1q25.1-q31.1CNV Type: Deletion
Largest CNV size: 11007551 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
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
The application of whole-exome sequencing in the early diagnosis of rare genetic diseases in children: a study from Southeastern China
Deletion
Minor Reports
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
han_22_ASD/DD/ID_discovery_cases
Probands with ASD or unexplained developmental delay/intellectual disability with or without other congenital anomalies from Shandong province in Northern China who were referred for genetic services from January 2014 to December 2018.
410
151 cases diagnosed with ASD (DSM-5 criteria, ADOS-2, confirmed by CARS score > 30) and 259 patients diagnosed with developmental delay/intellectual disability (DSM-5 criteria, confirmed by Gesell developmental scale DQ score < 75 and Wechsler Intelligence Scale for Children-Revised with IQ<70).
Mean age, 2 yrs. 11 mos.
68.78% Male
12291822
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
11007551
1
0
1
lai_24_DD/ID_discovery_cases
Pediatric patients assessed at the Clinical Genetics Laboratory of the Ganzhou Maternal and Child Health Hospital who were recruited between January 2021 and December 2023.
144
Clinical manifestations observed in this cohort included global developmental delay (HP:0001263; n=46, 31.94%), intellectual disability (HP:0001249; n=44, 30.56%), seizures (HP:0001250, n = 24, 16.67%), and autistic behavior (HP:0000729; n=19, 13.19%).
Median age 4yrs. (range 0-17 yrs.)
59.03% Male
14559913
1
0
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
han_22_ASD/DD/ID_discovery_cases
Han Chinese
Array SNP
Affymetrix SNP 6.0, Affymetrix CytoScan HD
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
lai_24_DD/ID_discovery_cases
China
WES
Illumina NovaSeq 6000
PCR or Sanger
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
han_22_ASD/DD/ID_discovery_cases-case19D0673
4 yrs.
M
Developmental delay/Intellectual disability
175653343
187945164
12291822
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001150
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
175035040
186042595
11007556
GRCh38
Deletion
Yes
lai_24_DD/ID_discovery_cases-case27
2 yrs.
F
Developmental delay and intellectual disability
Global developmental delay
Intellectual disability
174210482
188770394
14559913
GRCh38
Deletion
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
han_22_ASD/DD/ID_discovery_cases-case19D0673
De novo
