12q12-q13.11CNV Type: Deletion
Largest CNV size: 7961778 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
Rare singleton deletion within this region was found in a case 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
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
Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea
Deletion
ARID2-related disorder: further delineation of the clinical phenotype of 27 novel individuals and description of an epigenetic signature
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
akkus_24_ASD/DD/ID_discovery_cases
Patients with developmental delay/intellectual disability, autism spectrum disorder, and/or multiple congenital anomalies consulted by the Department of Medical Genetics at the Health Sciences University Kocaeli Derince Training and Research Hospital between January 1, 2017 and March 30, 2021.
1227
Patients presented with developmental delay/intellectual disability, autism spectrum disorder, and/or multiple congenital anomalies.
57.13% Male
641250
0
1
1
houdayer_25_DD/ID_discovery_cases
Individuals with interstitial deletions encompassing the ARID2 gene from an initial cohort of 27 previously unreported individuals with ARID2-related disorder who were recruited through the French network for rare developmental disorders (AnDDI-Rares) and GeneMatcher.
6
All of one individual presented with developmental delay with or without intellectual disability.
Range, 6 wks.-15 yrs. 2 mos.
66.67% Male
990341
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
7961778
1
0
1
lee_21_DD/ID/EP_discovery_cases
Patients evaluated at the Medical Genetic Center of the Asan Medical Childrens Hospital, Seoul, Korea, from March 2018 to October 2020 for pathogenic variants or microdeletions in the components of the SWI/SNF complex.
564
Cases presented with neurodevelopmental disorders, including developmental delay (DD), intellectual disability (ID), and epilepsy (EP).
NA
NA
3663029
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.
1563709
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
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
akkus_24_ASD/DD/ID_discovery_cases
Turkey
Array SNP
Affymetrix CytoScan Optima
ThermoFisher ChAS v.3.1.
houdayer_25_DD/ID_discovery_cases
4 Caucasian ancestry, 2 NA
aCGH, exome sequencing, genome sequencing
NovaSeq 6000, Illumina NextSeq-Novaseq, Agilent 4x180K, Affymetrix CytoScan
xHMM v.1.0
xHMM v.1.0, Agilent Feature Extraction and Cytogenomics, Cyto-B-N2.0.1.2 (r5919) NetAfx Build 33.1,
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
lee_21_DD/ID/EP_discovery_cases
Korea
CMA
ThermoFisher CytoScan 750KK
NA
ThermoFisher ChAS
None
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
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
akkus_24_ASD/DD/ID_discovery_cases-case25A
3 yrs.
M
ASD
Autism, triangular face, prominent ears, macrocephaly.
45798573
46439822
641250
GRCh38
Duplication
No
houdayer_25_DD/ID_discovery_cases-caseI-27
15 yrs. 2 mos.
M
Developmental delay and intellectual disability
Birth/neonatal history: intrauterine growth retardation, delivery by secondary C-section due to decelerations, small for gestational age (birth weight <5th %ile), birth length <5th %ile, proximal constriction of the penis neonatally. Developmental milestones: mild developmental delay/intellectual disability with delayed ability to sit (18 months) and delayed speech and language development. Language and communication evaluation: dysarthria. Motor and musculoskeletal evaluation: muscular hypotonia of the trunk, facial hypotonia, delayed skeletal maturation, short fifth finger, overlapping toe, hypoplastic fifth toenail. Behavioral/psychiatric evaluation: abnormal aggressive, impulsive, or violent behavior, short attention span, low frustration tolerance. Additional medical history: bilateral inguinal hernia, esodeviation. Dysmorphic features: broad forehead, broad eyebrow, downslanted palpebral fissures, small ears, low-set and posteriorly rotated ears, large earlobe, wide nasal bridge, prominent nasal tip, macrodontia of the permanent maxillary central incisor, thick vermillion border, open mouth, small philtrum, broad chin, retrognathia, long face, triangular face (as an infant), high palate, curly hair. Growth parameters: growth delay with short stature (height -2.9 SD). Family history: this deletion was inherited from an affected mother, and this patient had one healthy sister.
Mild intellectual disability (IQ 50 at 9 years 4 months)
45299856
46290196
990341
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004743
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
38590101
46551898
7961798
GRCh38
Deletion
Yes
lee_21_DD/ID/EP_discovery_cases-case11
15 yrs.
F
Developmental delay and intellectual disability
Birth/neonatal history: small for gestational age. Developmental milestones: developmental delay, language delay. Additional medical history: ventricular septal defect, inguinal hernia, feeding difficulties. Dysmorphic features: sparse hair, thick eyebrows, epicanthus, hypertelorism, flat and broad nasal bridge, low-set ears, long philtrum, large mouth, thick lips, micrognathia. Growth parameters: short stature, microcephaly.
Mild intellectual disability
42612189
46275217
3663029
GRCh38
Deletion
No
wu_24_ASD/ADHD/DD/ID_discovery_cases-case44
4.9 yrs.
F
ASD and developmental delay/intellectual disability
Severe-profound global developmental delay/intellectual disability, comorbid diagnosis of ASD, dysmorphic facial features (low-set ears, micrognathia, broad nasal bridge), microcephaly, short stature (height <-3 SD).
Severe-profound global developmental delay/intellectual disability
45216322
46780030
1563709
GRCh38
Deletion
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
akkus_24_ASD/DD/ID_discovery_cases-case25A
Unknown
SLC38A2,SLC38A1,ARID2,KNOP1P2,SLC38A2-AS1,RN7SL246P,SCAF11
houdayer_25_DD/ID_discovery_cases-caseI-27
Maternal
Maternal
Simplex
Segregated
SLC38A1,ARID2,ANO6,KNOP1P2,RN7SL246P,SCAF11
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00004743
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
CPNE8-AS1,RPL30P13,LINC02555,RNU6-713P,RNA5SP360,MTND2P17,MTND1P24,LINC02400,MIR7851,RNU6-249P,RPS27P21,MRPS36P5,EEF1A1P17,ZNF75BP,RACGAP1P,RNA5SP361,RN7SL246P,KNOP1P2,LINC02406,LINC02471,GXYLT1,ZCRB1,LINC02402,LINC02451,LINC02450,LINC02461,PUS7L,TWF1,DBX2,PLEKHA8P1,SCAF11,SLC38A2,KIF21A,ABCD2,LRRK2,MUC19,PDZRN4,YAF2,PPHLN1,PRICKLE1,ADAMTS20,IRAK4,NELL2,ANO6,ARID2,SLC38A1,CPNE8,C12orf40,SLC2A13,CNTN1,TMEM117
lee_21_DD/ID/EP_discovery_cases-case11
De novo
IRAK4,PLEKHA8P1,RACGAP1P1,SLC38A1,TMEM117,PUS7L,ADAMTS20,ARID2,ANO6,MRPS36P5,DBX2,EEF1A1P17,NELL2,RPS27P21,KNOP1P2,SSBL3P,RNA5SP361,LINC02402,TWF1,LINC02451,LINC02461,LINC02450,RN7SL246P,ZNF75BP,DBX2-AS1,SCAF11
wu_24_ASD/ADHD/DD/ID_discovery_cases-case44
CMA
De novo
Simplex
SLC38A2,SLC38A4,SLC38A1,ARID2,ANO6,OR7A19P,MARK3P1,KNOP1P2,SLC38A2-AS1,RN7SL246P,SCAF11
Controls
No Control Data Available
No Animal Model Data Available