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1q21.3-q22CNV Type: Deletion


Largest CNV size: 714527 bp

Statistics Box:
Number of Reports: 3



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
Performance of chromosomal microarray for patients with intellectual disabilities/developmental delay, autism, and multiple congenital anomalies in...
Deletion
Management of Severe Developmental Regression in an Autistic Child with a 1q21.3 Microdeletion and Self-Injurious Blindness.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type

No Minor Reports

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 chong_14_DD/ID/ASD/MCA_discovery_cases
 Patients referred to clinical genetics service and recruited for CMA application study
 105
 Developmental delay/intellectual disability (DD/ID), autism (ASD), and/or multiple congenital anomalies (MCA)
 N/A
 N/A
 1240000
 1
 0
 1
 cravero_17_ASD/ID_discovery_cases
 Last child in a family of six with five healthy sisters and healthy non-consanguineous parents with unremarkable family history that presented with a de novo 1q21.3-q22 microdeletion
 1
 Case initially diagnosed with autism at age of 3 years (based on communication and social interaction impairments and restricted, repetitive patterns of behavior and interests); psychiatric evaluation at age of 7 years 7 months confirmed original diagnosis of autism (CARS score of 38, indicating severe autism) and also led to a diagnosis of severe intellectual disability (Vineland-II developmental age equivalent to 12 months in areas of communication and social skills and 15 months in autonomy)
 7 years 7 months
 Male
 1400000
 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
 714527
 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
 chong_14_DD/ID/ASD/MCA_discovery_cases
  Chinese
 aCGH
  High-resolution 180K oligoarray
 
 
 aCGH (NimbleGen)
 cravero_17_ASD/ID_discovery_cases
  Congolese
 aCGH
  N/A
 
 
 FISH
 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

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
  chong_14_DD/ID/ASD/MCA_discovery_cases-caseaCGH4935
 N/A
 F
 DD and autistic features
 Severe developmental delay,autistic features, hypotonia, dysmorphic features
 Severe developmental delay
 154141542
 155388230
  1246689
 GRCh38
 Deletion
 Yes
  cravero_17_ASD/ID_discovery_cases-case1
 7 yrs. 7 mos.
 M
 Autism and intellectual disability
 Case initially diagnosed with autism at age of 3 years (based on communication and social interaction impairments and restricted, repetitive patterns of behavior and interests); diagnosis confirmed following psychiatric evaluation at age of 7 years 7 months (CARS score of 38, indicating severe autism). Birth/neonatal history: uneventful pregnancy; born at term at 38 weeks of gestation by emergency C-section; birth weight 2680 g, Apgar scores of 2-6; ventilation during first five minutes of life. Developmental milestones: began to walk at 23 months of age; delayed speech development (first words at age of 3 years, vocabulary later limited to three words); developmental regression noted after loss of sight at age of 4 years (increasingly important attachment to adults, grasping behavior, loss of walking, increased self-injurious behaviors, diet almost exclusively made up of dairy products). Motor and musculoskeletal evaluation: inability to walk (case moved on his back by jerking on the ground or requested to be carried); thin legs; genu valgus; genu recurvatum; hyperlaxity; clinodactyly of 4th and 5th fingers of the right hand and the left and right fifth toe. Behavioral/psychiatric evaluation: behavioral problems reported before the age of 2 years; self-injurious behaviors (intense and repeated mutilations of cheekbones and eyes culminating in bilateral blindness at age of 4 years by intumescent white cataract after numerous surgical complication; knee blows on face, punches against cheekbones, and head banging against walls noted following admission into dedicated neurodevelopmental child psychiatric unit at age of 7 years 7 months); mood fluctation, alternating between emotional outbursts with bursts of self-stimulatory behaviors (stereotypies) and significant irritability, intolerance to frustration, opposition behaviors, tantrums, and sleeping troubles. Epilepsy/seizures: epilepsy was not diagnosed by neuropediatric team. EEG: EEG after sleep deprivation identified a somewhat slow wake-up track for his age, with sleep figures and arrangements preserved; sleep plot showed predominant intermittent slow activity on the anterior and one or two spikes on temporal. Brain imaging: brain MRI detected multiple structural brain abnormalities (moderate enlargement of temporal horns and frontal horns of lateral ventricles, also associated with moderate expansion of hemispheric grooves, with thickening of cranial vault; moderate diffuse hyperintensity of supratentorial white matter and a change of intracranial visual ways associated with atrophy of the eyeballs). Additional medical history: xerostomia; feeding difficulties (regurgitation, vomiting, refusal of solid food, forced feeding, gastroesophageal reflux, constipation; altered intestinal transit with episodes of diarrhea, encopresis, and coprophagia); ear infections and inflammation of sinus mucosa; chronic rhinosinusitis; numerous cavity lesions. Dysmorphic features: broad-based flat nose, poor dental status, lanugo. Growth parameters: weight 25th %ile, height -0.5 SD, BMI of 14.2 kg/m(2), head circumference within normal range. Family history: last child in a family of six, with five healthy sisters; mother was 41 years old and father was 44 years old at time of birth; parents were not related, and family history was unremarkable.
 Severe intellectual disability (Vineland-II developmental age equivalent to 12 months in areas of communication and social skills and 15 months in autonomy at age of 7 years 7 months)
 154104996
 155539091
  1434096
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002379
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 154575689
 155292901
  717213
 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
 chong_14_DD/ID/ASD/MCA_discovery_cases-caseaCGH4935
 Nimblegen aCGH
 
