HELP     Sign In

19q13.3CNV Type: Deletion


Largest CNV size: 63800 bp

Statistics Box:
Number of Reports: 2



Summary Information

Deletions in this region including the SHANK1 gene were identified that segregated with ASD in males.

Additional Locus Information

Genome browsers

USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

References

Major Reports

Title
Author, Year
Report Class
CNV Type
SHANK1 Deletions in Males with Autism Spectrum Disorder.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Deletion-Duplication

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
 Patients from the Developmental Gene Anatomy Project at Harvard Medical School (DGAP), the Developmental Gene Discovery Project at Georgia Health Sciences University (DGDP), the National Institute of General Medical Sciences Human Genetic Cell Repository (NIGMS), the Signature Genomic Laboratories Genoglyphix Chromosome Aberration Database, and DECIPHER
 57365
 Predominant cohort diagnosis of developmental delay/intellectual disability and/or mulitple congenital anomalies (MCA); 5 cases with additional diagnosis of autism/ASD
 N/A
 N/A
 N/A
 3
 4
 7
 sato_12_ASD_discovery_cases_1
 Unrelated ASD cases from Canada (Hospital for Sick Children, McMaster University, Memorial University of Newfoundland, University of Alberta, and Montral Children's Hospital of McGill University Health Centre) and Europe (PARIS and specialized clincial centers in France, Sweden, Germany, Finland, and the UK).
 1614
 Diagnosis of ASD based on Autism Diagnostic Interview-Revised (ADI-R) and/or Autism Diagnostic Observation Schedule (ADOS). In some ASD cases from Sweden, the Diagnostic Interview for Social and Communication Disorders (DISCO-10) was applied instead of ADI-R.
 NA
 78.07% Male
 63800
 2
 0
 2
 sato_12_ASD_discovery_cases_2
 Three additional affected males from four-generation family with ASD/BAP
 3
 Two cases diagnosed with Asperger syndrome, 1 case with broader autism phenotype
 Range, 5 yrs. 8 mos.-95 yrs.
 100% Male
 63800
 3
 0
 3

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 nguyen_13_DD/ID/MCA/ASD_discovery_controls
 Control data from the Database of Genomic Variants (DGV, n=12,145) and a published dataset of 8,329 individuals from Moriarty et al., 1998.
 20474
 Control
 N/A
 N/A
 N/A
 2
 2
 4
 sato_12_ASD_discovery_controls
 Control cohort consisting of 2026 healthy individuals from CHOP, 2493 controls genotyped at University of Washington, and 10603 population-based controls including 1123 controls from Northern Germany, 1234 Canadian controls from Ottawa, 1120 controls from Ontario, 1056 HapMap samples, 4783 controls from WTCCC, and 1287 controls recruited by SAGE consortium.
 15122
 Control
 NA
 NA
 63800
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 nguyen_13_DD/ID/MCA/ASD_discovery_cases
  N/A
 aCGH
  SignatureChip BACs aCGH, SignatureChip Oligo whole-genome microarray
 
 
 N/A
 sato_12_ASD_discovery_cases_1
  Canadian (n=1158) and European (n=456)
 aCGH, array SNP, solid phase hybridization
  Affymetrix 6.0, Illumina 1M, Agilent SurePrint G3 Human CGH 1X1M, Illumina Human 1M-Duo BeadChip
 DNA Analytics, CBS/DNAcopy, Birdsuite, iPattern, Genotyping Console, PennCNV, QuantiSNP, iPattern
 
 qPCR
 sato_12_ASD_discovery_cases_2
  Canadian
 aCGH
  Agilent SurePrint G3 Human CGH 1x1M
 DNA Analytics, CBS/DNAcopy
 
 qPCR

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  nguyen_13_DD/ID/MCA/ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
  N/A
  sato_12_ASD_discovery_controls
  Predominantly European
  N/A
  N/A
 
