16q24.1-q24.3CNV Type: Deletion-Duplication
Largest CNV size: 5377249 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
A de novo deletion in an ASD case (Handrigan et al., 2012) and a duplication in a case with developmental delay (Kaminsky et al., 2012) were identified within this region.
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...
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Deletions in 16q24.2 are associated with autism spectrum disorder, intellectual disability and congenital renal malformation.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
handrigan_13_ASD/DD/ID_discovery_cases
Patients with 16q24.2 deletions recruited at the University of Alberta, Edmonton, the Hospital for Sick Children, Toronto, Signature Genomic Laboratories, and the Mayo Clinic).
35
22 patients with ASD (19 with pervasive developmental delay/PDD, 3 with autism), 3 patients with intellectual disability (defined as IQ<70 by DSM-IV); 11 patients with facial dysmorphisms.
Range, 0 mos.-20 yrs.
48.57% Male
2645900
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
5377249
0
1
1
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
4289000
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
handrigan_13_ASD/DD/ID_discovery_controls
Microarray data from population-based control individuals [4783 controls from the Wellcome Trust Case Control Consortium (WTCCC), 1123 PopGen controls from Germany, 1234 controls from the Ottawa Heart Institute, 1056 controls from HapMap, 1287 controls from SAGE, 1120 population controls from Ontario, and 416 controsl from the Ontario Population Genomics Platform]
11019
Control
NA
NA
0
0
0
0
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
handrigan_13_ASD/DD/ID_discovery_cases
NA
aCGH, solid phase hybridization
Illumina Omni 2.5M-Quad BeadChip, SignatureChipOS V1.0 105K, V2.0 135K, V3.0 135K, BACs aCGH, Agilent 4x180K ISCA V2, Agilent ISCA 44K, Agilent 180K
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
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
handrigan_13_ASD/DD/ID_discovery_controls
NA
N/A
N/A
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
handrigan_13_ASD/DD/ID_discovery_cases-patient1
9 yrs.
F
ASD
Neurodevelopmental abnormalities: PDD (pervasive developmental delay), mild language delay, gross and fine motor deficits. Urological abnormalities: bilateral hydronephrosis. Other features: intrauterine growth retardation, bilateral conductive hearing loss following chronic otitis media with perforation of the tympanic membranes requiring the use of hearing aids, bifid uvula, synophrys, up-slanted palpebral fissures, depressed nasal brdige, rounded nasal tip, slightly elongated philtrum, full upper lip, down-turned corners of the mouth, retro-micrognathia, evidence of dental crowding, mild kyphosis with exaggerated lordosis from increased body weight, hyperextensibility of lower extremities, inability to balance on either foot without assistance, cafe-au-lait macule on right thigh. Growth parameters: height <3rd %ile, weight 70th %ile. Family history: parents were second cousins once removed.
86739157
89382255
2643099
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004752
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
84707538
90081985
5374448
GRCh38
Duplication
Yes
maini_18_ASD/DD/ID_discovery_cases-case114
6 yrs.
M
Language delay and language disorder
Birth history: born at 40 weeks gestation, no reported pregnancy anomalies. Developmental milestones: language delay. Language and communication evaluation: language disorder. Behavioral/psychiatric evaluation: no reported behavioral or psychiatric abnormalities. Epilepsy/abnormal EEG: no reported epilepsy or EEG abnormalities. Additional medical history: neurological anomalies. Dysmorphic features: prominent forehead, overfolded helix of the ears, cowlick. Growth parameters: normal head circumference, normal growth. Family history: negative for consanguineity, negative for familiarity, family history negative for NDDs.
Normal (no intellectual disability or learning disorder)
85788576
90045000
4256425
GRCh38
Duplication
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
handrigan_13_ASD/DD/ID_discovery_cases-patient1
De novo
Unknown
Unknown
LINC02181,ZNF469,MIR5189,IL17C,CYBA,SNAI3,CTU2,MIR4722,CDT1,APRT,TRAPPC2L,PABPN1L,LINC02138,SLC22A31,LINC02188,FBXO31,MAP1LC3B,KLHDC4,SLC7A5,MIR6775,CA5A,LINC02182,MVD,SNAI3-AS1,RNF166,GALNS,CBFA2T3,LINC00304,CDH15,ZNF778,C16orf95,ZCCHC14,JPH3,BANP,ZFPM1,ZC3H18,PIEZO1,ANKRD11,ACSF3
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004752
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
COX6CP16,LINC00311,MIR5093,RN7SL381P,MIR1910,RNU1-103P,MIR6774,LINC02132,LINC02135,FOXF1,FOXC2-AS1,FOXC2,FOXL1,LINC02189,LINC02181,ZNF469,MIR5189,IL17C,CYBA,SNAI3,CTU2,MIR4722,CDT1,APRT,TRAPPC2L,PABPN1L,LINC02138,SLC22A31,RNU6-430P,RPL13,SNORD68,SPATA2L,VPS9D1-AS1,CENPBD1,GAS8-AS1,USP10,CRISPLD2,ZDHHC7,FAM92B,LINC02139,GINS2,EMC8,COX4I1,IRF8,LINC01082,LINC00917,MTHFSD,FLJ30679,LINC02188,FBXO31,MAP1LC3B,KLHDC4,SLC7A5,MIR6775,CA5A,LINC02182,MVD,SNAI3-AS1,RNF166,GALNS,CBFA2T3,LINC00304,CDH15,ZNF778,CPNE7,DPEP1,SPATA33,CDK10,LINC02166,VPS9D1,ZNF276,SPIRE2,TCF25,TUBB3,DEF8,AFG3L1P,DBNDD1,GAS8,PRDM7,KIAA0513,GSE1,C16orf74,LINC01081,FENDRR,C16orf95,ZCCHC14,JPH3,BANP,ZFPM1,ZC3H18,PIEZO1,ANKRD11,SPG7,CHMP1A,FANCA,MC1R,URAHP,LINC02176,ACSF3
maini_18_ASD/DD/ID_discovery_cases-case114
Unknown
Simplex
Unknown
MIR6774,LINC02132,LINC02135,FOXF1,FOXC2-AS1,FOXC2,FOXL1,LINC02189,LINC02181,ZNF469,MIR5189,IL17C,CYBA,SNAI3,CTU2,MIR4722,CDT1,APRT,TRAPPC2L,PABPN1L,LINC02138,SLC22A31,RNU6-430P,RPL13,SNORD68,SPATA2L,VPS9D1-AS1,CENPBD1,GAS8-AS1,EMC8,COX4I1,IRF8,LINC01082,LINC00917,MTHFSD,FLJ30679,LINC02188,FBXO31,MAP1LC3B,KLHDC4,SLC7A5,MIR6775,CA5A,LINC02182,MVD,SNAI3-AS1,RNF166,GALNS,CBFA2T3,LINC00304,CDH15,ZNF778,CPNE7,DPEP1,SPATA33,CDK10,LINC02166,VPS9D1,ZNF276,SPIRE2,TCF25,TUBB3,DEF8,AFG3L1P,DBNDD1,GAS8,LINC01081,FENDRR,C16orf95,ZCCHC14,JPH3,BANP,ZFPM1,ZC3H18,PIEZO1,ANKRD11,SPG7,CHMP1A,FANCA,MC1R,URAHP,ACSF3
Controls
No Control Data Available
No Animal Model Data Available