6q13CNV Type: Deletion
Largest CNV size: 50590 bp
Statistics Box:
Number of Reports: 9
Number of Reports: 9
Summary Information
Summary statement in development
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
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion-Duplication
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
Deletion
De novo 11q deletion including SHANK2 in a patient with global developmental delay.
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_discovery_cases
Affected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (362 cases from 311 families; 54 multiplex, 243 simplex) and the Simons Simplex 1 (SSC1) cohort (518 cases from simplex quad families)
880
REACH cohort: 285 cases diagnosed with ASD, 43 cases diagnosed with PDD-NOS, 10 cases diagnosed with ADHD, and 24 cases presenting with speech delay, epilepsy, anxiety, or other related developmental disorders that were classified as cases for bioinformatics analyses; Simons Simplex Collection 1 (SSC1) cohort: all 518 cases were diagnosed with ASD
N/A
N/A
7650
1
0
1
engchuan_15_ASD_discovery_cases
Samples from the Autism Genome Project (AGP)
1892
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
N/A
85.78% Male
245236
2
1
3
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
1451942
2
0
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
9512
0
1
1
marcou_17_DD/ID_discovery_cases
Third child born to parents with unremarkable family history presenting with a de novo 11q13.2-q13.4 deletion that included the SHANK2 gene
1
Case presented with global developmental delay, intellectual disability, microcephaly, and dysmorphic features
12 yrs.
Female
118775
0
1
1
mosca_16_DCD_discovery_cases
Participants recruited as part of a multidisciplinary study at the Alberta Children's Hospital (Calgary, Alberta, Canada)
82
All cases met diagnostic criteria for developmental coordination disorder (DCD) with or without co-occurring ADHD and/or reading disorder.
Range, 8-17 years (Mean, 10.06 2.92 yrs.)
N/A
23529
1
0
1
poultney_13_ASD_discovery_cases
ASD cases of European ancestry from AGRE retained after filtering (original cohort size of 432 cases)
299
Cases diagnosed with ASD
N/A
79.86% Male (before filtering)
18169
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
520944
1
0
1
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
50590
3
0
3
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_controls
Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)
2342
Controls; subjects had no previous psychiatric history
N/A
46.67% Male
605468
0
7
7
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
kanduri_15_ASD_discovery_controls
Unrelated Finnish samples from the cohort of Health 2000 survey from an initial sample of 288 individuals following quality control
269
Controls screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
N/A
N/A
17210
1
0
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
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.
15346
1
0
1
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)
178240
0
5
5
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)
520944
0
0
0
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
14214
1
0
1
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_discovery_cases
N/A
WGS
Illumina HiSeq X10 or HiSeq 2500
ForestSV, Lumpy, Manta, Mobster, SV2
PCR, array SNP
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
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
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
marcou_17_DD/ID_discovery_cases
N/A
Array SNP
Affymetrix Cytoscan HD
None
mosca_16_DCD_discovery_cases
Canada
Solid phase hybridization
Illumina HumanOmni2.5-Quad BeadChip
iPattern, PennCNV, QuantiSNP, CNVPartition
None
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
sanders_11_ASD_discovery_cases
White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
Solid phase hybridization
Illumina 1M v1, Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
kanduri_15_ASD_discovery_controls
Finnish
Solid phase hybridization
Illumina Infinium HD Human610-Quad BeadChip
QuantiSNP, PennCNV
Illumina BeadStudio
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
poultney_13_ASD_discovery_controls
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
brandler_18_ASD_discovery_cases-caseSSC11860
N/A
M
ASD
Case from SSC cohort
73390854
73398504
7651
GRCh38
Deletion
Yes
engchuan_15_ASD_discovery_cases-case20028_1134001
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
70695233
70940469
245237
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case3454_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
74336360
74399693
63334
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4258_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
73591913
73705353
113441
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001043
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
73479920
74931870
1451951
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001802
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
71961903
72268687
306785
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case11331.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
73756642
73766154
9513
GRCh38
Duplication
Yes
marcou_17_DD/ID_discovery_cases-case1
12 yrs.
