19p13.2-p13.13CNV Type: Deletion-Duplication
Largest CNV size: 4500218 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
CNVs within this region were identified in two cases from a study of 15,749 individuals from the International Standards for Cytogenomic Arrays (ISCA) consortium with unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome (Kaminsky et al., 2011).
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion-Duplication
Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.
Duplication
Behavioral characteristics associated with 19p13.2 microdeletions.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
4500218
1
1
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)
27101
0
1
1
welham_15_ASD_discovery_cases
Ten participants recruited through UNIQUE that were confirmed to have a 19p13.2 microdeletion
10
Diagnosis of ASD/autism based on meeting cut-off on Social Communication Questionnaire (SCQ); behavioral evaluation of cases made using the Challenging Behavior Questionnaire (CBQ), the Activity Questionnaire (TAQ), the Mood Interest and Pleasure Questionnaire Short-Form (MIPQ-S), the Repetitive Behavior Questionnaire (RBQ), and a modified version of the Sleep Questionnaire (ISQm); self-help subscale of Wessex scale used as an approximate indicator of intellectual disability.
Range, 2-20 yrs.
40% Male
1718000
1
0
1
wu_24_ASD/ADHD/DD/ID_discovery_cases
Children with unexplained neurodevelopmental disorders and one of more neurodevelopmental comorbidities who had undergone trio-WES and were admitted to the Children's Medical Center of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from October 2018 to December 2022.
163
Diagnoses of ASD, ADHD, and/or global developmental delay/intellectual disability were made following DSM-V diagnostic criteria.
1753288
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_controls
Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)
2342
Controls; subjects had no previous psychiatric history
N/A
46.67% Male
97189
1
0
1
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
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
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
poultney_13_ASD_discovery_cases
European
WES
Agilent SureSelect Human All Exon v.2
XHMM
None
welham_15_ASD_discovery_cases
5 from United Kingdom, 3 from United States, 1 from Australia, 1 from Canada
N/A
N/A
N/A
N/A
N/A
wu_24_ASD/ADHD/DD/ID_discovery_cases
China
WES
Illumina Novaseq 6000
Picard v.2.18.2, GATK Haplotype Caller v.4.0.4, ANNOVAR v2019/10/24
CMA
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
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
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002244
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
11517825
13225287
1707463
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004114
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
8831147
13331227
4500081
GRCh38
Duplication
Yes
poultney_13_ASD_discovery_cases-case04HI2999A
N/A
M
ASD
ASD case from AGRE (AGRE ID AU0916301; NDAR ID NDAR_INVET846NRU)
13778050
13805150
27101
GRCh38
Duplication
No
welham_15_ASD_discovery_cases-case2
3 yrs.
M
Not ASD
Language and communication evaluation: fewer than 30 words or signs. Motor and musculoskeletal evaluation: not walking independently. Behavioral/psychiatric evaluation: 3 clinically significant repetitive behaviors on RBQ; unusually low mood (5th %ile) on MIPQ-S; self-injurious behavior and aggressive behavior exhibited during previous month (CBQ); disruption or destruction of property (CBQ). Visual and auditory evaluation: vision reported to be normal; hearing reported to be normal. Additional medical history: ear problems, gastrointestinal difficulties, bowel problems, problems with genitalia.
Self-help category (Wessex self-help subscale): not able.
11642931
13361333
1718403
GRCh38
Deletion
N/A
wu_24_ASD/ADHD/DD/ID_discovery_cases-case50
2.8 yrs.
M
ASD, developmental delay/intellectual disability, and epilepsy
Severe-profound global developmental delay/intellectual disability, comorbid diagnosis of ASD, comorbid epilepsy (generalized seizures, generalized tonic-clonic seizures, Dravet syndrome), abnormal EEG (generalized spikes), dysmorphic facial features (low-set ears, hypertelorism, broad nasal bridge).
