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12p13.2-p13.1CNV Type: Deletion


Largest CNV size: 1776542 bp

Statistics Box:
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

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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
NA
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
  NA NA
 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
  NA NA
 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
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