F
Global developmental delay/intellectual disability
Birth/neonatal history: born to a 36-year-old, gravida three, para three mother via natural conception; pregnancy not complicated by maternal illness or exposure to known teratogens, although the mother did take birth control pills during the first trimester and an antidepressant medication throughout gestation; birth at 36-1/2 weeks gestation via spontaneous vaginal delivery; birth weight of 2814 g (5th %ile), length of 45.08 cm (5th %ile), and head circumference of 32 cm (25th %ile); postnatal complications included need for oxygen and resuscitation for first 5 minutes of life; no additional postnatal complications observed prior to release from hospital; normal newborn screening; weak cry and weak suck as an infant, resulting in feeding difficulties and failure to thrive (weight <5th %ile); microcephaly (head circumference fell from 25th %ile to <5th %ile), hypotonia, and global developmental delay noted at this time. Developmental milestones: global developmental delay; rolling from front to back at 7 months, unassisted sitting between 9-11 months, crawling at 1 year, began pulling to stand at 14 months, independent walking at 22 months, climbing stairs between 4-5 years; did not use words until 3-4 years, did not speak in complete sentences until 8 years; no developmental regression. Lanaguge and communication evaluation: severe language delay, receives speech therapy twice a week. Motor and musculoskeletal evaluation: hypotonia; hypermobility in the small joints of the hand, mild pectus excavatum, evidence of scoliosis, arachnodactyly, long and thin feet, long and slender figners, clinodactyly of both fifth fingers, mild pes planus, piezogenic apules. EEG: normal. Brain imaging: normal brain MRI. Dysmorphic features: microcephaly, mild dolichocephaly, mild malar hypoplasia, mild retrognathia, fine hair, posterior hair whorl, prominent forehead, bilateral epicanthal folds, long palpebral fissures, deep-set eyes, low-set ears, petite ears, long ears with over-folding of the superior helix and with no tags or pits, broad nasal tip, depressed nasal bridge, small mouth, slight downturned corners of the mouth, widely spaced teeth. Growth parameters: height of 148.3 cm (19th %ile), weight of 36.1 kg (15th %ile), and head circumference of 50 cm (<3rd %ile) at 12 years. Family history: third child of parents; family history on both the maternal and paternal side is unremarkable with no documentation of any congenital anomalies or developmental delay; 48-year-old mother, 51-year-old father, and 23-year-old sister are healthy, 28-year-old brother was treated for testicular cancer at 21 years of age and a recurrence at 26 years of age.
Moderate-severe intellectual disability; case currently in 6th grade but performs work at 1st grade level.
73593217
73711991
118775
GRCh38
Duplication
No
mosca_16_DCD_discovery_cases-case127604
N/A
F
DCD (with or without ADHD and/or RD)
Ancestry: unknown. Family history: maternal diagnosis unknown; paternal diagnosis unknown.
69535898
69559426
23529
GRCh38
Deletion
No
poultney_13_ASD_discovery_cases-case00HI1274A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU066104; NDAR ID NDAR_INVVV950VBW)
73479730
73497898
18169
GRCh38
Deletion
No
prasad_12_ASD_discovery_cases-case119974L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
73425268
73946211
520944
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11289.p1
6
M
Autism
NA
Full-scale IQ, 82; non-verbal IQ, 98; verbal IQ, 62
74939852
74990442
50591
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12003.p1
4.3
M
ASD
NA
Full-scale IQ, 115; non-verbal IQ, 120; verbal IQ, 103
69536309
69554719
18411
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12624.p1
7.3
M
Autism
NA
Full-scale IQ, 36; non-verbal IQ, 47; verbal IQ, 27
70908465
70922679
14215
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
engchuan_15_ASD_discovery_controls-controlB116679_1007853952
N/A
N/A
Control
No previous psychiatric history
71186742
71269626
82885
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB350610_1007873740
N/A
N/A
Control
No previous psychiatric history
74653517
74705493
51977
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlB764926_1007854164
N/A
N/A
Control
No previous psychiatric history