Severe-profound global developmental delay/intellectual disability
12046634
13799921
1753288
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
engchuan_15_ASD_discovery_controls-controlB306257_1007873482
N/A
N/A
Control
No previous psychiatric history
12571167
12668356
97190
GRCh38
Deletion
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002244
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
CNN1,ELOF1,ACP5,GAPDHP76,HNRNPA1P10,ZNF491,RNA5SP464,RNA5SP465,ZNF878,RNA5SP466,RSL24D1P8,RNA5SP467,ZNF625,RPS29P23,ZNF799,MTND2P40,MTCO1P27,MTCO2P27,MTATP6P27,PPIAP20,PGK1P2,RPL10P16,WDR83,WDR83OS,GNG14,FBXW9,SNORD41,TRIR,BEST2,MIR5684,JUNB,PRDX2,MIR6794,KLF1,MIR5695,FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,LYL1,STX10,IER2,RPL12P42,ECSIT,ZNF627,ZNF887P,ZNF833P,ZNF823,ZNF441,ZNF440,ZNF439,ZNF69,ZNF763,ZNF433-AS1,ZNF433,ZNF844,ZNF788P,ZNF20,ZNF625-ZNF20,ZNF44,ZNF442,ZNF443,ZNF709,ZNF564,ZNF791,MAN2B1,DHPS,ASNA1,THSD8,RNASEH2A,RTBDN,DNASE2,GCDH,RPS6P25,SYCE2,FARSA,CALR,NFIX,NACC1,ZNF700,ZNF136,ZNF563,TNPO2,HOOK2,MAST1,TRMT1,ZNF490,CACNA1A
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004114
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
MBD3L1,BOLA3P2,OR1M4P,OR7G2,OR7G1,OR7G15P,OR7G3,OR7D2,ELOCP29,OR7D4,OR7D1P,OR7E24,OR7E18P,OR7E19P,OR7H1P,ZNF426-DT,RPS4XP22,UBE2L4,RPL10P15,UBL5,RDH8,MIR5589,SNORD105,SNORD105B,P2RY11,EIF3G,MIR4322,ICAM4,ICAM5,FDX2,MIR1181,S1PR5,RNU7-140P,MIR1238,KRI1,ILF3-DT,QTRT1,MIR638,MIR4748,MIR199A1,MIR6793,TMED1,TIMM29,RN7SL192P,MIR6886,TMEM205,PLPPR2,SWSAP1,EPOR,CCDC151,MIR7974,RN7SL833P,CNN1,ELOF1,ACP5,GAPDHP76,HNRNPA1P10,ZNF491,RNA5SP464,RNA5SP465,ZNF878,RNA5SP466,RSL24D1P8,RNA5SP467,ZNF625,RPS29P23,ZNF799,MTND2P40,MTCO1P27,MTCO2P27,MTATP6P27,PPIAP20,PGK1P2,RPL10P16,WDR83,WDR83OS,GNG14,FBXW9,SNORD41,TRIR,BEST2,MIR5684,JUNB,PRDX2,MIR6794,KLF1,MIR5695,FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,LYL1,STX10,IER2,RPL12P42,ZNF558,OR1M1,ZNF317,OR7E16P,OR7E25P,ZNF559,ZNF559-ZNF177,ZNF177,ZNF266,ZNF560,ZNF426,ZNF561,ZNF561-AS1,ZNF562,ZNF846,FBXL12,PIN1,OLFM2,C3P1,PPAN-P2RY11,PPAN,MRPL4,ICAM1,ZGLP1,RAVER1,ICAM3,CDC37,PDE4A,KEAP1,ATG4D,CDKN2D,AP1M2,ILF3,C19orf38,YIPF2,LDLR,KANK2,DOCK6,ANGPTL8,TSPAN16,RAB3D,CCDC159,PRKCSH,ELAVL3,ZNF653,ECSIT,ZNF627,ZNF887P,ZNF833P,ZNF823,ZNF441,ZNF440,ZNF439,ZNF69,ZNF763,ZNF433-AS1,ZNF433,ZNF844,ZNF788P,ZNF20,ZNF625-ZNF20,ZNF44,ZNF442,ZNF443,ZNF709,ZNF564,ZNF791,MAN2B1,DHPS,ASNA1,THSD8,RNASEH2A,RTBDN,DNASE2,GCDH,RPS6P25,SYCE2,FARSA,CALR,NFIX,NACC1,MUC16,ZNF699,ZNF121,ZNF812P,COL5A3,C19orf66,ANGPTL6,DNMT1,S1PR2,TYK2,SLC44A2,DNM2,CARM1,SMARCA4,SPC24,RGL3,ZNF700,ZNF136,ZNF563,TNPO2,HOOK2,MAST1,TRMT1,ZNF490,CACNA1A
poultney_13_ASD_discovery_cases-case04HI2999A
Unknown
Unknown (likely multiplex/AGRE)
Unknown
C19orf53,ZSWIM4
welham_15_ASD_discovery_cases-case2
CNV validation not reported
Unknown
Unknown
Unknown
HNRNPA1P10,ZNF491,RNA5SP464,RNA5SP465,ZNF878,RNA5SP466,RSL24D1P8,RNA5SP467,ZNF625,RPS29P23,ZNF799,MTND2P40,MTCO1P27,MTCO2P27,MTATP6P27,PPIAP20,PGK1P2,RPL10P16,WDR83,WDR83OS,GNG14,FBXW9,SNORD41,TRIR,BEST2,MIR5684,JUNB,PRDX2,MIR6794,KLF1,MIR5695,FARSA-AS1,MIR6515,RAD23A,GADD45GIP1,DAND5,LYL1,STX10,IER2,RPL12P42,ZNF887P,ZNF833P,ZNF823,ZNF441,ZNF440,ZNF439,ZNF69,ZNF763,ZNF433-AS1,ZNF433,ZNF844,ZNF788P,ZNF20,ZNF625-ZNF20,ZNF44,ZNF442,ZNF443,ZNF709,ZNF564,ZNF791,MAN2B1,DHPS,ASNA1,THSD8,RNASEH2A,RTBDN,DNASE2,GCDH,RPS6P25,SYCE2,FARSA,CALR,NFIX,NACC1,ZNF700,ZNF136,ZNF563,TNPO2,HOOK2,MAST1,TRMT1,ZNF490,CACNA1A
wu_24_ASD/ADHD/DD/ID_discovery_cases-case50
CMA
De novo
Simplex
CALR,CACNA1A,GET3,DNASE2,DHPS,FARSA,SNORD41,WDR83OS,TNPO2,ZNF44,HOOK2,C19orf53,BEST2,TRMT1,ZNF490,ZSWIM4,TRIR,ZNF442,RTBDN,FBXW9,WDR83,YJU2B,MRI1,ZNF799,NACC1,GADD45GIP1,ZNF625,ZNF563,ZNF709,ZNF791,ZNF564,DAND5,GCDH,ZNF844,SYCE2,RPL10P16,ZNF788P,ZNF878,RPS6P25,RPL12P42,MAN2B1,JUNB,LYL1,NFIX,RPS29P23,PPIAP20,RSL24D1P8,ZNF625-ZNF20,MIR5695,MIR5684,RNA5SP466,RNA5SP467,PGK1P2,RAD23A,MIR6794,MIR6515,GNG14,FARSA-AS1,PRDX2,MTCO2P27,MTCO1P27,MTND2P40,MTATP6P27,THSD8,ZNF20,STX10,ZNF136,IER2,ZNF443,RNASEH2A,KLF1,MAST1
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlB306257_1007873482
Unknown
RPL10P16,WDR83,WDR83OS,ZNF791,MAN2B1,ZNF490
No Animal Model Data Available