Xp21.3-p21.2CNV Type: Duplication
Largest CNV size: 547408 bp
Statistics Box:
Number of Reports: 7
Number of Reports: 7
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Functional impact of global rare copy number variation in autism spectrum disorders.
Duplication
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Clinically relevant single gene or intragenic deletions encompassing critical neurodevelopmental genes in patients with developmental delay, mental...
Deletion
Intragenic ILRAPL1 deletion in a male patient with intellectual disability, mild dysmorphic signs, deafness, and behavioral problems.
Deletion
Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services.
Deletion
Intragenic rearrangements in X-linked intellectual deficiency: results of a-CGH in a series of 54 patients and identification of TRPC5 and KLHL15 as potential XLID genes
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
barone_13_ID/ASD_discovery_cases
First child of nonconsanguineous Italian parents
1
Intellectual disability, autistic features/behavioral problems, deafness, seizures, and dysmorphic features. Case considered to have autism in childhood (score of 68 of Childhood Behavior Checklist-ABC)
33 yrs.
Male
285000
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
703333
2
0
2
mignonravix_14_ASD/DD/ID_discovery_cases
Male patients presenting with intellectual disability and a family history suggesting X-linked inheritance or maternal skewed X-chromosome inactivation who were selected from a series of patients from the Centre of Reference for Developmental Abnormalities.
54
Cases presented with intellectual disability.
NA
100% Male
392983
1
0
1
mikhail_11_DD/ID_discovery_cases
Patients referred for clinical array CGH testing between January 2009 & December 2010 for various neurodevelopmental phenotypes (Univ. of Alabama-Birmingham)
1200
Developmental delay (DD), intellectual disability (ID), ASD, and/or multiple congenital anomalies
NA
NA
1070000
1
0
1
pinto_10_ASD_discovery_cases
Autism Genome Project (AGP) consortium patient cohort from families with at least two ASD individuals
996
ASD (ADI-R and ADOS): strict, broad, or spectrum ASD
547408
0
1
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
548350
0
1
1
roberts_13_ASD/DD/ID_discovery_cases
Consecutive patients referred with either ASD or learning disability for genetic services at the University of Kansas Medical Center from 2009-2012
215
ASD (n=65) or learning disability (LD; n=150); learning disability defined as developmental delay (infants & children) and/or intellectual disability (older children & adults)
Mean, 10 9.7 yrs.; Range 5 mos.-52 yrs.
65.12% Male
950000
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)
548350
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
barone_13_ID/ASD_discovery_cases
Italian
aCGH
Agilent SurePrint G3
Feature Extraction v10.7, DNA Analytics Software v4.0
MLPA, long-range PCR
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
mignonravix_14_ASD/DD/ID_discovery_cases
France
aCGH
X- chromosome-specific microarray (Roche Nimblegen)
NA
NA
qPCR
mikhail_11_DD/ID_discovery_cases
NA
aCGH
Agilent 4 X 44K, Agilent 2 X 105K
Feature Extraction V9.5, DNA Analytics V4.0
FISH
pinto_10_ASD_discovery_cases
European
Solid phase hybridization
Illumina Infinium 1M SNP microarray
QuantiSNP, iPattern
qPCR, long-range PCR (LR-PCR), MLPA, FISH, aCGH (Agilent 1M), array SNP (Affymetrix 500K)
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
roberts_13_ASD/DD/ID_discovery_cases
N/A
aCGH
105K or 180K oligonucleotide microarray
Nexus Copy Number (BioDiscovery)
BACs aCGH or FISH
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
barone_13_ID/ASD_discovery_cases-case1
33 yrs.
