9p24.3-p22.3CNV Type: N/A
Largest CNV size: 13925363 bp
Statistics Box:
Number of Reports: 6
Number of Reports: 6
Summary Information
De novo CNV identified in a case with developmental delay/intellectual disability (Girirajan et al., 2012)
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
Phenotypic heterogeneity of genomic disorders and rare copy-number variants.
NA
Minor Reports
Title
Author, Year
Report Class
CNV Type
Routine Chromosomal Microarray Analysis is Necessary in Korean Patients With Unexplained Developmental Delay/Mental Retardation/Autism Spectrum Dis...
Duplication
Genetic care in geographically isolated small island communities: 8 years of experience in the Dutch Caribbean
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chaves_24_ASD/DD/ID_discovery_cases
CMA read files performed by the Laboratrio Neurogene in Florianpolis, Santa Catarina, Brazil, upon request by medical geneticists and neurologists for investigative/diagnostic purposes, primarily from the Joana de Gusmo Children's Hospital, but also from MDs from the University Hospital Professor Polydoro Ernani de So Thiago and from private clinics in Florianpolis, State of Santa Catarina, betwee
1012
83% of cases presented with developmental delay (DD) and/or intellectual disability (ID), with 33% of cases presented with autism spectrum disorder.
Mean age, 10yrs. (median7.15 yrs., standard deviation10.2).
60.77% Male
15216536
1
0
1
girirajan_12_ASD/DD/ID_discovery_cases
Samples from affected children submitted to Signature Genomic Laboratories from 2008-2010.
32587
Developmental delay with or without congenital malformations
13925363
NA
NA
1
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
14539544
1
0
1
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
16360000
1
0
1
shin_15_ASD/DD/ID_discovery_cases
Patients with normal karyotype referred for further genetic testing from March 2012-April 2014
96
34 cases with ASD, 54 cases with DD/ID, 8 cases with ASD and DD/ID
N/A
69.8% Male
15891000
0
1
1
verberne_22_ASD/DD/ID_discovery_cases
Patients in the Dutch Caribbean referred to a visiting Dutch clinical geneticist between November 2011 and November 2019 by local pediatricians for a clinical genetic evaluation at the outpatient pediatric clinics of the Curacao Medical Center, Dr. Horacio E. Oduber Hospital (Aruba), Fundashon Mariadal (Bonaire), and St. Maarten Medical Center.
331
Common reasons for referral included developmental delay (DD) and/or intellectual disability (ID) (39%), with or without other anomalies, and congenital anomalies (24%); a subset of individuals also presented with autism spectrum disorder (ASD) and/or seizures.
Range, 0-18.7 yrs. (median age 3.95 yrs.)
NA
15827614
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
girirajan_12_ASD/DD/ID_discovery_controls
Persons found to have no overt neurological disorders during screening for other studies
8329
Control
13925363
NA
NA
NA
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chaves_24_ASD/DD/ID_discovery_cases
Brazil
Array SNP
Affymetrix CytoScan 750K, Affymetrix CytoScan HD
Affymetrix ChAS
girirajan_12_ASD/DD/ID_discovery_cases
aCGH
BACs aCGH, SignatureChipOS
FISH, aCGH, or confirmation by inheritance
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
mazzonetto_24_ASD/DD/ID_discovery_cases
Brazil
Low-pass WGS
Illumina NovaSeq 6000
SNP-FASST2 (HMM)
BioDiscovery NxClinical
shin_15_ASD/DD/ID_discovery_cases
Korean
Array SNP
Affymetrix CytoScan 750K
Affymetrix ChAS v.2.1, Nexus Copy Number v.7.5 (BioDiscovery)
None
verberne_22_ASD/DD/ID_discovery_cases
Dutch Caribbean
CMA
NA
NA
NA
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
girirajan_12_ASD/DD/ID_discovery_controls
aCGH
BACs ACGH (SignatureChipoWG) or oligoarray (SignatureChipOS)
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
chaves_24_ASD/DD/ID_discovery_cases-case1107
M
ASD
ASD. Karyotype: 46, XY, del(9)(~p22.2-pter).
208454
15424989
15216536
GRCh38
Deletion
No
girirajan_12_ASD/DD/ID_discovery_cases-case40242
NA
F
Developmental delay
NA
NA
214366
14139730
13925365
GRCh38
NA
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002176
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
111216
14650762
14539547
GRCh38
Deletion
Yes
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530529
F
Developmental delay
Global developmental delay (HP:0001263)
1
16360000
16360000
GRCh38
Deletion
No
shin_15_ASD/DD/ID_discovery_cases-case7
2 yrs.
