4q13.2-q13.3CNV Type: Deletion-Duplication
Largest CNV size: 4525417 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
CNVs within this region were found in three 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
Microdeletions of 5.5Mb (4q13.2-q13.3) and 4.1Mb (7p15.3-p21.1) associated with a saethre-chotzen-like phenotype, severe intellectual disability,...
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Copy number variation analysis of patients with intellectual disability from North-West Spain.
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
4525417
1
2
3
quintela_17_DD/ID_discovery_cases
Galician (NW Spain) patients recruited from the Complexo Hospitalario Universitario de Santiago de Compostela and referred to the Fundacion Publica Galega de Medicina Xenomica for genetic study
573
All participants had a clinical diagnosis of idiopathic intellectual disability (ID) or global developmental delay (DD) with or without another medical condition [e.g. autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), epilepsy, dysmorphic features, and/or congenital anomalies]
Range, 3 months-18 years
60.38% Male
6814223
1
0
1
shimada_13_DD/ASD_discovery_cases
First child of healthy parents presenting with typical Saethre-Chotzen syndrome (SCS) phenotype and additional severe neurological features; case present in DECIPHER database (DECIPHER #TWM264324).
1
Severe developmental delay, autistic behaviors (no formal diagnosis of ASD), and Seathre-Chotzen syndrome
5 yrs.
Male
4100000
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
240153
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
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
quintela_17_DD/ID_discovery_cases
North West Spain
Array SNP
Affymetrix Cytogenetics Whole-Genome 2M SNP array, Affymetrix CytoScan HD
Affymetrix ChAS v.1.2.2
None
shimada_13_DD/ASD_discovery_cases
Japanese
aCGH
Agilent SurePrint G3 + SNP180K
FISH, microsatellite analysis
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
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-ISCA00000538
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
66842408
70831557
3989150
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004113
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
68852530
69850009
997480
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004696
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
68852530
69850009
997480
GRCh38
Duplication
Yes
quintela_17_DD/ID_discovery_cases-caseID_533
11 yrs.
F
Developmental delay/intellectual disability
Patient originally reported in Quintela et al., 2015d (P2 in this report)
67341554
74155777
6814224
GRCh38
Deletion
No
shimada_13_DD/ASD_discovery_cases-case1
5 yrs.
M
Developmental delay and autistic behaviors
Case present in DECIPHER database (DECIPHER #TWM264324). Birth/neonatal history: born at 41 weeks gestation; birth weight of 3650 g (+1.0 SD), length of 51 cm (+0.5 SD), OFC of 34 cm (mean); surgery performed in infancy due to craniosynostosis. Developmental milestones: delay in psychomotor development apparent during early infancy; head control at 12 months, rolling over at 14 months, standing with support at 24 months, crawling at 26 months, standing alone at 30 months. Language and communication evaluation: unable to speak any meaningful words. Motor and musculoskeletal evaluation: unable to walk alone. Behavioral/psychiatric evaluation: autistic behaviors, interpersonal problems (no formal diagnosis of ASD). Epilepsy/seizures: no reported clinical epileptic seizures. EEG: spike discharges. Dysmorphic features: brachycephaly, acrocephaly, facial asymmetry, high and narrow forehead, sparse and arched eyebrows, hypertelorism, bilateral blepharophimosis and ptosis, epicanthus inversus, depressed and deviated nasal bridge, anteverted nares, maxillary hypoplasia, strabismus, low set and posteriorly angulated ear with uplifted lobe and prominent crus helixes, cutaneous syndactyly between 2nd and 3rd fingers. Growth parameters: weight of 15.3 kg (-0.1 SD), height of 102.5 cm (+0.9 SD), and OFC of 50 cm (-0.1 SD) at 5 years of age. Family history: first child of healthy parents. Karyotype: normal male karyotype of 46, XY.
