11q13.1CNV Type: Deletion
Largest CNV size: 13709 bp
Statistics Box:
Number of Reports: 12
Number of Reports: 12
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
A de novo 0.57 Mb microdeletion in chromosome 11q13.1 in a patient with speech problems, autistic traits, dysmorphic features and multiple endocrin...
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
A de novo 921Kb microdeletion at 11q13.1 including neurexin 2 in a boy with developmental delay, deficits in speech and language without autistic ...
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Deletion
The Role of mGluR Copy Number Variation in Genetic and Environmental Forms of Syndromic Autism Spectrum Disorder.
Deletion
Paternally inherited cis-regulatory structural variants are associated with autism.
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
79349
0
1
1
celestino-soper_11_ASD_discovery_cases
ASD probands from Simons Simplex Collection (SSC) trios. 90 of the probands in this study were also used in the Sanders et al. 2011 CNV report.
99
ASD
87.88% Male
2250
2
0
2
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
176540
1
0
1
han_22_ASD/DD/ID_discovery_cases
Probands with ASD or unexplained developmental delay/intellectual disability with or without other congenital anomalies from Shandong province in Northern China who were referred for genetic services from January 2014 to December 2018.
410
151 cases diagnosed with ASD (DSM-5 criteria, ADOS-2, confirmed by CARS score > 30) and 259 patients diagnosed with developmental delay/intellectual disability (DSM-5 criteria, confirmed by Gesell developmental scale DQ score < 75 and Wechsler Intelligence Scale for Children-Revised with IQ<70).
Mean age, 2 yrs. 11 mos.
68.78% Male
68367
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
239885
0
2
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
4267
1
1
2
mohrmann_11_DD_discovery_cases
21-year-old patient with speech problems, autistic traits, and additional anomalies; first-born to healthy unrelated parents with no family history of developmental delay or congenital anomalies.
1
Developmental delay. Case presented with speech problems, autistic traits (no formal diagnosis of autism/ASD), dysmorphic features, and multiple endocrine neoplasia type 1.
21 yrs.
Male
579260
1
0
1
nord_11_ASD_discovery_cases
Youth with ASD (as part of mother-father-child trios)
41
ASD
85.4% Male
343505
1
0
1
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
54318
0
1
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
13709
4
0
4
wenger_16_ASD_discovery_cases
ASD cases with CNVs containing genes involved in the mGluR network from an initial cohort of 539 cases
62
ASD
N/A
N/A
120810
1
0
1
yuan_18_DD_discovery_cases
Third child of healthy unrelated parents with unremarkable family history presenting with a de novo deletion encompassing the NRXN2 gene
1
Case presented with developmental delay, absent speech, short stature, failure to thrive, mild anxiety, and dysmorphic features; case did not present with autistic features, and evaluation with Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS), and Modified Checklist for Autism in Toddlers Revised (M-CHAT-R) did not support a diagnosis of ASD.
2 years 9 months
Male
921000
1
0
1
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
71853
0
1
1
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
krumm_13_ASD_discovery_controls
Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
46.47% Male
179
0
1
1
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
4526
1
0
1
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.
0
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.
10528
2
0
2
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
None
celestino-soper_11_ASD_discovery_cases
aCGH
Agilent 1M
ADM-2
Agilent Feature Extraction v10.7.3.1, Agilent DNA Analytics v4.0.76
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
han_22_ASD/DD/ID_discovery_cases
Han Chinese
Array SNP
Affymetrix SNP 6.0, Affymetrix CytoScan HD
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)
mohrmann_11_DD_discovery_cases
Caucasian
aCGH
Agilent 105A
Feature Extraction v9.5.3, CGH Analytics v3.5.14
FISH
nord_11_ASD_discovery_cases
29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
None (not tested or failure to confirm by qPCR)
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
wenger_16_ASD_discovery_cases
N/A
Solid phase hybridization
Illumina HumanHap 550 or Illumina Human610-Quad v1.0
PennCNV
None
yuan_18_DD_discovery_cases
Chinese
Array SNP
Affymetrix CytoScan 750K
Affymetrix ChAS
WES
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
krumm_13_ASD_discovery_controls
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
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-caseREACH000635
N/A
M
PDD-NOS
Case from REACH cohort
64053205
64132554
79350
GRCh38
Duplication
No (false positive)
celestino-soper_11_ASD_discovery_cases-11455
NA
M
ASD
NA
NA
65084125
65086375
2251
GRCh38
Deletion
No
celestino-soper_11_ASD_discovery_cases-11455
NA
M
ASD
NA
NA
64299544
64300448
905
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case4511_1
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
67074998
67251538
176541
GRCh38
Deletion
No
han_22_ASD/DD/ID_discovery_cases-caseY58
2 yrs. 3 mos.