ASTN1,ABL2,CACNA1E,DHX9,IER5,SWT1,RALGPS2,ODR4,KIAA1614,BRINP2,TOR3A,COP1,PAPPA2,TRMT1L,NPL,C1orf21,ACBD6,SHCBP1L,EDEM3,TEX35,HMCN1,SEC16B,LHX4,RGS8,ZNF648,TEDDM2P,TEDDM1,AXDND1,TSEN15,NIBAN1,OVAAL,FAM163A,TDRD5,TOR1AIP2,MR1,GLUL,LINC01686,SMG7-AS1,FDPSP1,KRT18P28,LINC00272,RGSL1,LINC01344,C1orf220,CLEC20A,APOBEC4,MIR488,PTPN2P1,RALGPS2-AS1,SCARNA3,RPL5P5,CRYZL2P,HMGN1P4,EIF1P3,YPEL5P1,MORF4L1P7,RPL22P24,EIF4A1P11,MEF2AP1,LAMC2,NCF2,LAMC1,RNU7-13P,RPS29P5,RPSAP16,RPS3AP8,LINC01699,SETP10,RASAL2-AS1,HNRNPA1P54,PTP4A1P7,FTH1P25,SLC4A1APP2,MIR3121,MIR4424,RNA5SP69,RNA5SP72,COX5BP8,RNU5F-2P,RNASEL,PDC,PTGS2,PLA2G4A,RGS16,RNF2,QSOX1,LINC01350,LINC01657,LINC01633,LINC01732,LINC01741,PACERR,KIAA1614-AS1,LINC01645,LINC01036,PDC-AS1,LINC01688,LINC02816,RNU6-41P,RN7SL230P,TPR,TNR,VDAC1P4,SOAT1,MCRIP2P2,RNU2-12P,RN7SL654P,RNU6-152P,RNU7-183P,RNA5SP70,RN7SKP229,RNU6-1240P,LINC02818,LINC02803,CRYZL2P-SEC16B,LAMC1-AS1,NPHS2,C1orf21-DT,CEP350,SMG7,FAM20B,XPR1,ARPC5,RASAL2,PRG4,ANGPTL1,STX6,IVNS1ABP,COLGALT2,TOR1AIP1,RGL1,NMNAT2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001150
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SDCCAG3P2,RPS29P4,LINC01657,RPS29P5,SCARNA3,RNU2-12P,MORF4L1P7,PTP4A1P7,MIR488,RASAL2-AS1,C1orf220,RNA5SP69,MIR4424,PTPN2P1,SETP10,EIF4A1P11,COX5BP8,MEF2AP1,RNU5F-2P,RN7SL230P,RPSAP16,VDAC1P4,MIR3121,OVAAL,KIAA1614-AS1,LINC01732,LINC01699,RNA5SP70,RN7SKP229,YPEL5P1,RNU6-152P,EIF1P3,TEDDM1,LINC00272,TEDDM2P,HMGN1P4,RNA5SP71,RNU6-41P,RN7SL654P,RNU7-13P,RNA5SP72,FTH1P25,RPL22P24,RPL5P5,GS1-279B7.1,RNU7-183P,MCRIP2P2,KIAA0040,TNR-IT1,LINC01645,LINC01741,SEC16B,CRYZL2P,CLEC20A,ANGPTL1,TOR3A,HNRNPA1P54,TDRD5,FAM163A,TOR1AIP2,TOR1AIP1,QSOX1,LHX4,KIAA1614,MR1,IER5,GLUL,RGS16,LINC01686,RGS8,NPL,SHCBP1L,KRT18P28,LAMC1-AS1,SMG7-AS1,NCF2,APOBEC4,TSEN15,EDEM3,LINC01633,TRMT1L,IVNS1ABP,TNR,PAPPA2,ASTN1,CRYZL2P-SEC16B,TEX35,RALGPS2,FAM20B,ABL2,AXDND1,NPHS2,CEP350,XPR1,STX6,ZNF648,LINC01344,RNASEL,LINC01688,DHX9,LAMC1,LAMC2,NMNAT2,ARPC5,RGL1,COLGALT2,FAM129A,RNF2,SWT1,HMCN1,TNN,BRINP2,RASAL2,SOAT1,ACBD6,CACNA1E,RGSL1,SMG7,LINC01350,COP1,C1orf21
lai_24_DD/ID_discovery_cases-case27
PCR or Sanger
De novo
ASTN1,ABL2,CACNA1E,DHX9,CACYBP,IER5,SWT1,RALGPS2,ODR4,KIAA1614,BRINP2,TNN,TOR3A,COP1,MRPS14,PAPPA2,TRMT1L,NPL,C1orf21,ACBD6,SHCBP1L,EDEM3,TEX35,HMCN1,SEC16B,LHX4,RGS8,ZNF648,TEDDM2P,TEDDM1,AXDND1,TSEN15,NIBAN1,OVAAL,FAM163A,TDRD5,TOR1AIP2,MR1,GLUL,LINC01686,SMG7-AS1,FDPSP1,KRT18P28,LINC00272,RGSL1,LINC01344,C1orf220,CLEC20A,APOBEC4,MIR488,ENTR1P2,PTPN2P1,RALGPS2-AS1,SCARNA3,RPL5P5,CRYZL2P,HMGN1P4,EIF1P3,YPEL5P1,NDUFAF4P4,MORF4L1P7,RPL22P24,EIF4A1P11,MEF2AP1,LAMC2,NCF2,LAMC1,RNU7-13P,RPS29P5,RPSAP16,RPS3AP9,RPS3AP8,RPS29P4,LINC01699,SETP10,RASAL2-AS1,HNRNPA1P54,PTP4A1P7,FTH1P25,SLC4A1APP2,MIR3121,MIR4424,RNA5SP69,BANF1P4,RNA5SP72,COX5BP8,TNR-IT1,RNU5F-2P,RNASEL,PDC,PTGS2,PLA2G4A,RGS16,RNF2,QSOX1,LINC01350,LINC01657,LINC01633,LINC01732,LINC01741,RABGAP1L-AS1,PACERR,KIAA1614-AS1,LINC01645,LINC01036,PDC-AS1,LINC01688,LINC02816,RNU6-41P,RN7SL230P,TPR,TNR,VDAC1P4,SOAT1,MCRIP2P2,RNU2-12P,RN7SL654P,RNU6-152P,RN7SKP156,RABGAP1L-IT1,RNU7-183P,RNA5SP70,RNU6-307P,RN7SKP229,RNU6-1240P,LINC02818,LINC02803,CRYZL2P-SEC16B,LAMC1-AS1,NPHS2,C1orf21-DT,CEP350,RABGAP1L,SMG7,FAM20B,GPR52,XPR1,ARPC5,RASAL2,PRG4,ANGPTL1,KIAA0040,STX6,IVNS1ABP,COLGALT2,TOR1AIP1,RGL1,NMNAT2
Controls
No Control Data Available
No Animal Model Data Available