M
Developmental delay
Developmental delay, torticollis, pes planovalgus, unilateral deafness (right side), downslanting palpebral fissures
208454
16099711
15891258
GRCh38
Duplication
No
verberne_22_ASD/DD/ID_discovery_cases-case352
NA
F
Facial dysmorphism
203860
16031473
15827614
GRCh38
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chaves_24_ASD/DD/ID_discovery_cases-case1107
Unknown
MLANA,DMRT1,RANBP6,CD274,AK3,SPATA6L,CDC37L1,PLGRKT,DMRT3,RIC1,ERMP1,DOCK8,PDCD1LG2,GLIS3-AS1,DMAC1,IL33,TPD52L3,UHRF2,ATP5PDP3,ATP5PDP2,LDHAP4,DOCK8-AS1,KIAA2026,FREM1,KCNV2,RPL4P5,TTC39B,GLIS3,INSL4,IGHEP2,GLDC,ZDHHC21,RPL7P33,LURAP1L,PSIP1P1,PES1P2,PPIAP33,GPS2P1,RPS26P3,PLPP6,SNRPEP2,MIR101-2,LINC01235,VLDLR-AS1,RPL23AP57,HMGN2P31,SELENOTP1,AKAP8P1,IMP3P1,JKAMPP1,LINC00583,TCF3P1,AK4P4,CARM1P1,RPL35AP20,HNRNPA1P41,PDSS1P1,JAK2,NFIB,GTF3AP1,RPL3P11,RNF2P1,RPL12P25,RPS27AP14,RNF152P1,ACTG1P14,CLCN3P1,ECM1P1,KLF4P1,CSNK1G2P1,CDCA4P1,EIF1P1,MIR4665,RNA5SP279,MTND5P14,MTND1P11,MTND4P14,RPS3AP54,PTPRD,RLN1,RN7SL5P,RFX3,RLN2,LURAP1L-AS1,CDC37L1-DT,LINC01231,PTPRD-AS1,PRELID3BP11,LINC01230,LINC02851,RN7SL25P,RNU7-185P,RN7SL123P,SLC1A1,PRDX1P1,SMARCA2,SNAPC3,TYRP1,VLDLR,RNU6-694P,RNU2-25P,RN7SL849P,MTND6P5,RNU2-47P,MTCO1P11,RN7SL592P,MTCO3P11,MTCO2P11,RNU6-1073P,RNU6-1260P,RNU6-1327P,RNU6-559P,MTATP6P11,MPDZ,H3P29,CER1,RCL1,PUM3,DMRT2,INSL6,KDM4C,KANK1
girirajan_12_ASD/DD/ID_discovery_cases-case40242
FISH, aCGH, or confirmation by inheritance
De novo
Unknown
Unknown
RPL12P25,RNU6-1327P,EIF1P1,RNU6-1073P,DMRT2,RPS27AP14,RNA5SP279,RNU2-25P,RN7SL592P,GPS2P1,ATP5PDP2,RNU6-694P,PLPP6,CDC37L1-DT,ECM1P1,KLF4P1,MIR101-2,HNRNPA1P41,CSNK1G2P1,PDSS1P1,MTND6P5,MTND1P11,MTCO1P11,MTCO2P11,MTATP6P11,MTCO3P11,MTND4P14,MTND5P14,IGHEP2,INSL4,RLN2,HMGN2P31,RLN1,RNF152P1,AK4P4,MIR4665,GTF3AP1,SELENOTP1,TPD52L3,RN7SL25P,RPL23AP57,RN7SL123P,RPS3AP54,RNF2P1,PRELID3BP11,SNRPEP2,ACTG1P14,RPL4P5,PPIAP33,RNU7-185P,PTPRD-AS1,RPS26P3,RN7SL5P,AKAP8P1,RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,C9orf66,DMRT3,VLDLR,KCNV2,LINC01231,GLIS3-AS1,SLC1A1,CDC37L1,INSL6,CD274,PDCD1LG2,RANBP6,IL33,IMP3P1,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,DOCK8,KANK1,DMRT1,VLDLR-AS1,PUM3,CARM1P1,RFX3,RFX3-AS1,SPATA6L,AK3,RCL1,JAK2,TCF3P1,PLGRKT,RIC1,ERMP1,KIAA2026,MLANA,UHRF2,GLDC,KDM4C,DMAC1,PTPRD-AS2,LURAP1L-AS1,MPDZ,NFIB,LINC01230,SMARCA2,GLIS3,PTPRD
