Yp11.2CNV Type: Deletion
Largest CNV size: 220000 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Non-syndromic language delay in a child with disruption in the Protocadherin11X/Y gene pair.
Deletion
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
Copy number variation in Han Chinese individuals with autism spectrum disorder.
Deletion-Duplication
Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation.
Duplication
RYR2, PTDSS1 and AREG genes are implicated in a Lebanese population-based study of copy number variation in autism.
Duplication
Chromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of cou...
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brand_15_ASD_discovery_cases
ASD cases who had been previously been screened by CNVs by CMA as part of the Simons Simplex Collection (SSC) in Sanders et al., 2011
259
Diagnosis of ASD
N/A
N/A
233568
0
2
2
digregorio_17_DD/ID_discovery_cases
Consecutive cases examined in the Medical Genetics Unit at the "Citta della Salte e della Scienza" University Hospital (Turin, Italy) from 2008 to 2014 (cases with CNVs are present in DECIPHER database)
1015
Cases diagnosed with idiopathic developmental delay and/or intellectual disability (DD/ID)
N/A
N/A
341000
0
1
1
gazzellone_14_ASD_discovery_cases
ASD-affected individuals referred to the Children Development and Behavior Research Center (CDRBC) at Harbin Medical University, China, between January 2007 and June 2011.
104
Diagnosis of ASD made using Autism Behavior Checklist (ABC) and Childhood Autism Rating Scale (CARS)
Mean age at enrollment, 4.31 1.80 yrs.
87.5% Male
207592
4
1
5
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
2282325
2
0
2
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
114000
0
2
2
soueid_16_ASD_discovery_cases
Autistic children; 37/41 from 35 fully analyzed families (33 simplex, 2 multiplex)
41
All cases fulfilled DSM-V criteria for autism
Range, 3-18 yrs.
92.68% Male
298000
0
2
2
soueid_16_DD/ID_discovery_cases
Individuals referred to clinical neurogenetics service with non-syndromic developmental delay and intellectual disabilities (DD/ID) or rare neurological syndromes
35
Cases present with non-syndromic developmental delay and intellectual disabilities (DD/ID) or rare neurological syndromes
N/A
N/A
121000
0
1
1
speevak_11_DD_discovery_cases
Patient referred to genetics clinic (Dept. of Genetics & Laboratory Medicine, Credit Valley Hospital, Ontario, Canada) for non-syndromic speech delay
1
Developmental delay (non-syndromic significant speech delay). Differential diagnosis of ASD ruled out by psychiatric assessment at 3.5 yrs., but no specific diagnosis suggested.
4.5 yrs.
Male
220000
1
0
1
xu_16_ASD/DD/ID_discovery_cases
Patients referred to the Duke Autism Genetics Clinic for clinical genetic evaluation of ASD and DD/ID from 2010-2014
115
66 cases with confirmed primary diagnosis of ASD (DSM-IV, DSM-5, ADOS, and ADI-R used to support ASD diagnosis), 49 cases with primary diagnosis of DD or ID (based on IQ and DQ scores).
Range, 18 months-15.1 years (mean age, 5.7 years)
72.17% Male
575000
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
nord_11_ASD_discovery_controls
Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
123
Controls (no history of psychiatric symptoms by self-report)
30 yrs.
84866
0
2
2
soueid_16_ASD_discovery_controls
Control cohort of normal participants
37
Control
N/A
51.35% Male
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brand_15_ASD_discovery_cases
N/A
Long-insert WGS
Long-insert whole genome sequencing
LUMPY, cn.MOPS, SV classifier
None
digregorio_17_DD/ID_discovery_cases
Italian
aCGH
Agilent 60K (SurePrint G3 Human CGH Microarray 8x60K)
ADM-2
Agilent CGH Analytics software ver. 4.0.81
None
gazzellone_14_ASD_discovery_cases
Han Chinese
Array SNP
Affymetrix CytoScan HD
ChAS, iPattern, Nexus, Partek
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
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
soueid_16_ASD_discovery_cases
Lebanon
Array SNP
Affymetrix 2.7M, Affymetrix CytoScan
Affymetrix ChAS
None
soueid_16_DD/ID_discovery_cases
Lebanon
Array SNP
Affymetrix 2.7M, Affymetrix CytoScan
Affymetrix ChAS
None
speevak_11_DD_discovery_cases
NA
FISH
microsatellite, PCR
xu_16_ASD/DD/ID_discovery_cases
N/A
aCGH, array SNP
BlueGnome CytoChip v2, Affymetrix 6.0, Affymetrix Cytoscan HD
Affymeytrix Genotyping Console v3.0.2
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
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
soueid_16_ASD_discovery_controls
Lebanon
Array SNP
Affymetrix 2.7M, Affymetrix CytoScan
Affymetrix ChAS
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
brand_15_ASD_discovery_cases-case4
N/A
N/A
ASD
Long-insert WGS identified a dupINVdup involving chromosome Y in this case. Duplication previously identified by aCGH (chrY:5060531-5269790; hg19).
5158663
5392231
233569
GRCh38
Duplication
No
brand_15_ASD_discovery_cases-case4
N/A
N/A
ASD
Long-insert WGS identified a dupINVdup involving chromosome Y in this case. Duplication not previously identified by aCGH.
