3p14.1-p12.3CNV Type: Deletion
Largest CNV size: 13819974 bp
Statistics Box:
Number of Reports: 2
Number of Reports: 2
Summary Information
Deletions within this region were found in two cases 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
Minor Reports
Title
Author, Year
Report Class
CNV Type
FOXP1-related intellectual disability syndrome: a recognisable entity.
Deletion
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
13819974
2
0
2
meerschaut_17_ID_discovery_cases
Previously unreported cases with de novo deletions affecting the FOXP1 gene
11
10/11 cases presented with intellectual disability (ID), motor delay, and delayed speech and language development, 5/11 cases presented with autistic features. One case (patient 9) died due to complications from diaphragmatic hernia at age of 5 months.
Range, 5 mos.-10 yrs.
72.72% Male
5001991
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
poultney_13_ASD_discovery_controls
Controls matched for European ancestry from NIMH and CEPH retained after filtering (original cohort size of 379 controls)
260
Control
N/A
47.49% Male (before filtering)
5787975
1
0
1
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
meerschaut_17_ID_discovery_cases
N/A
aCGH
N/A
None
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
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
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
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002116
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
64761248
78410098
13648851
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002197
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
70296167
74865078
4568912
GRCh38
Deletion
Yes
meerschaut_17_ID_discovery_cases-patient9
5 mos.
M
Multiple congenital anomalies
Case also present in DECIPHER database (DECIPHER ID 255792). Birth/neonatal history: born at 28 + 1 weeks; birth weight of 1150 g (25th-50th %ile), birth head circumference of 27 cm (50th-75th %ile); feeding difficulties. Brain imaging: abnormal brain imaging. Congenital anomalies: diaphragmatic hernia (patient died due to complications at age of 5 months). Cardiac abnormalities: pulmonary hypertension, patent ductus arteriosus.
69268686
74270676
5001991
GRCh38
Deletion
No
Controls
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
poultney_13_ASD_discovery_controls-control04C36576A
N/A
M
Control
NIMH Control (NIMH ID 91174)
68733140
74521114
5787975
GRCh38
Deletion
No
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-ISCA00002116
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
ILF2P1,RPL17P17,RNU6-787P,RN7SL482P,RPL21P41,MIR4272,NDUFB4P1,COPS8P2,PSMC1P1,RNA5SP135,MIR3136,RBM43P1,RN7SL418P,UQCRHP4,COX6CP6,HMGB1P36,RNU6-281P,MIR1284,FOXP1-IT1,GPR27,UBE2Q2P9,RNU1-62P,RNA5SP136,PSMD12P,LAPTM4BP2,FTH1P23,RNU7-19P,EBLN2,RNU6-557P,RNU2-64P,CCDC75P1,RNU6-1270P,RNU7-119P,PDZRN3-AS1,LINC02047,AKR1B1P2,NIPA2P2,RN7SL294P,MIR4444-2,HNRNPA3P6,OR7E66P,OR7E22P,OR7E55P,LSP1P2,SNRPCP10,RPS3AP15,OR7E121P,UNC93B3,CLUHP10,MIR1324,AGGF1P3,RARRES2P1,FRG2C,DUX4L26,MIR4273,RNU6-386P,VDAC1P7,RNU6-217P,LINC02077,RN7SL647P,RN7SKP61,LINC02040,MAGI1-AS1,KBTBD8,EOGT,TMF1,ARL6IP5,LMOD3,PROK2,LINC00870,RYBP,SHQ1,GXYLT2,LINC02005,MYLKP1,ALG1L6P,FAM86DP,LINC02018,ENPP7P2,LINC00960,MAGI1,MAGI1-IT1,SLC25A26,LRIG1,SUCLG2,SUCLG2-AS1,FAM19A4,UBA3,MITF,EIF4E3,RN7SL271P,LINC00877,PPP4R2,RPL23AP49,ZNF717,ADAMTS9-AS2,FAM19A1,FRMD4B,SAMMSON,MDFIC2,FOXP1,FOXP1-AS1,PDZRN3,CNTN3,ROBO2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002197
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
COX6CP6,HMGB1P36,RNU6-281P,MIR1284,FOXP1-IT1,GPR27,UBE2Q2P9,RNU1-62P,RNA5SP136,PSMD12P,LAPTM4BP2,FTH1P23,RNU7-19P,EBLN2,RNU6-557P,RNU2-64P,CCDC75P1,RNU6-1270P,RNU7-119P,PDZRN3-AS1,LINC02047,AKR1B1P2,PROK2,LINC00870,RYBP,SHQ1,GXYLT2,LINC02005,EIF4E3,RN7SL271P,LINC00877,PPP4R2,SAMMSON,MDFIC2,FOXP1,FOXP1-AS1,PDZRN3,CNTN3
meerschaut_17_ID_discovery_cases-patient9
De novo
RBM43P1,RN7SL418P,UQCRHP4,COX6CP6,HMGB1P36,RNU6-281P,MIR1284,FOXP1-IT1,GPR27,UBE2Q2P9,RNU1-62P,RNA5SP136,PSMD12P,LAPTM4BP2,FTH1P23,RNU7-19P,EBLN2,RNU6-557P,RNU2-64P,CCDC75P1,RNU6-1270P,RNU7-119P,PDZRN3-AS1,LINC02047,AKR1B1P2,PROK2,LINC00870,RYBP,SHQ1,GXYLT2,LINC02005,MITF,EIF4E3,RN7SL271P,LINC00877,PPP4R2,FRMD4B,SAMMSON,MDFIC2,FOXP1,FOXP1-AS1,PDZRN3,CNTN3
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
poultney_13_ASD_discovery_controls-control04C36576A
Unknown
RNA5SP135,MIR3136,RBM43P1,RN7SL418P,UQCRHP4,COX6CP6,HMGB1P36,RNU6-281P,MIR1284,FOXP1-IT1,GPR27,UBE2Q2P9,RNU1-62P,RNA5SP136,PSMD12P,LAPTM4BP2,FTH1P23,RNU7-19P,EBLN2,RNU6-557P,RNU2-64P,CCDC75P1,RNU6-1270P,RNU7-119P,PDZRN3-AS1,LINC02047,AKR1B1P2,EOGT,TMF1,ARL6IP5,LMOD3,PROK2,LINC00870,RYBP,SHQ1,GXYLT2,LINC02005,FAM19A4,UBA3,MITF,EIF4E3,RN7SL271P,LINC00877,PPP4R2,FRMD4B,SAMMSON,MDFIC2,FOXP1,FOXP1-AS1,PDZRN3,CNTN3
No Animal Model Data Available