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002176
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC01388,FOXD4,RPL12P25,RNU6-1327P,EIF1P1,RNU6-1073P,DMRT2,RPS27AP14,RNA5SP279,RNU2-25P,RN7SL592P,GPS2P1,ATP5PDP2,RNU6-694P,PLPP6,CDC37L1-DT,ECM1P1,KLF4P1,MIR101-2,HNRNPA1P41,CSNK1G2P1,PDSS1P1,MTND6P5,MTND1P11,MTCO1P11,MTCO2P11,MTATP6P11,MTCO3P11,MTND4P14,MTND5P14,IGHEP2,INSL4,RLN2,HMGN2P31,RLN1,RNF152P1,AK4P4,MIR4665,GTF3AP1,SELENOTP1,TPD52L3,RN7SL25P,RPL23AP57,RN7SL123P,RPS3AP54,RNF2P1,PRELID3BP11,SNRPEP2,ACTG1P14,RPL4P5,PPIAP33,RNU7-185P,PTPRD-AS1,RPS26P3,RN7SL5P,AKAP8P1,RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,C9orf66,DMRT3,VLDLR,KCNV2,LINC01231,GLIS3-AS1,SLC1A1,CDC37L1,INSL6,CD274,PDCD1LG2,RANBP6,IL33,IMP3P1,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,CBWD1,DOCK8,KANK1,DMRT1,VLDLR-AS1,PUM3,CARM1P1,RFX3,RFX3-AS1,SPATA6L,AK3,RCL1,JAK2,TCF3P1,PLGRKT,RIC1,ERMP1,KIAA2026,MLANA,UHRF2,GLDC,KDM4C,DMAC1,PTPRD-AS2,LURAP1L-AS1,MPDZ,NFIB,LINC01230,SMARCA2,GLIS3,ZDHHC21,PTPRD
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530529
Unknown
MLANA,DMRT1,FOXD4,RANBP6,CD274,AK3,SPATA6L,CDC37L1,PLGRKT,DMRT3,RIC1,CBWD1,ERMP1,DOCK8,PDCD1LG2,GLIS3-AS1,DMAC1,IL33,TPD52L3,UHRF2,ATP5PDP3,ATP5PDP2,LDHAP4,CCDC171,DOCK8-AS1,KIAA2026,FREM1,KCNV2,RPL4P5,TTC39B,GLIS3,INSL4,IGHEP2,GLDC,FTH1P12,ZDHHC21,RPL7P33,LURAP1L,PSIP1P1,PES1P2,PPIAP33,GPS2P1,RPS26P3,PLPP6,SNRPEP2,MIR101-2,LINC01235,VLDLR-AS1,RPL23AP57,HMGN2P31,SELENOTP1,AKAP8P1,IMP3P1,FAM138C,HMGN2P16,JKAMPP1,LINC00583,TCF3P1,AK4P4,C9orf92,CARM1P1,RPL35AP20,HNRNPA1P41,PDSS1P1,JAK2,NFIB,GTF3AP1,RPL3P11,RNF2P1,RPL12P25,DDX11L5,RPS27AP14,WASHC1,RNF152P1,ACTG1P14,CLCN3P1,ECM1P1,KLF4P1,CSNK1G2P1,CDCA4P1,MIR1302-9,EIF1P1,MIR4665,RNA5SP279,MTND5P14,MTND1P11,MTND4P14,RNU6-14P,RPS3AP54,PTPRD,RLN1,RN7SL5P,RFX3,RLN2,LURAP1L-AS1,CDC37L1-DT,LINC01231,LINC01388,PTPRD-AS1,PGM5P3-AS1,PRELID3BP11,LINC01230,LINC02851,RN7SL25P,RNU7-185P,RN7SL123P,RN7SL98P,SLC1A1,PRDX1P1,SMARCA2,SNAPC3,TYRP1,VLDLR,RNU6-694P,RNU2-25P,RN7SL849P,MTND6P5,RNU2-47P,RNU6-319P,MTCO1P11,RN7SL592P,MTCO3P11,MTCO2P11,RNU6-246P,RNU6-1073P,RNU6-1260P,RNU6-1327P,RNU6-559P,MTATP6P11,MIR1302-9HG,MPDZ,H3P29,CER1,RCL1,PUM3,PSIP1,DMRT2,INSL6,KDM4C,KANK1
