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9q21.12CNV Type: Deletion-Duplication


Largest CNV size: 7723 bp

Statistics Box:
Number of Reports: 5


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
Excess of rare, inherited truncating mutations in 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-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion
Genetic Diagnostic Yield in Autism Spectrum Disorder (ASD) and Epilepsy Phenotypes in Children with Genetically Defined ASD
Duplication
Genetic Variant Analyses Identify Novel Candidate Autism Risk Genes from a Highly Consanguineous Cohort of 104 Families from Oman
Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 gupta_25_ASD_discovery_cases
 ASD probands recruited primarily from the clinics in the Genetics and Developmental Medicine departments at Sultan Qaboos University hospitals between 2015 and 2022 in the Muscat and Batinah governates; all participants were Omani nationals, and all parents were negative for autistic traits.
 104
 Cases received a clinical diagnosis of ASD based on DSM-5 criteria.
 
 66.35% Male
 1184
 0
 1
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 145626
 1
 0
 1
 lob_24_ASD_discovery_cases
 Patients with ASD whose electronic medical records (EMRs) were queried from April 1, 2015 through March 31, 2020 and who had at least one genetic testing result documented in their chart; study completed at the Children's Neurodevelopmental Center, Hasbro Children's Hospital, Providence, RI.
 523
 Cases diagnosed with ASD (ICD-10 code F.84), with the majority of diagnoses made using the ADOS-2 followed by CARS.
 Range, 1-18 yrs.
 76.67% Male
 489690
 0
 1
 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
 82631
 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
 7723
 1
 22
 23

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 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)
 82631
 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.
 
 2258
 2
 16
 18

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 gupta_25_ASD_discovery_cases
  Oman
 Genome sequencing
  Illumina HiSeq4000
 
 DRAGEN v.4.2.4, GATK Germline CNV caller
 
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 lob_24_ASD_discovery_cases
  United States
 CMA
 
 
 
 
 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
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, 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
  gupta_25_ASD_discovery_cases-case74
 
 M
 ASD
 Case diagnosed with ASD based on DSM-5 criteria.
 
 71289426
 71290609
  1184
 GRCh38
 Duplication
 No
  krumm_15_ASD_discovery_cases-case13077.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 70535952
 70681578
  145627
 GRCh38
 Deletion
 Yes
  lob_24_ASD_discovery_cases-caseASD275
 
 
 ASD, ADHD, and developmental delay
 Case diagnosed with ASD (ICD-10 code F.84) and also presented with facial asymmetry, global developmental delay, aggression, sensory processing disorder, anxiety, and ADHD.
 
 70198514
 70688203
  489690
 GRCh38
 Duplication
 No
  prasad_12_ASD_discovery_cases-case71182
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
 
