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12q24.13CNV Type: Deletion


Largest CNV size: 32936 bp

Statistics Box:
Number of Reports: 7



Summary Information

Summary statement in development

Additional Locus Information

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USCS Symbol             NCBI Symbol

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            Decipher Symbol

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...
Duplication
Excess of rare, inherited truncating mutations in autism.
Duplication
Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder
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
Global increases in both common and rare copy number load associated with autism.
Duplication
Transmission disequilibrium of small CNVs in simplex autism.
Duplication
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 girirajan_13b_ASD_discovery_cases
 Children with autism ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (274 initial cases)
 243
 Diagnosis of autism confirmed by ADOS and ADI-R. Exclusion criteria: children with developmental delay but lacking symptoms and autism, as well as children with ASD as defined by the CHARGE protocol
 N/A
 N/A
 302210
 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
 415436
 0
 2
 2
 krumm_13_ASD_discovery_cases
 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
 Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
 N/A
 81.265% Male
 107437
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 121560
 0
 1
 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)
 19497
 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
 32936
 9
 0
 9
 schmitz-abe_20_ASD_discovery_cases
 ASD probands rom 187 families from the Homozygosity Mapping Collaborative of Autism (HMCA); 22% of families had more than one affected child, and 66% of families were consanguineous.
 255
 Diagnosis of autism or ASD made by a neurologist, child psychiatrist, or psychologist; DSM-IV-R criteria confirmed in all individuals with an Autism diagnosis
 N/A
 N/A
 5601
 2
 0
 2

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 brandler_18_ASD_discovery_controls
 Unaffected individuals from the Relating Genes with Adolescent and Child Health (REACH) cohort (112 individuals from 311 families) and the Simons Simplex 1 (SSC1) cohort (518 controls from simplex quad families)
 630
 Control
 N/A
 N/A
 7268
 1
 0
 1
 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
 297834
 0
 2
 2
 girirajan_13b_ASD_discovery_controls
 Controls ascertained from the Childhood Autism Risks from Genetics and Environment (CHARGE) study conducted through the Medical Investigation of Neurodevelopmental Disorders (MIND) Institute at UC-Davis after passing QC criteria (242 initial controls)
 223
 Control
 N/A
 N/A
 0
 0
 0
 0
 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
 0
 0
 0
 0
 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
 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)
 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.
 
 32936
 3
 0
 3

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 girirajan_13b_ASD_discovery_cases
  133 European, 57 Hispanic, 27 Mixed Race, 20 Asian, 6 African-American
 aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
 DNA Copy Number v1.6
 
 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_13_ASD_discovery_cases
  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_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 poultney_13_ASD_discovery_cases
  European
 WES
  Agilent SureSelect Human All Exon v.2
 XHMM
 
 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
 
 
 schmitz-abe_20_ASD_discovery_cases
  Middle Eastern
 Array SNP
  Affymetrix 6.0, Affymetrix 500K
 
 
 qPCR

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  brandler_18_ASD_discovery_controls
  N/A
  WGS
  Illumina HiSeq X10 or HiSeq 2500
  ForestSV, Lumpy, Manta, Mobster, SV2
 
  None
  engchuan_15_ASD_discovery_controls
  Caucasian
  Solid phase hybridization
  Illumina 1M
 
 
  None
  girirajan_13b_ASD_discovery_controls
  116 European, 70 Hispanic, 27 Mixed Race, 7 Asian, 3 African-American
  aCGH
  Roche NimbleGen custom targeted hotspot array comprised of 135,000 probes with higher density probe coverage in genomic hotspots (regions flanked by segmental duplications)
  DNA Copy Number v1.6
 
 
  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
 
  None
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
 
  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
  girirajan_13b_ASD_discovery_cases-28504101060
 N/A
 N/A
 Autism
 Diagnosis of autism confirmed by ADOS and ADI-R. Ethnicity: Hispanic
 N/A
 113807584
 114109794
  302211
 GRCh38
 Duplication
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001722
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 112307532
 112722967
  415436
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002120
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 112303430
 112676526
  373097
 GRCh38
 Duplication
 Yes
  krumm_13_ASD_discovery_cases-case13322.p1
 N/A
 M
 ASD
 ASD proband from SSC quad family 13322. SRS score of 77.
 Full-scale IQ (FSIQ) score of 59.
 113858790
 113966227
  107438
 GRCh38
 Duplication
 No (not tested)
  krumm_15_ASD_discovery_cases-case13322.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 113844667
 113966227
  121561
 GRCh38
 Duplication
 Yes
  poultney_13_ASD_discovery_cases-case99HI0694B
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU038203; NDAR ID NDAR_INVXX733FLA)
 