 
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient228
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Deletion
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient229
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Deletion
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient230
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Deletion
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient231
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Duplication
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient232
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Duplication
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient233
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Duplication
 N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient234
 N/A
 N/A
 DD/ID/MCA
 N/A
 N/A
 N/A
 N/A
  N/A
 GRCh37
 Duplication
 N/A
  sato_12_ASD_discovery_cases_1-family1caseIII-5
 32 yrs.
 M
 Asperger
 Diagnosis of Asperger disorder based on ADI-R and ADOS-4 at 25 years; initial diagnosis of PDD-NOS at 16 years (impairment in social communication, not enough repetitive stereotyped behaviors for diagnosis of autism or Asperger). Developmental milestones: engaged in repetitive paly and speech at 12-24 months; single words at 24 months, phrases by 36 months; no lost langauge or loss in other skills. Language and communication evaluation: normal language development; no history of echolalia, pronoun reversal, or neologisms. Behavioral/psychiatric evaluation: anxiety disorder (currently takes olanzapine and paroxetine); poor eye contact, persistent lack of social smile, facial affect, joint attention, and empathy. Additional genetic evaluation: nonsense mutation in PCDHGA11 gene that segregates with SHANK1 deletion. Family history: mother exhibited anxiety and shyness, but not considered to have ASD or BAP; sister with diagnosis of anxiety disorder and a generalized anxiety disorder (no evidence of ASD or BAP); sister has two children with ASD/Asperger; maternal grandfather with BAP.
 Leiter-R brief non-verbal IQ of 83 (13th %ile, low average range). Adaptive behavior scores (as measured by Vineland Adaptive Behavior Scales/VABS-I): adaptive behavior composite score of 52 (<1st %ile); communication score of 43 (<1st %ile); daily living skills score of 63 (1st %ile); socialization score of 65 (1st %ile).
 50677120
 50740926
  63807
 GRCh38
 Deletion
 Yes
  sato_12_ASD_discovery_cases_1-family2caseII-1
 2.5 yrs.
 M
 ASD
 Diagnosis of high-functioning ASD (based on ADI-R); diagnosis of mild autism using CARS. Birth/neonatal history: born two months before term. Developmental milestones: abnormalities identified during first year (did not babble, made no eye contact, refused to be touched); started to walk with poor motor coordination at 2 years of age; started to talk at 2.5 years of age. Language and communication evaluation: formal, pedantic style of speech with abnormal prosody. Behavioral/psychiatric evaluation: uninterested in other children; repeated routines and rituals, accumulated facts on certain subjects such as astronomy; hand-flapping or stereotypic body movements when upset; periods of depression. Brain imaging: positron emission tomography (PET) detected mild hyperfusion temporal left. Family history: younger maternal half-sister with autism and mild intellectual disability (sister lacks SHANK1 deletion).
 Wechsler Intelligence Scale for Children (WISC): full-scale IQ of 115 (84th %ile, high average range); verbal IQ of 120 (93rd %ile); performance IQ of 100 (50th %ile). Verbal IQ > peformance IQ.
 50613238
 50676640
  63403
 GRCh38
 Deletion
 Yes
  sato_12_ASD_discovery_cases_2-family1caseI-1
 95 yrs. (age at death)
 M
 Broader autism phenotype (BAP)
 Possible diagnosis of broader autism phenotype or high-functioning ASD. Beahvioral/psychiatric evaluation: no history of psychiatric illness: quiet and withdrawn throughout adult life, no close relationships, did not use interest in stamp collecting to engage in social interactions. Deceased at 95 years of age. Family history: grandson with Asperger disorder, great-grandchildren with ASD/Asperger disorder.
 Difficulty in school
 50677120
 50740926
  63807
 GRCh38
 Deletion
 Yes
  sato_12_ASD_discovery_cases_2-family1caseIV-1
 10 yrs.
 M
 Asperger
 Diagnosis of Asperger disorder based on ADI-R (met all cut-ffos for autistic disorder except for nonverbal total); ADOS scores below ASD cut-off due to strengths in communication domain; Social Responsiveness Scale (SRS) T-score of 68T (mild-to-moderate concerns). Birth/neonatal history: born by C-section 10 days late. Developmental milestones: early milestones within normal limits; developmental differences detected at 3 years (no interest in other children, preoccupation with objects). Language and communication evaluation: Oral and Written Language Scales (OWLS) total language score of 93, receptive language score of 82 (12th %ile), and expressive language score of 107 (68th %ile); Peabody Picture Vocabulary Test (PPVT) 4th edition receptive vocabulary score of 97 (42th %ile); descriptive gestures present but were vague and infrequent. Behavioral/psychiatric evaluation: continued impairment in reciprocal social interaction; approached other children but tended to play beside them; became upset with changes in routine; difficulties with eye contact and understanding social cues and rules. Family history: brother with ASD/Asperger disorder; mother with diagnosis of anxiety disorder and generalized anxiety disorder (no ASD or BAP); maternal uncle with Asperger disorder; great-grandfather with BAP.
 Wechsler Abbreviated Scale of Intelligence (WASI): verbal IQ of 114 (82nd %ile, high average range); performance IQ of 86 (18th %ile, low average range). Adaptive behavior scores (as determined by Vineland Adaptive Behavior Scales/VABS-II): adaptive behavior composite score of 85 (16th %ile); communication score of 92 (30th %ile); daily living skills score of 85 (16th %ile); socialization score of 85 (16th %ile).
 50677120
 50740926
  63807
 GRCh38
 Deletion
 Yes
  sato_12_ASD_discovery_cases_2-family1caseIV-3
 5 yrs. 8 mos.
 M
 Asperger
 Diagnosis of Asperger syndrome; positive for autism on ADI-R and ASD on the ADOS. Developmental milestones: not talking at 18 months, developed single words at 24 months. Language and communication evaluation: expressive language consisted of short sentences and phrases, some echoed speech, and mild articulation difficulties; Oral and Written Language Scales (OWLS) total language score of 80 (9th %ile), receptive language score of 78 (7th %ile), and expressive language score of 86 (18th %ile); Peabody Picture Vocabulary Test (PPVT) 4th edition receptive vocabulary score of 91 (27th %ile). Behavioral/psychiatric evaluation: exhibition of repetitive behaviors; failure to offer comfort or empathy; failure to initiate social interaction, although did play with parents; had made good progress in social interaction at 5 years 8 months of age. Additional genetic evaluation: nonsense mutation in PCDHGA11 gene that segregates with SHANK1 deletion. Family history: brother with ASD/Asperger disorder; mother with diagnosis of anxiety disorder and generalized anxiety disorder (no ASD or BAP); maternal uncle with Asperger disorder; great-grandfather with BAP.
 Wechsler Preschool and Primary Scale of Intelligence (WPPSI): full-scale IQ of 89 (23rd %ile, low average range); verbal Iqof 89 (23rd %ile); performance IQ of 91 (27th %ile). Adaptive behavior scores (as determined by Vineland Adaptive Behavior Scales/VABS-II): adaptive behavior composite score of 86 (18th %ile); communication score of 91 (27th %ile); daily living skills score of 89 (23rd %ile); socialization score of 85 (16th %ile); motor score of 91 (27th %ile).
 50677120
 50740926
  63807
 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
  nguyen_13_DD/ID/MCA/ASD_discovery_controls-control51
  N/A
  N/A
  Control
  N/A
  N/A
  N/A
  N/A
  N/A
  GRCh37
  Deletion
  N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_controls-control52
  N/A
  N/A
  Control
  N/A
  N/A
  N/A
  N/A
  N/A
  GRCh37
  Deletion
  N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_controls-control53
  N/A
  N/A
  Control
  N/A
  N/A
  N/A
  N/A
  N/A
  GRCh37
  Duplication
  N/A
  nguyen_13_DD/ID/MCA/ASD_discovery_controls-control54
  N/A
  N/A
  Control
  N/A
  N/A
  N/A
  N/A
  N/A
  GRCh37
  Duplication
  N/A