74657556
74705493
47938
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900106_900106
N/A
N/A
Control
No previous psychiatric history
74648642
74696917
48276
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900258_900258
N/A
N/A
Control
No previous psychiatric history
71179168
71231638
52471
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900578_900578
N/A
N/A
Control
No previous psychiatric history
69447099
69523816
76718
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_900623_900623
N/A
N/A
Control
No previous psychiatric history
70250307
70855775
605469
GRCh38
Duplication
No
kanduri_15_ASD_discovery_controls-control_split2019
N/A
N/A
Control
Control screened for DSM-IV mental disorders using the Composite International Diagnostic Interview and psychotic disorders using the research version of the Structured Clinical Interview for DSM-IV
75077150
75094359
17210
Unknown
Deletion
No
nord_11_ASD_discovery_controls-04C28417
Control
72011581
72026926
15346
Unknown
Deletion
poultney_13_ASD_discovery_controls-control04C31170A
N/A
F
Control
NIMH Control (NIMH ID 59702)
73595075
73697574
102500
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C31170A
N/A
F
Control
NIMH Control (NIMH ID 59702)
73461853
73492354
30502
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control04C38268A
N/A
M
Control
NIMH Control (NIMH ID 16691)
73756641
73766156
9516
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C45305
N/A
F
Control
NIMH Control (NIMH ID 26586)
73519335
73697574
178240
GRCh38
Duplication
No
poultney_13_ASD_discovery_controls-control05C45305
N/A
F
Control
NIMH Control (NIMH ID 26586)
73461853
73492354
30502
GRCh38
Duplication
No
sanders_11_ASD_discovery_controls-12624.s1
4.1
F
Control (matched sibling)
NA
NA
70908465
70922679
14215
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_cases-caseSSC11860
SNP VCF
De novo
RPS6P8,OOEP,DDX43
engchuan_15_ASD_discovery_cases-case20028_1134001
Unknown
NDUFAB1P1,SMAP1,B3GAT2
engchuan_15_ASD_discovery_cases-case3454_3
Unknown
engchuan_15_ASD_discovery_cases-case4258_1
Unknown
RPS27P15,SLC17A5,CD109
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001043
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SL827P,EEF1A1,RPS27P15,TXNP7,MTO1,SLC17A5,CD109
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001802
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RIMS1
krumm_15_ASD_discovery_cases-case11331.p1
Illumina 1M
Paternal
Simplex
Segregated
CD109
marcou_17_DD/ID_discovery_cases-case1
Unknown
Simplex
Unknown
RPS27P15,SLC17A5,CD109
mosca_16_DCD_discovery_cases-case127604
Unknown
Unknown
Unknown
poultney_13_ASD_discovery_cases-case00HI1274A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
RN7SL827P,MTO1
prasad_12_ASD_discovery_cases-case119974L
Unknown
Unknown
Unknown
KCNQ5,MIR4282
sanders_11_ASD_discovery_cases-11289.p1
Paternal
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12003.p1
Paternal
Simplex (trio)
NA
sanders_11_ASD_discovery_cases-12624.p1
Maternal
Simplex (quad-proband matched)
Not segregated
B3GAT2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB116679_1007853952
Unknown
engchuan_15_ASD_discovery_controls-controlB350610_1007873740
Unknown
engchuan_15_ASD_discovery_controls-controlB764926_1007854164
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900106_900106
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900258_900258
Unknown
RNU6-411P
engchuan_15_ASD_discovery_controls-controlHABC_900578_900578
Unknown
engchuan_15_ASD_discovery_controls-controlHABC_900623_900623
Unknown
RNU7-48P,NDUFAB1P1,SDHAF4,SLC25A6P6,FAM135A,SMAP1,COL9A1
kanduri_15_ASD_discovery_controls-control_split2019
Unknown
Intergenic CNV: nearest genes, CD109(dist=539109),COL12A1(dist=699683)
nord_11_ASD_discovery_controls-04C28417
0 genes
poultney_13_ASD_discovery_controls-control04C31170A
Unknown
RPS27P15,SLC17A5,CD109
poultney_13_ASD_discovery_controls-control04C31170A
Unknown
RNU6-975P,RN7SL827P,MTO1
poultney_13_ASD_discovery_controls-control04C38268A
Unknown
CD109
poultney_13_ASD_discovery_controls-control05C45305
Unknown
EEF1A1,RPS27P15,SLC17A5,CD109
poultney_13_ASD_discovery_controls-control05C45305
Unknown
RNU6-975P,RN7SL827P,MTO1
sanders_11_ASD_discovery_controls-12624.s1
Maternal
Simplex (quad)
NA
B3GAT2
No Animal Model Data Available