F
ASD and intellectual disability
Intellectual disability
65226708
65295074
68367
GRCh38
Duplication
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002692
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
67016543
67256428
239886
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003778
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
65881597
65893890
12294
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case11916.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
65014207
65018474
4268
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case12299.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
65018363
65021855
3493
GRCh38
Duplication
Yes
mohrmann_11_DD_discovery_cases-case1
21 yrs.
M
Developmental delay
Birth/neonatal history: unremarkable pregnancy; normal birth measurements; Apgar scores of 7/8/8; temporary episode of bradyarrhythmia noted after birth. Developmental milestones: delayed psychomotor development noted at 2 yrs (walked unsupported at 18 months); speech delay (spoke only several words at 4 yrs.); delay in comprehension of spoken language. Behavioral/psychiatric characteristics: autistic traits (aggression following changes in routine); no formal diagnosis of autism/ASD. Other health concerns: development of Zollinger-Ellison syndrome caused by gastrinoma of pancreas at 18 years; fusiform aneurysm of aortic arch that did not require treatment noted at 10 years; abdominal CT scan showed horseshoe kidney. Dysmorphic features: broad nasal base, slight synophrys, retrognathia, multiple naevi distributed all over body, digital abnormalities (broad thumb with short distal phalanx & short middle phalanx of 5th finger at left hand). Growth parameters: height, 170 cm (-1.1 SD); weight, 77 kg (+1 SD); head circumference, 55.5 cm (-0.6 SD); all within normal range. Family history: case was born to healthy, unrelated parents and has 19-yr-old normally-developing sister; no family history of developmental delay, congenital anomalies, or miscarriages.
Nonverbal IQ (as measured by culture fair test at 13 yrs.): 113
64591193
65160454
569262
GRCh38
Deletion
Yes
nord_11_ASD_discovery_cases-256-1
ASD
64914514
65258018
343505
Unknown
Deletion
No
sajan_13_ACC/CBLH/PMG_discovery_cases-case1641-0
N/A
N/A
PMG
Diagnosis of polymicrogyria (PMG).
64004528
64058845
54318
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11363.p1
5.9
F
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 78; verbal IQ 77
65026266
65039975
13710
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11860.p1
6
M
Autism
NA
Full-scale IQ, 86; non-verbal IQ, 95; verbal IQ, 75
64915478
64926132
10655
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11986.p1
10.5
M
Autism
NA
Full-scale IQ, 109; non-verbal IQ, 101; verbal IQ, 123
65639939
65650803
10865
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12454.p1
5.5
M
Autism
NA
Full-scale IQ, 72; non-verbal IQ, 82; verbal IQ, 62
67352625
67357752
5128
GRCh38
Deletion
No
wenger_16_ASD_discovery_cases-case35
N/A
N/A
ASD
Prior clinical diagnosis of genetic syndrome: n/a
64139607
64260416
120810
GRCh38
Deletion
No
yuan_18_DD_discovery_cases-case1
2 yrs. 9 mos.
M
Developmental delay
Birth/neonatal history: mother treated with progesterone while pregnany due to signs of spontaneous abortion; delivered at 38 weeks gestation by normal delivery; birth weight of 3000 g (-1 SD) and length of 50 cm (-0.8 SD); Apgar scores 9; no feeding problems noted; referred to clinic at 9 months due to difficulty gaining weight and global developmental delay. Developmental milestones: delayed milestones (raised head at 4 months, sat alone at 10 months, could not independently stand, no language development. Language and communication evaluation: absent speech (no language development at 2 years 9 months). Motor and musculoskeletal evaluation: delayed closure of cranial fontanelles and sutures; able to walk without assistance with unsteady gait and frequent falls. Behavioral/psychiatric evaluation: mild-anxiety like behavior in the open field; no autistic features (good eye contact, showed signs of empathy, no repetitive or stereotyped behavior); evaluation with Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS), and Modified Checklist for Autism in Toddlers Revised (M-CHAT-R) did not support a diagnosis of ASD. Brain imaging: normal brain MRI. Additional medical history: nocturnal urine and fecal incontinence; reduced levels of IGF1 and IGFBP3. Dysmorphic features: protruding forehead, flat facial profile, low-set ears, ptosis, broad nose with anteverted nares, downturned corners of the mouth, teeth dysplasia, retrognathia. Growth parameters: short stature, failure to thrive; weight of 11.2 kg (< -2 SD), height of 88.0 cm (-2 SD), and head circumference of 46.4 cm (< -2 SD). Family history: third child of healthy unrelated parents (both sisters were healthy); unremarkable family history.
Appeared to have normal cognitive competence
64354519
65275167
920649
GRCh38
Deletion
Yes
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-controlHABC_902862_902862
N/A
N/A
Control
No previous psychiatric history
64363404
64435257
71854
GRCh38
Duplication
No
krumm_13_ASD_discovery_controls-control14110.s1
N/A
F
Control
Unaffected sibling from SSC quad family 14110. SRS score of 39.