3542962
3568305
25344
GRCh38
Duplication
No
digregorio_17_DD/ID_discovery_cases-DECIPHER_300158
N/A
M
Developmental delay/intellectual disability
6848760
7189494
340735
GRCh38
Duplication
No
gazzellone_14_ASD_discovery_cases-case505-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
6664556
6709862
45307
GRCh38
Duplication
No
gazzellone_14_ASD_discovery_cases-case527-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
4083611
4291203
207593
GRCh38
Deletion
No
gazzellone_14_ASD_discovery_cases-case577-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
9471034
9505219
34186
GRCh38
Deletion
No
gazzellone_14_ASD_discovery_cases-case577-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
9399486
9467379
67894
GRCh38
Deletion
No
gazzellone_14_ASD_discovery_cases-case693-3
N/A
M
ASD
ASD; no other clinical information provided
N/A
9655203
9685107
29905
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001239
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
6724827
9007152
2282326
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005273
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
4246296
5511861
1265566
GRCh38
Deletion
Yes
maini_18_ASD/DD/ID_discovery_cases-case_unknown250
N/A
N/A
NDD/MCA/dysmorphic features
CNV was identified in an individual with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features (detailed clinical information was not available). CNV classified as variant of unknown significance-likely benign (VOUS-LB)
6760650
6874888
114239
GRCh38
Triplication
No
soueid_16_ASD_discovery_cases-caseBAK41
N/A
M
Autism
Case fulfilled DSM-V criteria for autism; no other information available
4105083
4403332
298250
GRCh38
Duplication
No
soueid_16_ASD_discovery_cases-caseLAS17
N/A
M
Autism
Case fulfilled DSM-V criteria for autism; no other information available
9361112
9482315
121204
GRCh38
Duplication
No
soueid_16_DD/ID_discovery_cases-case10
N/A
N/A
Developmental delay/intellectual disability
9361112
9482315
121204
GRCh38
Duplication
No
speevak_11_DD_discovery_cases-case1
4.5 yrs.
M
Developmental delay/speech delay
Developmental milestones: significant speech delay (first words at 2 yrs.; at 4.5 yrs., patient was only able to use a few words in a sentence, which were not easily understood). Behavioral characteristics: aggressive behavior, autistic traits (spitting and rocking with excessive hand movements and solitary play noted at 3.5 yrs.; however, a differential diagnosis of ASD ruled out by psychiatric assessment at the time, but no specific diagnosis was suggested). Dysmorphic features: no major dysmorphic or congenitally abnormal features, other than mild 2-3 toe syndactyly. Growth parameters: height, 90th %ile; wieght, 50th %ile; head circumference, 10th %ile.
5111632
5310008
198377
GRCh38
Deletion
Yes
xu_16_ASD/DD/ID_discovery_cases-case35
N/A
N/A
Developmental delay
Primary diagnosis of developmental delay based on DQ scores.
6532152
7107031
574880
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
nord_11_ASD_discovery_controls-04C27090
Control
7535471
7583267
47797
Unknown
Duplication
nord_11_ASD_discovery_controls-04C27265
Control
7495620
7580485
84866
Unknown
Duplication
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brand_15_ASD_discovery_cases-case4
Paternal
Simplex
Unknown
VDAC1P6,EIF4A1P2,PCDH11Y
brand_15_ASD_discovery_cases-case4
Paternal
Simplex
Unknown
PRRC2CP1
digregorio_17_DD/ID_discovery_cases-DECIPHER_300158
Unknown
AMELY,ATP5PFP1,GPR143P,TBL1Y
gazzellone_14_ASD_discovery_cases-case505-3
Unknown
Unknown
Unknown
gazzellone_14_ASD_discovery_cases-case527-3
Unknown
Unknown
Unknown
RNU6-303P
gazzellone_14_ASD_discovery_cases-case577-3
Unknown
Unknown
Unknown
FAM197Y4,TSPY9P,FAM197Y3
gazzellone_14_ASD_discovery_cases-case577-3
Unknown
Unknown
Unknown
TSPY3,FAM197Y5,TSPY1
gazzellone_14_ASD_discovery_cases-case693-3
Unknown
Unknown
Unknown
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001239
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
GOT2P5,AMELY,ATP5PFP1,GPR143P,RN7SKP282,RNU6-941P,RNU6-521P,RBMY2HP,TSPY12P,TTTY12,ZNF92P1Y,BPY2DP,ZNF736P7Y,ZNF736P9Y,TSPY24P,ZNF736P6Y,MTND6P1,MTCYBP1,MTND1P1,MTND2P3,TRIM60P3Y,ZNF736P10Y,LINC00279,TTTY19,TTTY16,ZNF736P8Y,RBMY2JP,RBMY2KP,TTTY18,TTTY11,TBL1Y,RFTN1P1,PRKY
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005273
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SERBP1P2,RNU2-57P,VDAC1P6,EIF4A1P2,PCDH11Y
maini_18_ASD/DD/ID_discovery_cases-case_unknown250
Paternal
Unknown
Unknown
GOT2P5,AMELY
soueid_16_ASD_discovery_cases-caseBAK41
Paternal
Simplex
RNU6-303P
soueid_16_ASD_discovery_cases-caseLAS17
De novo
Simplex
TSPY7P,FAM197Y6,TSPY3,FAM197Y5,TSPY1,FAM197Y4,FAM197Y7
soueid_16_DD/ID_discovery_cases-case10
Unknown
Unknown
Unknown
TSPY7P,FAM197Y6,TSPY3,FAM197Y5,TSPY1,FAM197Y4,FAM197Y7
speevak_11_DD_discovery_cases-case1
microsatellite, PCR
De novo
NA
Possibly segregated
VDAC1P6,PCDH11Y
xu_16_ASD/DD/ID_discovery_cases-case35
Paternal
SRIP3,GOT2P5,AMELY,ATP5PFP1,GPR143P,TBL1Y
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
nord_11_ASD_discovery_controls-04C27090
0 genes
nord_11_ASD_discovery_controls-04C27265
0 genes
No Animal Model Data Available