 113268740
 113288236
  19497
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11216.p1
 4.7
 M
 ASD
 NA
 Full-scale IQ, 77; non-verbal IQ, 97; verbal IQ, 57
 113213463
 113232741
  19279
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11447.p1
 6.6
 M
 Autism
 NA
 Full-scale IQ, 89; non-verbal IQ, 97; verbal IQ, 82
 113410729
 113434639
  23911
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-11918.p1
 9.8
 F
 Autism
 NA
 Full-scale IQ, 48; non-verbal IQ, 59; verbal IQ, 39
 113130992
 113150326
  19335
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12219.p1
 7.2
 M
 Autism
 NA
 Full-scale IQ, 121; non-verbal IQ, 110; verbal IQ, 136
 113231058
 113263994
  32937
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12582.p1
 6.3
 M
 Autism
 NA
 Full-scale IQ, 57; non-verbal IQ, 73; verbal IQ, 45
 113134361
 113156910
  22550
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12596.p1
 4.9
 M
 Autism
 NA
 Full-scale IQ, 61; non-verbal IQ, 89; verbal IQ, 32
 113134361
 113158204
  23844
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12597.p1
 6.4
 M
 Autism
 NA
 Full-scale IQ, 70; non-verbal IQ, 77; verbal IQ, 66
 113130992
 113158204
  27213
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12941.p1
 4.5
 M
 Autism
 NA
 Full-scale IQ, 92; non-verbal IQ, 93; verbal IQ, 96
 113134361
 113156910
  22550
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-13056.p1
 4.6
 M
 Autism
 NA
 Full-scale IQ, 64; non-verbal IQ, 65; verbal IQ, 58
 113134361
 113136469
  2109
 GRCh38
 Deletion
 No
  schmitz-abe_20_ASD_discovery_cases-caseAU-19601
 N/A
 M
 ASD
 Proband born to non-consanguineous parents of Middle Eastern descent from the HMCA cohort. Homozygous deletion segregated with ASD in this family.
 
 111995070
 112000670
  5601
 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
  brandler_18_ASD_discovery_controls-controlSSC00082
  N/A
  F
  Control
  Control from SSC_phase1 cohort
 
  112478880
  112486148
  7269
  GRCh38
  Deletion
  No
  engchuan_15_ASD_discovery_controls-controlB475222_1007872252
  N/A
  N/A
  Control
  No previous psychiatric history
 
  113823248
  114121082
  297835
  GRCh38
  Duplication
  No
  engchuan_15_ASD_discovery_controls-controlB884573_1007852580
  N/A
  N/A
  Control
  No previous psychiatric history
 
  111902039
  112039251
  137213
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11216.s1
  6.4
  M
  Control (matched sibling)
  NA
  NA
  113213463
  113231058
  17596
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12219.s1
  11.4
  F
  Control (matched sibling)
  NA
  NA
  113231058
  113263994
  32937
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12798.s1
  8.1
  F
  Control (matched sibling)
  NA
  NA
  113134361
  113159115
  24755
  GRCh38
  Deletion
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 girirajan_13b_ASD_discovery_cases-28504101060
 
 
 Unknown
 Unknown
 Unknown
 GLULP5,HAUS8P1,RBM19
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00001722
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Paternal
 Unknown
 Unknown
 MIR1302-1,RPL6,PTPN11,RPH3A,HECTD4
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002120
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 RPL6,PTPN11,RPH3A,HECTD4
 
 krumm_13_ASD_discovery_cases-case13322.p1
 
 
 Maternal
 Simplex
 Segregated
 RBM19
 
 krumm_15_ASD_discovery_cases-case13322.p1
 Illumina 1MDuo
 
 Maternal
 Simplex
 Segregated
 RBM19
 
 poultney_13_ASD_discovery_cases-case99HI0694B
 
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 TPCN1
 
 sanders_11_ASD_discovery_cases-11216.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 IQCD,TPCN1
 
 sanders_11_ASD_discovery_cases-11447.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Segregated
 SDS,SDSL
 
 sanders_11_ASD_discovery_cases-11918.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 CFAP73,RASAL1
 
 sanders_11_ASD_discovery_cases-12219.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TPCN1
 
 sanders_11_ASD_discovery_cases-12582.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 CFAP73,RASAL1
 
 sanders_11_ASD_discovery_cases-12596.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 CFAP73,DDX54,RASAL1
 
 sanders_11_ASD_discovery_cases-12597.p1
 
 
 Unknown
 Simplex (quad-proband matched)
 Not segregated
 CFAP73,DDX54,RASAL1
 
 sanders_11_ASD_discovery_cases-12941.p1
 
 
 Maternal
 Simplex (trio)
 NA
 CFAP73,RASAL1
 
 sanders_11_ASD_discovery_cases-13056.p1
 
 
 Maternal
 Simplex (trio)
 NA
 RASAL1
 
 schmitz-abe_20_ASD_discovery_cases-caseAU-19601
 qPCR
 
 Both parents
 Simplex
 Segregated
 TMEM116
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC00082
  Not available
 
  Maternal
 
 
  PTPN11
 
engchuan_15_ASD_discovery_controls-controlB475222_1007872252
 
 
  Unknown
 
 
  GLULP5,HAUS8P1,RBM19
 
engchuan_15_ASD_discovery_controls-controlB884573_1007852580
 
 
  Unknown
 
 
  ADAM1B,SLC25A3P2,MIR3657,MAPKAPK5,ERP29,TMEM116,NAA25
 
sanders_11_ASD_discovery_controls-11216.s1
 
 
  Maternal
  Simplex (quad)
  NA
  IQCD,TPCN1
 
sanders_11_ASD_discovery_controls-12219.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TPCN1
 
sanders_11_ASD_discovery_controls-12798.s1
 
 
  Unknown
  Simplex (quad)
  NA
  CFAP73,MIR7106,DDX54,RASAL1
 

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