shin_15_ASD/DD/ID_discovery_cases-case7
Unknown
Unknown
RPL12P25,RNU6-1327P,EIF1P1,RNU6-1073P,DMRT2,RPS27AP14,RNA5SP279,RNU2-25P,RN7SL592P,GPS2P1,ATP5PDP2,RNU6-694P,PLPP6,CDC37L1-DT,ECM1P1,KLF4P1,MIR101-2,HNRNPA1P41,CSNK1G2P1,PDSS1P1,MTND6P5,MTND1P11,MTCO1P11,MTCO2P11,MTATP6P11,MTCO3P11,MTND4P14,MTND5P14,IGHEP2,INSL4,RLN2,HMGN2P31,RLN1,RNF152P1,AK4P4,MIR4665,GTF3AP1,SELENOTP1,TPD52L3,RN7SL25P,RPL23AP57,RN7SL123P,RPS3AP54,RNF2P1,PRELID3BP11,SNRPEP2,ACTG1P14,RPL4P5,PPIAP33,RNU7-185P,PTPRD-AS1,RPS26P3,RN7SL5P,AKAP8P1,RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,C9orf66,DMRT3,VLDLR,KCNV2,LINC01231,GLIS3-AS1,SLC1A1,CDC37L1,INSL6,CD274,PDCD1LG2,RANBP6,IL33,IMP3P1,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,SNAPC3,DOCK8,KANK1,DMRT1,VLDLR-AS1,PUM3,CARM1P1,RFX3,RFX3-AS1,SPATA6L,AK3,RCL1,JAK2,TCF3P1,PLGRKT,RIC1,ERMP1,KIAA2026,MLANA,UHRF2,GLDC,KDM4C,DMAC1,PTPRD-AS2,LURAP1L-AS1,MPDZ,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,LINC01230,SMARCA2,GLIS3,ZDHHC21,CCDC171,PTPRD
verberne_22_ASD/DD/ID_discovery_cases-case352
Unknown
MLANA,DMRT1,RANBP6,CD274,AK3,SPATA6L,CDC37L1,PLGRKT,DMRT3,RIC1,ERMP1,DOCK8,PDCD1LG2,GLIS3-AS1,DMAC1,IL33,TPD52L3,UHRF2,ATP5PDP3,ATP5PDP2,LDHAP4,CCDC171,DOCK8-AS1,KIAA2026,FREM1,KCNV2,RPL4P5,TTC39B,GLIS3,INSL4,IGHEP2,GLDC,FTH1P12,ZDHHC21,RPL7P33,LURAP1L,PSIP1P1,PES1P2,PPIAP33,GPS2P1,RPS26P3,PLPP6,SNRPEP2,MIR101-2,LINC01235,VLDLR-AS1,RPL23AP57,HMGN2P31,SELENOTP1,AKAP8P1,IMP3P1,HMGN2P16,JKAMPP1,LINC00583,TCF3P1,AK4P4,CARM1P1,RPL35AP20,HNRNPA1P41,PDSS1P1,JAK2,NFIB,GTF3AP1,RPL3P11,RNF2P1,RPL12P25,RPS27AP14,RNF152P1,ACTG1P14,CLCN3P1,ECM1P1,KLF4P1,CSNK1G2P1,CDCA4P1,EIF1P1,MIR4665,RNA5SP279,MTND5P14,MTND1P11,MTND4P14,RNU6-14P,RPS3AP54,PTPRD,RLN1,RN7SL5P,RFX3,RLN2,LURAP1L-AS1,CDC37L1-DT,LINC01231,PTPRD-AS1,PRELID3BP11,LINC01230,LINC02851,RN7SL25P,RNU7-185P,RN7SL123P,RN7SL98P,SLC1A1,PRDX1P1,SMARCA2,SNAPC3,TYRP1,VLDLR,RNU6-694P,RNU2-25P,RN7SL849P,MTND6P5,RNU2-47P,RNU6-319P,MTCO1P11,RN7SL592P,MTCO3P11,MTCO2P11,RNU6-246P,RNU6-1073P,RNU6-1260P,RNU6-1327P,RNU6-559P,MTATP6P11,MPDZ,H3P29,CER1,RCL1,PUM3,PSIP1,DMRT2,INSL6,KDM4C,KANK1
Controls
No Control Data Available
No Animal Model Data Available