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3p21.2CNV Type: Deletion


Largest CNV size: 3152 bp

Statistics Box:
Number of Reports: 3



Summary Information

A deletion within this region affecting the ABHD14A gene was identified in a female ASD case from AGRE (Poultney et al., 2013).

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
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Deletion
Excess of rare, inherited truncating mutations in autism.
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion

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
 17389
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 608507
 0
 2
 2
 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)
 3152
 1
 0
 1

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
 17389
 1
 0
 1
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 63081
 0
 1
 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)
 0
 0
 0
 0

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
 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
 
 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
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
  poultney_13_ASD_discovery_controls
  European
  WES
  Agilent SureSelect Human All Exon v.2
  XHMM
 
 

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-caseSSC11525
 N/A
 M
 ASD
 Case from SSC_phase1 cohort
 
 51347212
 51364601
  17390
 GRCh38
 Deletion
 No
  krumm_15_ASD_discovery_cases-case12208.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 51633576
 51635789
  2214
 GRCh38
 Duplication
 Yes
  krumm_15_ASD_discovery_cases-case12215.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Trio
 
 158460934
 159069441
  608508
 GRCh38
 Duplication
 Yes
  poultney_13_ASD_discovery_cases-case98HI0029B
 N/A
 F
 ASD
 ASD case from AGRE (AGRE ID AU012104; NDAR ID NDAR_INVNC573ATM)
 
 51977869
 51981020
  3152
 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-controlSSC11537
  N/A
  M
  Control
  Control from SSC_phase1 cohort
 
  51347212
  51364601
  17390
  GRCh38
  Deletion
  No
  krumm_15_ASD_discovery_controls-control11172.s1
  N/A
  Female
  Control
  Unaffected sibling from the Simons Simplex Collection (SSC)
 
  50778666
  50841747
  63082
  GRCh38
  Duplication
  Yes

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 brandler_18_ASD_discovery_cases-caseSSC11525
 Determined to be false positive after PCR or SNP data validation
 
 Paternal
 
 
 DOCK3
 
 krumm_15_ASD_discovery_cases-case12208.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 RAD54L2
 
 krumm_15_ASD_discovery_cases-case12215.p1
 Illumina 1MDuo
 
 Paternal
 Simplex
 Segregated
 MTAPP1,GPR79,GFM1,LXN,MFSD1,MLF1,RARRES1,IQCJ,RSRC1,IQCJ-SCHIP1
 
 poultney_13_ASD_discovery_cases-case98HI0029B
 qPCR
 
 Unknown
 Unknown (likely multiplex/AGRE)
 Unknown
 ABHD14A,ABHD14B,ABHD14A-ACY1
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_discovery_controls-controlSSC11537
  Determined to be false positive after PCR or SNP data validation
 
  Paternal
 
 
  DOCK3
 
krumm_15_ASD_discovery_controls-control11172.s1
  Illumina 1M
 
  De novo
 
 
  ZNF652P1,DOCK3
 

No Animal Model Data Available
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