19p13.13CNV Type: Deletion
Largest CNV size: 2199 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
Summary statement in development
Additional Locus Information
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
Complex Diagnostics of Non-Specific Intellectual Developmental Disorder
Deletion
The application of whole-exome sequencing in the early diagnosis of rare genetic diseases in children: a study from Southeastern China
Deletion
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
lai_24_DD/ID_discovery_cases
Pediatric patients assessed at the Clinical Genetics Laboratory of the Ganzhou Maternal and Child Health Hospital who were recruited between January 2021 and December 2023.
144
Clinical manifestations observed in this cohort included global developmental delay (HP:0001263; n=46, 31.94%), intellectual disability (HP:0001249; n=44, 30.56%), seizures (HP:0001250, n = 24, 16.67%), and autistic behavior (HP:0000729; n=19, 13.19%).
Median age 4yrs. (range 0-17 yrs.)
59.03% Male
406831
1
0
1
levchenko_22_DD/ID_discovery_cases
Individuals with non-specific intellectual developmental disorder from the Research Centre for Medical Genetics consulted from 2017 to 2020.
198
Cases presented with non-specific intellectual developmental delay (DD/ID).
Range, 6 mos.-65 yrs.
63.63% Male
80865
1
0
1
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
mazzonetto_24_ASD/DD/ID_discovery_cases
Patients from a total of 15 non-profit organizations and university centers located in different states of Brazil who were enrolled between July 2021 and June 2022 and referred with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorder (ASD), and/or multiple congenital anomalies.
1363
"95% of individuals in this cohort reported with the HPO phenotype ""Abnormality of the nervous system"" (HP:0000707); the HPO phenotypes ""Intellectual disability"" (HP:0001249; 36%), ""Global developmental delay"" (HP:0001263; 32%), and ""Autism"" (HP:0000717; 28%) were the most frequently reported phenotype subcategories within this subset of individuals."
63.17% Male
500000
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
9353
1
0
1
sanchis_juan_23_ASD/DD/ID_discovery_cases
Individuals affected with a neurodevelopmental disorder (NDD) from the National Institute for Health and Care Research (NIHR) BioResource project.
489
73% (357/489) of the participants in this study had autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID), a movement disorder or dystonia, and/or seizures.
NA
NA
4618
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
lai_24_DD/ID_discovery_cases
China
WES
Illumina NovaSeq 6000
PCR or Sanger
levchenko_22_DD/ID_discovery_cases
Russia
WES
NA
NA
NA
MLPA
malan_10_ID_discovery_cases
N/A
aCGH
Agilent 244K
FISH
mazzonetto_24_ASD/DD/ID_discovery_cases
Brazil
Low-pass WGS
Illumina NovaSeq 6000
SNP-FASST2 (HMM)
BioDiscovery NxClinical
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
sanchis_juan_23_ASD/DD/ID_discovery_cases
United Kingdom
Short-read WGS
Illumina HiSeq 2500/Illumina HiSeq X
Canvas v.1.1.0.5, Manta v.0.23.15
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
lai_24_DD/ID_discovery_cases-case53
3 yrs.
F
Intellectual disability
Dysmorphic facial features, abnormal vertebral morphology
Intellectual disability
12703848
13110678
406831
GRCh38
Deletion
Yes
levchenko_22_DD/ID_discovery_cases-caseD1020
NA
NA
Developmental delay/intellectual disability
Case presented with non-specific intellectual developmental disorder. Motor and musculoskeletal evaluation: hypotonia, varus feet. Brain imaging: hypoplasia of the cerebellum. Dysmorphic features: narrow forehead, moderately upturned nose, macrotomia, low-set ears, transverse palmar crease.
13073018
13153882
80865
GRCh38
Deletion
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
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530976
M
Autism and developmental delay
Autism (HP:0000717), global developmental delay (HP:0001263), abnormal cardiovascular system morphology (HP:0030680), abnormal facial shape (HP:0001999)
12810001
13310000
500000
GRCh38
Duplication
No
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
sanchis_juan_23_ASD/DD/ID_discovery_cases-caseG017082
NA
M
Developmental delay and seizures
Patient was of European ancestry and presented with seizures and developmental delay.
13454516
13459133
4618
GRCh38
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
lai_24_DD/ID_discovery_cases-case53
PCR or Sanger
De novo
CALR,GET3,DNASE2,FARSA,SNORD41,TNPO2,HOOK2,BEST2,TRMT1,TRIR,RTBDN,GADD45GIP1,DAND5,GCDH,SYCE2,RPS6P25,JUNB,LYL1,NFIX,MIR5695,MIR5684,RAD23A,MIR6794,MIR6515,FARSA-AS1,PRDX2,THSD8,RNASEH2A,KLF1,MAST1
levchenko_22_DD/ID_discovery_cases-caseD1020
MLPA
De novo
Simplex
Segregated
TRMT1,NACC1,LYL1,NFIX,STX10,IER2
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
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530976
Unknown
CALR,CACNA1A,DNASE2,FARSA,HOOK2,TRMT1,RTBDN,NACC1,GADD45GIP1,DAND5,GCDH,SYCE2,RPS6P25,RPL12P42,LYL1,NFIX,MIR5695,RAD23A,MIR6794,MIR6515,FARSA-AS1,THSD8,STX10,IER2,RNASEH2A,KLF1,MAST1
prasad_12_ASD_discovery_cases-case126173
Unknown
Unknown
Unknown
C19orf53,MRI1
sanchis_juan_23_ASD/DD/ID_discovery_cases-caseG017082
Unknown
Simplex
CACNA1A
Controls
No Control Data Available
No Animal Model Data Available