6q25.2-q27CNV Type: Deletion
Largest CNV size: 14500000 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
A de novo deletion in this region contains the ARID1B gene was identified in a female with developmental delay.
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-Duplication
Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, ...
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Corpus callosum abnormalities, intellectual disability, speech impairment, and autism in patients with haploinsufficiency of ARID1B.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
battaglia_13_DD/ID/ASD_discovery_cases
Patients affected by DD/ID/ASD/dysmorphic features of unknown origin observed at the Stella Maris Institute (Pisa, Italy) between May 2004 & December 2011
349
34 cases with borderline intellectual disability, 237 cases with mixed intellectual disability, 78 cases with intellectual disability and ASD (cases referred with a provisional diagnosis of ASD evaluated with ADI-R and ADOS-G)
Range, 5 mos.-19 yrs.
63.9% Male
12700000
1
0
1
halgren_11_ASD/DD/ID_discovery_cases
Patients referred to genetic evaluation due to developmental delay
7
All cases diagnosed with developmental delay/intellectual disability (DD/ID). Two cases with diagnosis of ASD, two cases with autistic traits.
Range, 3 yrs.-46 yrs.
14.3% Male
14500000
1
0
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
17995061
2
1
3
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
battaglia_13_DD/ID/ASD_discovery_cases
Italy
aCGH, array SNP
BACs aCGH, Agilent 44K, Agilent 180K, Affymetrix 6.0
FISH, qPCR
halgren_11_ASD/DD/ID_discovery_cases
European
aCGH, array SNP, solid phase hybridization
Agilent Oligoarray 400K, Affymetrix 250K, Agilent 44K, Affymetrix 250K and Illumina Sentrix HumanHap300, Agilent Human Genome CGH Micorarray 44B, Agilent Oligoarray 244K
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
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
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
battaglia_13_DD/ID/ASD_discovery_cases-case72
8 yrs. 5 mos.
F
Developmental delay/intellectual disability and epilepsy
Autism: no. Epilepsy: yes. Dysmorphic features: yes.
Moderate-severe DD/ID
153567607
166122268
12554662
GRCh38
Deletion
Yes
halgren_11_ASD/DD/ID_discovery_cases-patient8
10 yrs.
F
Developmental delay/intellectual disability
First child to healthy unrelated Caucasian parents. Prenatal ultrasound examination revealed increased nuchal translucency and a chromosome analysis was performed. She was born by uncomplicated vaginal delivery at term with BW of 2,640 g, BL 45.5 cm, and OFC 32.5 cm. The child was hypotonic, and webbed neck and a right preauricular pit were noticed. Developmental milestones were markedly delayed; e.g. she walked independently at 4 years of age. She suffered from renal lithiasis from the age of 4, and she developed bilateral cataract at the age of 6 years. She suffered from partial seizure epilepsy. At the most recent examination at age 9 years she had microcephaly, hyperactivity, and speech impairment (spoke only 2-3 words). Dysmorphic features included a very low posterior hair line, low set posteriorly rotated ears, deviated nasal septum, broad nasal tip, and a long flat philtrum. The mouth was frequently open with a protruding tongue. She had slender fingers, joint contractures of the knees, general joint laxity, pectus excavatum, and hypertrichosis. Height was 112 cm (-4 SD), weight 19.5 kg (-2 SD), and OFC 48.5 cm (-2.5 SD). Brain MRI showed hypoplasia of corpus callosum, moderate vermis hypoplasia, large ventricles.