Severe developmental delay
66140532
70202818
4062287
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-controlHABC_900461_900461
N/A
N/A
Control
No previous psychiatric history
69445504
69685657
240154
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-ISCA00000538
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,MT2P1,UGT2B29P,UGT2B25P,UGT2A3P7,STATH,HTN3,ODAM,FDCSP,CSN3,SMR3A,AMTN,UTP3,RNU6-520P,RNU6-784P,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,APOOP4,YTHDC1,TMPRSS11E,UGT2B15,UGT2B10,UGT2B27P,UGT2B26P,UGT2B28,UGT2B24P,UGT2B4,SULT1D1P,SULT1E1,CSN1S1,CSN2,HTN1,CSN1S2AP,PRR27,CABS1,OPRPN,MUC7,AMBN,JCHAIN,GRSF1,CENPC,UBA6,UBA6-AS1,UGT2B17,UGT2A3,UGT2B7,UGT2A1,UGT2A2,SULT1B1,SMR3B,ENAM,RUFY3,UGT2B11
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004113
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Paternal
Unknown
Unknown
UGT2B25P,UGT2A3P7,UGT2B27P,UGT2B26P,UGT2B28,UGT2B24P,UGT2B4,SULT1D1P,SULT1E1,UGT2A3,UGT2B7,UGT2A1,UGT2A2,SULT1B1,UGT2B11
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004696
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
UGT2B25P,UGT2A3P7,UGT2B27P,UGT2B26P,UGT2B28,UGT2B24P,UGT2B4,SULT1D1P,SULT1E1,UGT2A3,UGT2B7,UGT2A1,UGT2A2,SULT1B1,UGT2B11
quintela_17_DD/ID_discovery_cases-caseID_533
De novo
Possibly segregated
RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,MT2P1,UGT2B29P,UGT2B25P,UGT2A3P7,STATH,HTN3,ODAM,FDCSP,CSN3,SMR3A,AMTN,UTP3,RNU6-520P,RNU6-784P,RNU6-891P,LDHAL6EP,RNA5SP163,HNRNPA1P67,RNU4ATAC9P,RNU6ATAC5P,HMGA1P2,CXCL8,PPBPP1,PF4V1,CXCL1,HNRNPA1P55,CXCL1P1,PF4,PPBP,CXCL5,RN7SL218P,CXCL3,PPBPP2,CXCL2,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,APOOP4,YTHDC1,TMPRSS11E,UGT2B15,UGT2B10,UGT2B27P,UGT2B26P,UGT2B28,UGT2B24P,UGT2B4,SULT1D1P,SULT1E1,CSN1S1,CSN2,HTN1,CSN1S2AP,PRR27,CABS1,OPRPN,MUC7,AMBN,JCHAIN,GRSF1,DCK,GC,COX18,AFP,AFM,RASSF6,CXCL6,CENPC,UBA6,UBA6-AS1,UGT2B17,UGT2A3,UGT2B7,UGT2A1,UGT2A2,SULT1B1,SMR3B,ENAM,RUFY3,MOB1B,NPFFR2,ANKRD17,LINC02499,MTHFD2L,UGT2B11,SLC4A4,ADAMTS3,ALB
shimada_13_DD/ASD_discovery_cases-case1
FISH, microsatellite analysis
De novo
Simplex
Likely segregated
MIR1269A,RPS23P3,RNU6-699P,RNU1-63P,RNA5SP527,ST3GAL1P1,TMPRSS11CP,RNU6-95P,GCOM2,MTND2P41,SYT14P1,MT2P1,UGT2B29P,UGT2B25P,UGT2A3P7,STATH,HTN3,ODAM,STAP1,GNRHR,TMPRSS11D,TMPRSS11A,TMPRSS11GP,TMPRSS11F,FTLP10,TMPRSS11BNL,TMPRSS11B,APOOP4,YTHDC1,TMPRSS11E,UGT2B15,UGT2B10,UGT2B27P,UGT2B26P,UGT2B28,UGT2B24P,UGT2B4,SULT1D1P,SULT1E1,CSN1S1,CSN2,HTN1,CSN1S2AP,PRR27,CENPC,UBA6,UBA6-AS1,UGT2B17,UGT2A3,UGT2B7,UGT2A1,UGT2A2,SULT1B1,UGT2B11
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_900461_900461
Unknown
UGT2A3P7,UGT2B4,UGT2A1,UGT2A2
No Animal Model Data Available