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient228
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient229
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient230
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient231
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient232
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient233
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 nguyen_13_DD/ID/MCA/ASD_discovery_cases-patient234
 
 
 Unknown
 Unknown
 Unknown
 Minimum CNV gene content: DHX34
 
 sato_12_ASD_discovery_cases_1-family1caseIII-5
 qPCR
 Possibly maternal
 Maternal
 Simplex for ASD; multiplex for anxiety disorder
 ASD: segregated in males, but not females (sister with deletion); anxiety disorder: segregated.
 SHANK1,CLEC11A
 
 sato_12_ASD_discovery_cases_1-family2caseII-1
 qPCR
 
 De novo, maternal chromosome
 Multiplex (maternal half-sister with ASD & ID)
 Not segregated
 C19orf81,SYT3,SHANK1
 
 sato_12_ASD_discovery_cases_2-family1caseI-1
 qPCR
 
 Unknown
 Unknown
 Unknown
 SHANK1,CLEC11A
 
 sato_12_ASD_discovery_cases_2-family1caseIV-1
 qPCR
 Possibly maternal
 Maternal
 Multiplex (brother with Asperger)
 Segregated
 SHANK1,CLEC11A
 
 sato_12_ASD_discovery_cases_2-family1caseIV-3
 qPCR
 Possibly maternal
 Maternal
 Multiplex (brother with Asperger)
 Segregated
 SHANK1,CLEC11A
 

Controls

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
nguyen_13_DD/ID/MCA/ASD_discovery_controls-control51
 
 
  Unknown
  Unknown
 
  Minimum CNV gene content: DHX34
 
nguyen_13_DD/ID/MCA/ASD_discovery_controls-control52
 
 
  Unknown
  Unknown
 
  Minimum CNV gene content: DHX34
 
nguyen_13_DD/ID/MCA/ASD_discovery_controls-control53
 
 
  Unknown
  Unknown
 
  Minimum CNV gene content: DHX34
 
nguyen_13_DD/ID/MCA/ASD_discovery_controls-control54
 
 
  Unknown
  Unknown
 
  Minimum CNV gene content: DHX34
 

No Animal Model Data Available
HELP
Copyright © 2017 MindSpec, Inc.