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Yp11.2CNV Type: Deletion


Largest CNV size: 220000 bp

Statistics Box:
Number of Reports: 8



Summary Information

Summary statement in development

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

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
NA
Duplication
NA
Duplication

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
  NA NA
 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
  NA NA
 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
  NA NA
 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
  NA NA
 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
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