64801578
64801757
180
GRCh38
Duplication
No (not tested)
krumm_15_ASD_discovery_controls-control11916.s1
N/A
Female
Control
Unaffected sibling from the Simons Simplex Collection (SSC)
65014207
65018733
4527
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_controls-11330.s1
11.8
F
Control (matched sibling)
NA
NA
65504361
65510990
6630
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11445.s1
9.5
F
Control (matched sibling)
NA
NA
67141279
67151807
10529
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-caseREACH000635
SNP VCF
Unknown
FLRT1,MACROD1
celestino-soper_11_ASD_discovery_cases-11455
Unknown
Simplex
NA
ZFPL1,TMEM262,CDCA5
celestino-soper_11_ASD_discovery_cases-11455
Unknown
Simplex
NA
KCNK4,KCNK4-TEX40,CATSPERZ
engchuan_15_ASD_discovery_cases-case4511_1
Unknown
KDM2A
han_22_ASD/DD/ID_discovery_cases-caseY58
Unknown
SLC22A20P,POLA2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002692
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
MIR6860,SYT12,RHOD,KDM2A
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00003778
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
FIBP,CCDC85B,CTSW,FOSL1
krumm_15_ASD_discovery_cases-case11916.p1
Illumina 1MDuo
Paternal
Simplex
Not segregated (CNV in unaffected sibling)
ARL2,ARL2-SNX15
krumm_15_ASD_discovery_cases-case12299.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
ARL2,MIR6879,ARL2-SNX15
mohrmann_11_DD_discovery_cases-case1
FISH
De novo
Simplex
Likely segregated
MEN1,MIR194-2HG,MIR192,MIR194-2,MIR6750,MIR6749,GPHA2,ARL2,MIR6879,NAALADL1,ZFPL1,TMEM262,TM7SF2,ZNHIT2,FAU,MIR6751,HIGD1AP10,RNU2-23P,PDCL2P2,SLC22A12,RASGRP2,SF1,MAP4K2,CDC42BPG,ATG2A,PPP2R5B,MAJIN,BATF2,ARL2-SNX15,SNX15,SAC3D1,CDCA5,VPS51,SYVN1,MRPL49,NRXN2,PYGM,EHD1
nord_11_ASD_discovery_cases-256-1
Paternal
EHBP1L1,FAM89B,KAT5,KCNK7,LTBP3,MALAT1,MAP3K11,NEAT1,PCNXL3,RELA,RNASEH2C,SCYL1,SIPA1,SSSCA1,FRMD8
sajan_13_ACC/CBLH/PMG_discovery_cases-case1641-0
qPCR (CNV not detected)
Bi-parental
Unknown
Unknown
MACROD1
sanders_11_ASD_discovery_cases-11363.p1
Unknown
Simplex (trio)
NA
ARL2-SNX15,SNX15
sanders_11_ASD_discovery_cases-11860.p1
Unknown
Simplex (quad-proband matched)
Segregated
ATG2A,PPP2R5B
sanders_11_ASD_discovery_cases-11986.p1
Both parents
Simplex (quad-proband matched)
Segregated
MIR4489,SIPA1
sanders_11_ASD_discovery_cases-12454.p1
Paternal
Simplex (trio)
NA
POLD4,RAD9A
wenger_16_ASD_discovery_cases-case35
Unknown
NUDT22,DNAJC4,VEGFB,PPP1R14B,STIP1,FERMT3,FKBP2,PLCB3,MACROD1,TRPT1
yuan_18_DD_discovery_cases-case1
WES
De novo
Simplex
Segregated
RPS6KA4,MIR1237,MEN1,MIR194-2HG,MIR192,MIR194-2,MIR6750,MIR6749,GPHA2,ARL2,MIR6879,NAALADL1,ZFPL1,TMEM262,TM7SF2,ZNHIT2,FAU,MIR6751,HIGD1AP10,RNU2-23P,PDCL2P2,SPDYC,SLC22A11,SLC22A12,RASGRP2,SF1,MAP4K2,CDC42BPG,ATG2A,PPP2R5B,MAJIN,BATF2,ARL2-SNX15,SNX15,SAC3D1,CDCA5,VPS51,SYVN1,MRPL49,PGAM1P8,CAPN1,SLC22A20P,CCDC88B,NRXN2,PYGM,EHD1,POLA2
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_902862_902862
Unknown
RPS6KA4,MIR1237
krumm_13_ASD_discovery_controls-control14110.s1
Paternal
Simplex
MAP4K2
krumm_15_ASD_discovery_controls-control11916.s1
Illumina 1MDuo
Paternal
ARL2,MIR6879,ARL2-SNX15
sanders_11_ASD_discovery_controls-11330.s1
Maternal
Simplex (quad)
NA
MALAT1
sanders_11_ASD_discovery_controls-11445.s1
Maternal
Simplex (quad)
NA
KDM2A
No Animal Model Data Available