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19p13.13CNV Type: Deletion


Largest CNV size: 2199 bp

Statistics Box:
Number of Reports: 4



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
Distinct effects of allelic NFIX mutations on nonsense-mediated mRNA decay engender either a Sotos-like or a Marshall-Smith syndrome.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication

Minor Reports

Title
Author, Year
Report Class
CNV Type
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Deletion
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 2199
 1
 0
 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
 440359
 0
 2
 2
 malan_10_ID_discovery_cases
 Cases with unexplained overgrowth evaluated by aCGH
 18
 Inclusion criteria for cases: (1) unrelated parents; (2) developmental delay; (3) height >95th %ile and/or OFC >95th %ile; and (4) at least two of the following features: (i) advanced bone age, (ii) dysmorphic features, and (iii) congential malformations.
 N/A
 N/A
 107789
 2
 0
 2
 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
 9353
 1
 0
 1

Controls

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 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
 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)
 9353
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 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
 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
 malan_10_ID_discovery_cases
  N/A
 aCGH
  Agilent 244K
 
 
 FISH
 prasad_12_ASD_discovery_cases
  Canada
 aCGH
  Agilent 1M
 ADM-2, DNAcopy (R Bioconductor)
 DNA Analytics v4.0.85 (Agilent), DNAcopy
 None

Controls

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
  kaminsky_11_DD/ID/ASD_discovery_controls
  NA
  aCGH
  Agilent 44K, Agilent 105K
 
  Feature Extraction, DNA Analytics
 
  prasad_12_ASD_discovery_controls
  NA
  aCGH
  Agilent 1M
  ADM-2, DNAcopy (R Bioconductor)
  DNA Analytics v4.0.85 (Agilent), DNAcopy
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  celestino-soper_11_ASD_discovery_cases-11327
 NA
 M
 ASD
 NA
 NA
 13772128
 13774327
  2200
 GRCh38
 Deletion
 No
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002051
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 12813597
 13119698
  306102
 GRCh38
 Duplication
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002134
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 12850595
 13290954
  440360
 GRCh38
 Duplication
 Yes
  malan_10_ID_discovery_cases-case1
 14 yrs.
 M
 Intellectual disability and autistic features
 Birth/neonatal history: birth weight 4500 g (>95th %ile), length 53 cm (95th %ile), OFC 38 cm (>95th %ile); neonatal feeding problems. Developmental milestones: speech delay, motor retardation. Motor and musculoskeletal evaluation: hypotonia, abdominal wall hypotonia; pectus excavatum, scoliosis, advanced bone age, coxa valga, long fingers. Behavioral/psychiatric evaluation: autistic traits, behavioral anomalies. Brain imaging: ventricular dilatation and hypoplasia of the corpus callosum on brain MRI. Visual evaluation: hypermetropia, strabismus. Dysmorphic features: macrocephaly, long narrow face, high forehead, down-slanting palpebral fissures, small mouth, everted lower lip, prognathia, malformed nails, premature eruption of teeth. Growth parameters: height >98th %ile, OFC >98th %ile, height/weight ratio <25th %ile.
 Intellectual disability
 12926937
 13034725
  107789
 GRCh38
 Deletion
 Yes
  malan_10_ID_discovery_cases-case2
 10 yrs.
 M
 Intellectual disability and autistic features
 Birth/neonatal history: neonatal feeding problems. Developmental milestones: speech delay. Motor and musculoskeletal evaluation: hypotonia; pectus excavatum, advanced bone age, coxa valga, long fingers. Behavioral/psychiatric evaluation: autistic traits, behavioral anomalies. Visual evaluation: hypermetropia, astigmatism. Dysmorphic features: macrocephaly, long narrow face, high forehead, generalized livedo. Growth parameters: height >98th %ile, OFC >98th %ile, height/weight ratio <25th %ile.
 Intellectual disability
 13050544
 13154694
  104151
 GRCh38
 Deletion
 Yes
  prasad_12_ASD_discovery_cases-case126173
 NA
 M
 ASD
 Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
 
 13745886
 13755238
  9353
 Unknown
 Deletion
 No

Controls

No Control Data Available

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 celestino-soper_11_ASD_discovery_cases-11327
 
 
 Unknown
 Simplex
 NA
 MRI1,C19orf53
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002051
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 MIR6794,KLF1,MIR5695,FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,LYL1,RNASEH2A,RTBDN,DNASE2,GCDH,RPS6P25,SYCE2,FARSA,CALR,NFIX,NACC1,HOOK2,MAST1,TRMT1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002134
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 MIR6794,KLF1,MIR5695,FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,LYL1,STX10,IER2,RPL12P42,DNASE2,GCDH,RPS6P25,SYCE2,FARSA,CALR,NFIX,NACC1,HOOK2,MAST1,TRMT1,CACNA1A
 
 malan_10_ID_discovery_cases-case1
 FISH
 
 De novo
 Simplex
 Segregated
 FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,FARSA,CALR,NFIX
 
 malan_10_ID_discovery_cases-case2
 FISH
 
 De novo
 Simplex
 Segregated
 LYL1,STX10,IER2,NFIX,NACC1,TRMT1
 
 prasad_12_ASD_discovery_cases-case126173
 
 
 Unknown
 Unknown
 Unknown
 C19orf53,MRI1
 

Controls

No Control Data Available
No Animal Model Data Available
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