1p36.11-p35.3CNV Type: Deletion
Largest CNV size: 878199 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
Deletions overlapping the AHDC1 and FGR genes were identified in two cases (one with developmental delay, one with ASD) from two recent reports (Kaminsky et al., 2011; Prasad 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
Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
guo_18_ASD/DD/ID_discovery_cases
Patients from 180 families (153 simplex, 27 multiplex) with at least one proband diagnosed with ASD who had been been clinically evaluated at the Seattle Children's Autism Center from SAGE collection
213
Patients were ascertained based on the presence of a diagnosis of ASD, intellectual disability (ID) or developmental delay (DD). ASD diagnoses were confirmed by meeting cutoff criteria on the Autism Diagnostic Observation Schedule and DSM-5 criteria; cognitive abilities were assessed using age-appropriate cognitive batteries, including DAS-2, Wechsler tests (WPPSI-IV, WISC-V, WASI-2), and Mullen.
N/A
N/A
833399
0
1
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
878199
1
0
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
30954
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
prasad_12_ASD_discovery_controls
PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
5139
Control
NA
NA (PDx controls 50.2% male)
30954
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
guo_18_ASD/DD/ID_discovery_cases
N/A
WGS
Illumina HiSeq X Ten
dCGH, Genome STRiP, LUMPY, WHAMG, CNVnator, DELLY
aCGH, Sanger sequencing
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
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
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
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
guo_18_ASD/DD/ID_discovery_cases-caseBK-364-03
N/A
M
ASD
GI problems
26958401
27791800
833400
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002086
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
26807012
27685191
878180
GRCh38
Deletion
Yes
prasad_12_ASD_discovery_cases-case103953
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
27787128
27818081
30954
Unknown
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
guo_18_ASD/DD/ID_discovery_cases-caseBK-364-03
aCGH, Sanger sequencing
De novo
Simplex
Segregated
RPL12P13,OSTCP2,TENT5B,CHCHD3P3,NPM1P39,SNRPEP7,RNU6-48P,ACTG1P20,FCN3,CD164L2,LINC02574,IFI6,RNU6-949P,CHMP1AP1,RNU6-424P,RPEP3,KDF1,TMEM222,SYTL1,MAP3K6,WASF2,AHDC1,FGR,FAM76A,TRNP1,SLC9A1,GPR3,STX12,WDTC1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002086
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SL165P,SFN,GPATCH3,NR0B2,RPL12P13,OSTCP2,TENT5B,CHCHD3P3,NPM1P39,SNRPEP7,RNU6-48P,ACTG1P20,FCN3,CD164L2,LINC02574,IFI6,RNU6-949P,ZDHHC18,GPN2,NUDC,KDF1,TMEM222,SYTL1,MAP3K6,WASF2,AHDC1,FGR,TRNP1,SLC9A1,GPR3,WDTC1
prasad_12_ASD_discovery_cases-case103953
Unknown
Unknown
Unknown
AHDC1,FGR
Controls
No Control Data Available
No Animal Model Data Available