Developmental delay
152863961
167313899
14449939
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001772
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
154118058
170602152
16484095
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001850
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
154118058
170602152
16484095
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004145
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
152376338
170583214
18206877
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
battaglia_13_DD/ID/ASD_discovery_cases-case72
FISH or qPCR
De novo
Unknown
Unknown
MTCO2P31,MTATP6P31,MTCO3P31,MTND3P20,MTND4LP20,MTND4P13,RNU6-896P,HMGB3P19,RPS4XP8,RNU6-824P,MIR1273C,RNU7-152P,MIR1202,SNORD28B,MIR4466,LDHAL6FP,MIR3692,HSPE1P26,RNU6-786P,SYNJ2-IT1,SRP72P2,RN7SL173P,CACYBPP3,MIR7161,DYNLT1,AMZ2P2,MIR3918,EZR-AS1,RNU6-293P,FNDC1-IT1,HNRNPH1P1,RNU4ATAC18P,TCP1,SNORA20,SNORA29,AGPAT4-IT1,KRT8P44,DKFZp451B082,CAHM,RN7SL366P,RNA5SP226,RNU6-730P,LINC00602,GAPDHP72,TFB1M,CLDN20,TMEM242,SERAC1,GTF2H5,TATDN2P2,EZR,OSTCP1,C6orf99,TAGAP,SOD2,WTAP,SOD2-OT1,MRPL18,PNLDC1,AIRN,SLC22A1,SLC22A2,LPAL2,PLG,IPCEF1,CNKSR3,SCAF8,NOX3,ARID1B,ZDHHC14,SNX9,SYNJ2,TMEM181,SYTL3,RSPH3,FNDC1,ACAT2,MAS1,IGF2R,LPA,MAP3K4,AGPAT4,PACRG,PACRG-AS2,PACRG-AS3,PACRG-AS1,C6orf118,OPRM1,TIAM2,TULP4,SLC22A3,PRKN,QKI,PDE10A,LINC02529
halgren_11_ASD/DD/ID_discovery_cases-patient8
De novo
Simplex
Likely segregated
TUBB4BP7,RNA5SP224,RNA5SP225,MTCO2P31,MTATP6P31,MTCO3P31,MTND3P20,MTND4LP20,MTND4P13,RNU6-896P,HMGB3P19,RPS4XP8,RNU6-824P,MIR1273C,RNU7-152P,MIR1202,SNORD28B,MIR4466,LDHAL6FP,MIR3692,HSPE1P26,RNU6-786P,SYNJ2-IT1,SRP72P2,RN7SL173P,CACYBPP3,MIR7161,DYNLT1,AMZ2P2,MIR3918,EZR-AS1,RNU6-293P,FNDC1-IT1,HNRNPH1P1,RNU4ATAC18P,TCP1,SNORA20,SNORA29,AGPAT4-IT1,KRT8P44,DKFZp451B082,CAHM,RN7SL366P,RNA5SP226,RNU6-730P,LINC00602,GAPDHP72,RNU6-153P,GNG5P1,PRR18,HNRNPA1P49,MIR1913,RAMACL,MIR3939,GPR31,FBXO5,MTRF1L,TFB1M,CLDN20,TMEM242,SERAC1,GTF2H5,TATDN2P2,EZR,OSTCP1,C6orf99,TAGAP,SOD2,WTAP,SOD2-OT1,MRPL18,PNLDC1,AIRN,SLC22A1,SLC22A2,LPAL2,PLG,TBXT,MPC1,RPS6KA2-AS1,RNASET2,FGFR1OP,TCP10L2,HPAT5,UNC93A,IPCEF1,CNKSR3,SCAF8,NOX3,ARID1B,ZDHHC14,SNX9,SYNJ2,TMEM181,SYTL3,RSPH3,FNDC1,ACAT2,MAS1,IGF2R,LPA,MAP3K4,AGPAT4,PACRG,PACRG-AS2,PACRG-AS3,PACRG-AS1,C6orf118,SFT2D1,RPS6KA2-IT1,CCR6,RGS17,OPRM1,TIAM2,TULP4,SLC22A3,PRKN,QKI,PDE10A,RPS6KA2,LINC02529
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001772