 72726673
 72809303
  82631
 Unknown
 Deletion
 No
  sanders_11_ASD_discovery_cases-11025.p1
 4.6
 F
 ASD
 NA
 Full-scale IQ, 98; non-verbal IQ, 102; verbal IQ, 92
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11197.p1
 10.1
 M
 Autism
 NA
 Full-scale IQ, 112; non-verbal IQ, 110; verbal IQ, 110
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11266.p1
 4.3
 F
 Autism
 NA
 Full-scale IQ, 71; non-verbal IQ, 73; verbal IQ, 78
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11267.p1
 13.2
 F
 Autism
 NA
 Full-scale IQ, 85; non-verbal IQ, 91; verbal IQ, 79
 71287232
 71294955
  7724
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11355.p1
 8.8
 M
 ASD
 NA
 Full-scale IQ, 69; non-verbal IQ, 73; verbal IQ, 67
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11561.p1
 5.9
 M
 Autism
 NA
 Full-scale IQ, 109; non-verbal IQ, 103; verbal IQ, 114
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11843.p1
 14.3
 F
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 113; verbal IQ, 117
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-11855.p1
 14.8
 M
 Autism
 NA
 Full-scale IQ, 75; non-verbal IQ, 94; verbal IQ, 48
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12061.p1
 7
 F
 Autism
 NA
 Full-scale IQ, 92; non-verbal IQ, 89; verbal IQ, 101
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12068.p1
 12.5
 M
 Autism
 NA
 Full-scale IQ, 35; non-verbal IQ, 39; verbal IQ, 26
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12154.p1
 4
 M
 Autism
 NA
 Full-scale IQ, 90; non-verbal IQ, 95; verbal IQ, 87
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12215.p1
 4.5
 M
 Autism
 NA
 Full-scale IQ, 108; non-verbal IQ, 113; verbal IQ, 96
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12350.p1
 11.8
 M
 Autism
 NA
 Full-scale IQ, 86; non-verbal IQ, 102; verbal IQ, 61
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12414.p1
 4.4
 M
 ASD
 NA
 Full-scale IQ, 116; non-verbal IQ, 129; verbal IQ, 90
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12445.p1
 10.9
 M
 Autism
 NA
 Full-scale IQ, 104; non-verbal IQ, 111; verbal IQ, 91
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12568.p1
 14.6
 M
 Autism
 NA
 Full-scale IQ, 51; non-verbal IQ, 75; verbal IQ, 26
 71152109
 71154367
  2259
 GRCh38
 Deletion
 No
  sanders_11_ASD_discovery_cases-12613.p1
 12.6
 M
 Autism
 NA
 Full-scale IQ, 77; non-verbal IQ, 78; verbal IQ, 79
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12647.p1
 6.8
 M
 Autism
 NA
 Full-scale IQ, 72; non-verbal IQ, 73; verbal IQ, 81
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12722.p1
 11.6
 M
 Autism
 NA
 Full-scale IQ, 72; non-verbal IQ, 73; verbal IQ, 77
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-12742.p1
 4.8
 M
 ASD
 NA
 Full-scale IQ, 105; non-verbal IQ, 103; verbal IQ, 106
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13010.p1
 7.9
 M
 Autism
 NA
 Full-scale IQ, 115; non-verbal IQ, 122; verbal IQ, 99
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13080.p1
 8.3
 F
 Autism
 NA
 Full-scale IQ, 111; non-verbal IQ, 104; verbal IQ, 121
 71292709
 71294955
  2247
 GRCh38
 Duplication
 No
  sanders_11_ASD_discovery_cases-13153.p1
 9.3
 M
 Autism
 NA
 Full-scale IQ, 75; non-verbal IQ, 86; verbal IQ, 59
 71292709
 71294955
  2247
 GRCh38
 Duplication
 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
  sanders_11_ASD_discovery_controls-11124.s1
  13.3
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11266.s1
  5.8
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11355.s1
  5.4
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11711.s1
  7
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11843.s1
  16.9
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11855.s1
  15.9
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11860.s1
  14.1
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-11981.s1
  8.6
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12061.s1
  8.4
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12154.s1
  9.1
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12175.s1
  6.7
  F
  Control (matched sibling)
  NA
  NA
  71152109
  71154367
  2259
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12568.s1
  15.7
  F
  Control (matched sibling)
  NA
  NA
  71152109
  71154367
  2259
  GRCh38
  Deletion
  No
  sanders_11_ASD_discovery_controls-12613.s1
  12.6
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12722.s1
  6.8
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-12865.s1
  5.8
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13010.s1
  5.8
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13080.s1
  6.8
  F
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No
  sanders_11_ASD_discovery_controls-13153.s1
  11.8
  M
  Control (matched sibling)
  NA
  NA
  71292709
  71294955
  2247
  GRCh38
  Duplication
  No

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 gupta_25_ASD_discovery_cases-case74
 
 
 De novo
 Simplex
 
 TRPM3
 
 krumm_15_ASD_discovery_cases-case13077.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 RN7SL726P,TRPM3
 
 lob_24_ASD_discovery_cases-caseASD275
 
 
 Unknown
 
 
 KLF9,TRPM3,MAMDC2,RPL24P8,SMC5-DT,RN7SL726P,SMC5
 
 prasad_12_ASD_discovery_cases-case71182
 
 
 Unknown
 Unknown
 Unknown
 TRPM3
 
 sanders_11_ASD_discovery_cases-11025.p1
 
 
 Maternal
 Simplex (trio)
 NA
 TRPM3
 
 sanders_11_ASD_discovery_cases-11197.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11266.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11267.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11355.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11561.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11843.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-11855.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12061.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12068.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12154.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12215.p1
 
 
 Paternal
 Simplex (trio)
 NA
 TRPM3
 
 sanders_11_ASD_discovery_cases-12350.p1
 
 
 Maternal
 Simplex (trio)
 NA
 TRPM3
 
 sanders_11_ASD_discovery_cases-12414.p1
 
 
 Paternal
 Simplex (trio)
 NA
 TRPM3
 
 sanders_11_ASD_discovery_cases-12445.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12568.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12613.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12647.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12722.p1
 
 
 Paternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-12742.p1
 
 
 Paternal
 Simplex (trio)
 NA
 TRPM3
 
 sanders_11_ASD_discovery_cases-13010.p1
 
 
 Both parents
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-13080.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 
 sanders_11_ASD_discovery_cases-13153.p1
 
 
 Maternal
 Simplex (quad-proband matched)
 Not segregated
 TRPM3
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
sanders_11_ASD_discovery_controls-11124.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11266.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11355.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11711.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11843.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11855.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11860.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-11981.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12061.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12154.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12175.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12568.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12613.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12722.s1
 
 
  Paternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-12865.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-13010.s1
 
 
  Both parents
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-13080.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 
sanders_11_ASD_discovery_controls-13153.s1
 
 
  Maternal
  Simplex (quad)
  NA
  TRPM3
 

No Animal Model Data Available
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