,EIF5P1,MIR23C,GOT2P7,MIR3690,MIR4770,MIR4768,ARSD-AS1,MDM4P1,SETP15,MIR548AX,MIR4767,MIR548AM,RNA5SP499,PTCHD1-AS,PPEF1-AS1,RNU5F-7P,GYG2-AS1,FRMPD4-AS1,PHEX-AS1,PRKX-AS1,WWC3-AS1,HMGN1P33,EIF1AX-AS1,NHS-AS1,TMSB10P2,RPS6KA3,RBBP7,PHKA2,PIGA,PDHA1,RS1,PRPS2,PRKX,PPEF1,PHEX,MIR6089,MIR6086,LINC01456,KRT18P53,DHRSX-IT1,RN7SKP20,TMSB4X,CDKL5,TBL1X,SMS,SCML1,TRAPPC2,SHOX,RN7SL578P,RN7SKP183,FABP5P13,RN7SL658P,RNA5SP498,RN7SKP290,RPL12P49,RNU6-146P,RNU6-114P,RN7SL48P,RNU6-800P,RNU6-133P,MTCYBP12,RARRES2P3,MTND6P12,FAM136GP,SNORA48B,LINC02154,PNPLA4,GYG2,ZRSR2,OFD1,XG,INE2,AKAP17A,ASMTL,AP1S2,PUDP,PIR,RPS24P21,CHP1P3,REPS2,ADGRG2,ZBED1,FRMPD4,RAB9A,MSL3,CA5B,RAI2,SCML2,CNKSR2,EGFL6,SMPX,MXRA5
Controls
No Control Data Available
No Animal Model Data Available