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPS4XP8,RNU6-824P,MIR1273C,RNU7-152P,MIR1202,SNORD28B,MIR4466,LDHAL6FP,MIR3692,HSPE1P26,RNU6-786P,SYNJ2-IT1,SRP72P2,RN7SL173P,CACYBPP3,MIR7161,DYNLT1,AMZ2P2,MIR3918,EZR-AS1,RNU6-293P,FNDC1-IT1,HNRNPH1P1,RNU4ATAC18P,TCP1,SNORA20,SNORA29,AGPAT4-IT1,KRT8P44,DKFZp451B082,CAHM,RN7SL366P,RNA5SP226,RNU6-730P,LINC00602,GAPDHP72,RNU6-153P,GNG5P1,PRR18,HNRNPA1P49,MIR1913,RAMACL,MIR3939,GPR31,AFDN-DT,HGC6.3,KIF25-AS1,CTAGE13P,LINC01615,VTA1P1,C6orf120,TCTE3,LINC00242,LINC00574,RPL12P23,MIR4644,PDCD2,TFB1M,CLDN20,TMEM242,SERAC1,GTF2H5,TATDN2P2,EZR,OSTCP1,C6orf99,TAGAP,SOD2,WTAP,SOD2-OT1,MRPL18,PNLDC1,AIRN,SLC22A1,SLC22A2,LPAL2,PLG,TBXT,MPC1,RPS6KA2-AS1,RNASET2,FGFR1OP,TCP10L2,HPAT5,UNC93A,TTLL2,LINC02538,LINC02487,LINC01558,FRMD1,LINC02544,THBS2,LINC02519,PHF10,ERMARD,LINC01624,DLL1,PSMB1,TBP,IPCEF1,CNKSR3,SCAF8,NOX3,ARID1B,ZDHHC14,SNX9,SYNJ2,TMEM181,SYTL3,RSPH3,FNDC1,ACAT2,MAS1,IGF2R,LPA,MAP3K4,AGPAT4,PACRG,PACRG-AS2,PACRG-AS3,PACRG-AS1,C6orf118,SFT2D1,RPS6KA2-IT1,CCR6,TCP10,AFDN,KIF25,DACT2,SMOC2,WDR27,FAM120B,OPRM1,TIAM2,TULP4,SLC22A3,PRKN,QKI,PDE10A,RPS6KA2,LINC02529
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001850
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RPS4XP8,RNU6-824P,MIR1273C,RNU7-152P,MIR1202,SNORD28B,MIR4466,LDHAL6FP,MIR3692,HSPE1P26,RNU6-786P,SYNJ2-IT1,SRP72P2,RN7SL173P,CACYBPP3,MIR7161,DYNLT1,AMZ2P2,MIR3918,EZR-AS1,RNU6-293P,FNDC1-IT1,HNRNPH1P1,RNU4ATAC18P,TCP1,SNORA20,SNORA29,AGPAT4-IT1,KRT8P44,DKFZp451B082,CAHM,RN7SL366P,RNA5SP226,RNU6-730P,LINC00602,GAPDHP72,RNU6-153P,GNG5P1,PRR18,HNRNPA1P49,MIR1913,RAMACL,MIR3939,GPR31,AFDN-DT,HGC6.3,KIF25-AS1,CTAGE13P,LINC01615,VTA1P1,C6orf120,TCTE3,LINC00242,LINC00574,RPL12P23,MIR4644,PDCD2,TFB1M,CLDN20,TMEM242,SERAC1,GTF2H5,TATDN2P2,EZR,OSTCP1,C6orf99,TAGAP,SOD2,WTAP,SOD2-OT1,MRPL18,PNLDC1,AIRN,SLC22A1,SLC22A2,LPAL2,PLG,TBXT,MPC1,RPS6KA2-AS1,RNASET2,FGFR1OP,TCP10L2,HPAT5,UNC93A,TTLL2,LINC02538,LINC02487,LINC01558,FRMD1,LINC02544,THBS2,LINC02519,PHF10,ERMARD,LINC01624,DLL1,PSMB1,TBP,IPCEF1,CNKSR3,SCAF8,NOX3,ARID1B,ZDHHC14,SNX9,SYNJ2,TMEM181,SYTL3,RSPH3,FNDC1,ACAT2,MAS1,IGF2R,LPA,MAP3K4,AGPAT4,PACRG,PACRG-AS2,PACRG-AS3,PACRG-AS1,C6orf118,SFT2D1,RPS6KA2-IT1,CCR6,TCP10,AFDN,KIF25,DACT2,SMOC2,WDR27,FAM120B,OPRM1,TIAM2,TULP4,SLC22A3,PRKN,QKI,PDE10A,RPS6KA2,LINC02529
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004145
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SYNE1-AS1,RNA5SP223,NANOGP11,HSPD1P16,VIP,TUBB4BP7,RNA5SP224,RNA5SP225,MTCO2P31,MTATP6P31,MTCO3P31,MTND3P20,MTND4LP20,MTND4P13,RNU6-896P,HMGB3P19,RPS4XP8,RNU6-824P,MIR1273C,RNU7-152P,MIR1202,SNORD28B,MIR4466,LDHAL6FP,MIR3692,HSPE1P26,RNU6-786P,SYNJ2-IT1,SRP72P2,RN7SL173P,CACYBPP3,MIR7161,DYNLT1,AMZ2P2,MIR3918,EZR-AS1,RNU6-293P,FNDC1-IT1,HNRNPH1P1,RNU4ATAC18P,TCP1,SNORA20,SNORA29,AGPAT4-IT1,KRT8P44,DKFZp451B082,CAHM,RN7SL366P,RNA5SP226,RNU6-730P,LINC00602,GAPDHP72,RNU6-153P,GNG5P1,PRR18,HNRNPA1P49,MIR1913,RAMACL,MIR3939,GPR31,AFDN-DT,HGC6.3,KIF25-AS1,CTAGE13P,LINC01615,VTA1P1,C6orf120,TCTE3,LINC00242,LINC00574,RPL12P23,MIR4644,PDCD2,FBXO5,MTRF1L,TFB1M,CLDN20,TMEM242,SERAC1,GTF2H5,TATDN2P2,EZR,OSTCP1,C6orf99,TAGAP,SOD2,WTAP,SOD2-OT1,MRPL18,PNLDC1,AIRN,SLC22A1,SLC22A2,LPAL2,PLG,TBXT,MPC1,RPS6KA2-AS1,RNASET2,FGFR1OP,TCP10L2,HPAT5,UNC93A,TTLL2,LINC02538,LINC02487,LINC01558,FRMD1,LINC02544,THBS2,LINC02519,PHF10,ERMARD,LINC01624,DLL1,PSMB1,TBP,SYNE1,MYCT1,IPCEF1,CNKSR3,SCAF8,NOX3,ARID1B,ZDHHC14,SNX9,SYNJ2,TMEM181,SYTL3,RSPH3,FNDC1,ACAT2,MAS1,IGF2R,LPA,MAP3K4,AGPAT4,PACRG,PACRG-AS2,PACRG-AS3,PACRG-AS1,C6orf118,SFT2D1,RPS6KA2-IT1,CCR6,TCP10,AFDN,KIF25,DACT2,SMOC2,WDR27,FAM120B,RGS17,OPRM1,TIAM2,TULP4,SLC22A3,PRKN,QKI,PDE10A,RPS6KA2,LINC02529
Controls
No Control Data Available
No Animal Model Data Available