12p13.2-p13.1CNV Type: Deletion
Largest CNV size: 1776542 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
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
Chromosome 12p Deletion Spanning the GRIN2B Gene Presenting With a Neurodevelopmental Phenotype: A Case Report and Review of Literature.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
A 12p13 GRIN2B deletion is associated with developmental delay and macrocephaly.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chaves_19_ASD/DD/ID_discovery_cases
Patients from the south of Brazil with neurodevelopmental disorders
420
Developmental delay/intellectual disability present in 80% of cases, ASD in 32%
Range, 0-49 years (mean 9.5 9.73 years)
61.90% Male
2014470
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
1776542
1
0
1
mishra_17_DD_discovery_cases
3-year-old male patient with de novo 12p13.2-p13.2 deletion encompassing the entire GRIN2B gene
1
Case presented with global developmental delay (with motor skills and expressive speech more delayed than receptive speech), hypotonia, and facial dysmorphic features, as well as mild repetitive behaviors
3 yrs.
Male
3110000
1
0
1
morisada_16_ASD/ID_discovery_cases
First child of healthy, non-consanguineous Japanese parents
1
Case presented with mild intellectual disability and macrocephaly and was diagnosed with autism spectrum disorder (ASD).
6 yrs.
Male
2000000
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
chaves_19_ASD/DD/ID_discovery_cases
Brazil
Array SNP
Affymetrix CytoScan 750K, Affymetrix CytoScan HD
Affymetrix ChAS
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
mishra_17_DD_discovery_cases
N/A
aCGH
N/A
FISH
morisada_16_ASD/ID_discovery_cases
Japanese
aCGH
Agilent 180K
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
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
chaves_19_ASD/DD/ID_discovery_cases-case339
N/A
F
Dysmorphic features
Slender build, facial dysmorphism, and alopecia. Karyotype: 46, XX, Inv (12)(p13q24.1).
10769917
12784386
2014470
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000831
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
11771233
13547775
1776543
GRCh38
Deletion
Yes
mishra_17_DD_discovery_cases-case1
3 yrs.
M
Global developmental delay
Birth/neonatal history: born at term via spontaneous vaginal delivery; antental ultrasound during 33rd week of gestation detected a large head circumference and improper closure of the cerebral ventricles (not seen on postnatal head ultrasound); light meconium present at delivery, bit no resuscitation was required; transient respiratory distress; birth weight of 8 lbs. 7 ozs. (90th %ile); patent foramen ovale detected by echocardiogram at this time. Developmental milestones: global developmental delay noted since early infancy, predominantly affecting motor and language domains; no developmental regression; adequate head control around 6 months, able to sit with support by 9 months, able to sit unsupported by 12 months, could transition from supine to sitting at 18 months, started to pull-to-stand at 24 months; started ambulating independently at 3 years (frequent falls due to poor balance); bilateral pincer grasp at around 15 months; able to spoon-feed himself by 24 months; scribbling with a pen at 3 years (could not draw discrete lines or shapes); significanly delayed language development; social smile developed in infancy; began to laugh around 11 months; not toilet trained and unable to dress himself at 3 years. Langauge and communication evaluation: vocabulary of approximately 5 words at 2 years, which expanded to 10-20 single spontaneous words by 3 years; main method of communication was nonverbal with gestures; receptive lanaguge was comparatively better than expressive language but delayed. able to spontaneously produce few meaningful words at 3 years. Motor and musculoskeletal evaluation: central hypotonia since first week of life; mild truncal hypotonia; poor balance while walking; clinodactyly of fifth digits bilaterally; third and fourth right toe incomplete syndactyly, second toe on right foot is shorter than first and third toes. Behavioral/psychiatric evaluation: social interest in peers, able to initiate and interact in reciprocal play; engaged in some simple pretend play by 24 months; mild repetitive behaviors (turning on/off switches, closing door repeatedly by age 2, restricted play themes); some sensory aversions, including aversion to certain tactile and auditory stimuli; interactive with interest in external environment on neurological examination at 3 years. Epilepsy/seizures: no clinical seizures. EEG: spike and wave discharges over the right posterior parietal head region. Brain imaging: brain MRI not performed. Ophthalmological evaluation: normal. Auditory evaluation: normal. Dysmorphic features: broad forehead, mild frontal bossing, scaphocephaly, hypoplastic supraorbital ridge, prominent nasal bridge, bulbous nose, mild micrognathia, slightly wide mouth, downturned corners of the mouth, deep-set eyes, posteriorly rotated right ear compared to the left, high anterior hairline, single posterior hair whorl, sacro-coccygeal dimple. Growth parameters: height and weight near 50th %ile, head circumference just above 97th %ile. Family history: born to nonconsanguineous parents; significant for developmental delay and primary gastrointestinal malignancies in some family members; case's eldest brother was diagnosed with ASD and ADHD and presented with moderate-to-severe language delay, fine motor delay, motor planning difficulties, and academic challenges; younger brother had isolated speech delay; paternal grandfather had a history of speech and langage delay; paternal grandmother had benign colon tumor removed at age of 21 years; paternal nephew found to have appendiceal tumor at age of 16 years; paternal uncle diagnosed with gastrointestinal cancer in mid-50s.