M
ID and autistic features
Case considered to have autism in childhood (score of 68 of Childhood Behavior Checklist-ABC). Birth/neonatal history: born by spontaneous labor at 40 weeks; birth weight, lenght, and head circumference at 50th %ile. Developmental milestones: delayed psychomotor development; sitting at 10 months of age, independent walking at 16 months of age; use of single words at age of 12 months, complete sentences at 3 years of age. Language and communication evaluation: nasal speech. Behavioral/psychiatric evaluation: significant short attention span since childhood; lack of reciprocal social interaction and communication exhibited at 33 years of age. Epilepsy/seizures: pharmacologically-treated seizures since age of 25 years. Other features: bilateral progessive neurosensorial deafness requiring use of hearing aids since age of 5 years. Dysmorphic features: mild left divergent strabismus, convex nasal bridge, short philtrum, large ear lobules. Growth parameters: weight of 75 kg, height of 164 cm, and OFC of 55 cm at 33 years of age. Family history: first child of nonconsanguineous parents.
Intellectual disability; IQ of 41
29056705
29349382
292678
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002450
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
29128906
29515069
386164
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002789
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
29207382
29910715
703334
GRCh38
Deletion
Yes
mignonravix_14_ASD/DD/ID_discovery_cases-case1
3.5 yrs.
M
Developmental delay and intellectual disability
Birth/neonatal history: uneventful pregnancy and delivery at 40 weeks gestation; birth weight 3360 g (50th %ile), length 50 cm (30th %ile), and head circumference 35.5 cm (85th %ile); strabismus and myopia diagnosed soon after birth. Developmental milestones: significant motor and language delay with delayed ability to walk (22 months) and absent speech at 3.5 years. Dysmorphic features: high frontal hairline, anteverted nares, short and upturned philtrum, thick lip vermillion, everted lower lip. Growth parameters: microcephaly (head circumference <5th %ile). Family history: first child of healthy unrelated 28-year-old mother and 52-year-old father; family history notable for a healthy maternal half-sister and a maternal half-brother reported to have developmental delay.
Intellectual disability
29011033
29404015
392983
GRCh38
Deletion
Yes
mikhail_11_DD/ID_discovery_cases-patient8
6 yrs.
M
Intellectual disability + developmental delay
Language delay. Microcephaly. Diminished tone & strength. Dysmorphic features: triangular-shaped face, mild hypertelorism, upslated palpebral fissures. Growth parameters: height, 109 cm (10th %ile); weight, 19 kg (25th %ile); head circumference, 48.8 cm (2nd %ile).
Intellectual disability, developmental delay
28755881
29825327
1069447
GRCh38
Deletion
Yes
pinto_10_ASD_discovery_cases-case5126_4
NA
M
Autism
Anxiety disorder, delayed language development, sat at 6 m and walked at 12 m, health history uneventful except for asthma as an infant. When last evaluated at age 10 y, no obvious muscular difficulJes were noted.
Low average IQ (5%ile)
29003521
29550928
547408
GRCh38
Duplication
Yes
prasad_12_ASD_discovery_cases-case128832
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
28931383
29479732
548350
Unknown
Duplication
No
roberts_13_ASD/DD/ID_discovery_cases-DD/IDcase28
15 yrs.
M
Learning disability (developmental delay/intellectual disability)
Dysmorphism
29206009
30156196
950188
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
barone_13_ID/ASD_discovery_cases-case1
MLPA, long-range PCR
De novo
Simplex
Segregated
IL1RAPL1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002450
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
IL1RAPL1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002789
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MIR4666B,IL1RAPL1
mignonravix_14_ASD/DD/ID_discovery_cases-case1
qPCR
Maternal
IL1RAPL1
mikhail_11_DD/ID_discovery_cases-patient8
FISH
Maternal
Unknown
Unknown
RNA5SP500,MIR4666B,IL1RAPL1
pinto_10_ASD_discovery_cases-case5126_4
qPCR-Maternal,Agilent1M
maternal
Multiplex
NA
IL1RAPL1
prasad_12_ASD_discovery_cases-case128832
Unknown
Unknown
Unknown
IL1RAPL1
roberts_13_ASD/DD/ID_discovery_cases-DD/IDcase28
BACs aCGH or FISH
Maternal
Unknown
Unknown
MIR4666B,PIGFP3,IL1RAPL1
Controls
No Control Data Available
No Animal Model Data Available