10995116
14105396
3110281
GRCh38
Deletion
Yes
morisada_16_ASD/ID_discovery_cases-case1
6 yrs.
M
Intellectual disability and ASD
Birth/neonatal history: gestational age 40 weeks 0 days; birth weight of 4112 g (+2.91 SD), length of 53 cm (+1.48 SD), and head circumference of 36 cm (+2.2 SD). Developmental milestones: referred to hospital at age of 7 months due to motor developmental delay and intellectual disability; unable to hold his hea dup at 7 months; unable to sit alone at age of 1 year. Behavioral/psychiatric evaluation: diagnosed with autism spectrum disorder (ASD); diagnostic tools not reported. Epilepsy/seizures: no epileptic convulsions. Brain imaging: no significant abnormalities on cranial MRI. Dysmorphic features: macrocephaly. Growth parameters: height of 90.9 cm (+1.8 SD), weight of 13.28 kg (+1.4 SD), and head circumference of 54.0 cm (+4.8 SD) at age of 2 years. Family history: first child of non-consanguineous Japanese parents: both parents and a younger sister were healthy. Additional genetic information: normal male karyotype detected by standard G-band karyotyping; inherited missense variant in NFIX (c.830G>A;p.Arg277His).
Mild intellectual disability. Developmental quotient, as assessed by the Kyoto Scale of Psychological Development 2001, was 60 (age of 3 years 6 months), 65 (age of 5 years), and 67 (age of 6 years 1 month).
12330022
14283265
1953244
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
chaves_19_ASD/DD/ID_discovery_cases-case339
Unknown
HSPE1P12,TAS2R7,TAS2R8,TAS2R9,TAS2R10,TAS2R13,PRH2,TAS2R15P,TAS2R50,TAS2R20,TAS2R19,TAS2R31,TAS2R63P,TAS2R46,TAS2R64P,TAS2R30,TAS2R42,PRB3,PRB4,HIGD1AP8,DDX55P1,RNU7-60P,PTMAP9,MIR1244-4,RNU6-545P,RNU6-318P,RPL23AP66,LOH12CR2,CDKN1B,MIR613,STX8P1,LINC02366,PRR4,TAS2R43,SMIM10L1,PRB1,LINC01252,MANSC1,DUSP16,CREBL2,RPL21P136,GPR19,APOLD1,PRH1,TAS2R14,PRB2,ETV6,BCL2L14,LRP6,BORCS5
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000831
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
MIR1244-4,RNU6-545P,RNU6-318P,RPL23AP66,LOH12CR2,CDKN1B,MIR613,STX8P1,RPL13AP20,MIR614,HTR7P1,RNA5SP353,RNU6-590P,MANSC1,DUSP16,CREBL2,RPL21P136,GPR19,APOLD1,DDX47,GPRC5A,GPRC5D,GSG1,EMP1,LINC01559,ETV6,BCL2L14,LRP6,BORCS5,GPRC5D-AS1,HEBP1,FAM234B,GRIN2B
mishra_17_DD_discovery_cases-case1
FISH
De novo
Multiplex
Not segregated (deletion not observed in eldest brother diagnosed with ASD and ADHD and presenting with with moderate-to-severe language delay, fine motor delay, motor planning difficulties, and academic challenges)
TAS2R20,TAS2R19,TAS2R31,TAS2R63P,TAS2R46,TAS2R64P,TAS2R30,TAS2R42,PRB3,PRB4,HIGD1AP8,DDX55P1,RNU7-60P,MIR1244-4,RNU6-545P,RNU6-318P,RPL23AP66,LOH12CR2,CDKN1B,MIR613,STX8P1,RPL13AP20,MIR614,HTR7P1,RNA5SP353,RNU6-590P,RN7SKP162,TAS2R43,SMIM10L1,PRB1,LINC01252,MANSC1,DUSP16,CREBL2,RPL21P136,GPR19,APOLD1,DDX47,GPRC5A,GPRC5D,GSG1,EMP1,LINC01559,PRH1,PRH1-PRR4,TAS2R14,PRB2,ETV6,BCL2L14,LRP6,BORCS5,GPRC5D-AS1,HEBP1,FAM234B,GRIN2B
morisada_16_ASD/ID_discovery_cases-case1
De novo
Simplex
Segregated
RPL23AP66,LOH12CR2,CDKN1B,MIR613,STX8P1,RPL13AP20,MIR614,HTR7P1,RNA5SP353,RNU6-590P,RN7SKP162,MRPS18CP4,RNU6-491P,GNAI2P1,MANSC1,DUSP16,CREBL2,RPL21P136,GPR19,APOLD1,DDX47,GPRC5A,GPRC5D,GSG1,EMP1,LINC01559,BORCS5,GPRC5D-AS1,HEBP1,FAM234B,GRIN2B
Controls
No Control Data Available
No Animal Model Data Available