 De novo
 Unknown
 Unknown
 RN7SL431P,MIR190B,C1orf43,SNORA58B,HAX1,RNU6-239P,RNU6-121P,AQP10,RNU7-57P,RPSAP17,PSMD8P1,UBE2Q1-AS1,CHRNB2,PBXIP1,SHC1,MIR4258,LENEP,DCST1-AS1,EFNA4,EFNA3,EFNA1,SLC50A1,HMGN2P18,TRIM46,MIR92B,MTX1,MTX1P1,SCAMP3,PKLR,RUSC1,MIR555,RNU6-106P,TPM3,C1orf189,UBAP2L,ATP8B2,IL6R,SHE,UBE2Q1,ADAR,PYGO2,CKS1B,FLAD1,ZBTB7B,DCST2,DCST1,DPM3,KRTCAP2,THBS3,GBAP1,GBA,FAM189B,CLK2,HCN3,IL6R-AS1,TDRD10,KCNN3,PMVK,ADAM15,FDPS,RUSC1-AS1,ASH1L,NUP210L,MUC1
 
 cravero_17_ASD/ID_discovery_cases-case1
 FISH
 
 De novo
 Simplex
 Segregated
 RN7SL431P,MIR190B,C1orf43,SNORA58B,HAX1,RNU6-239P,RNU6-121P,AQP10,RNU7-57P,RPSAP17,PSMD8P1,UBE2Q1-AS1,CHRNB2,PBXIP1,SHC1,MIR4258,LENEP,DCST1-AS1,EFNA4,EFNA3,EFNA1,SLC50A1,HMGN2P18,TRIM46,MIR92B,MTX1,MTX1P1,SCAMP3,PKLR,RUSC1,MIR555,RNU6-106P,ASH1L-IT1,RNU6-1297P,POU5F1P4,TPM3,C1orf189,UBAP2L,ATP8B2,IL6R,SHE,UBE2Q1,ADAR,PYGO2,CKS1B,FLAD1,ZBTB7B,DCST2,DCST1,DPM3,KRTCAP2,THBS3,GBAP1,GBA,FAM189B,CLK2,HCN3,IL6R-AS1,TDRD10,KCNN3,PMVK,ADAM15,FDPS,RUSC1-AS1,ASH1L,NUP210L,MUC1
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002379
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 CHRNB2,PBXIP1,SHC1,MIR4258,LENEP,DCST1-AS1,EFNA4,EFNA3,EFNA1,SLC50A1,HMGN2P18,TRIM46,MIR92B,MTX1,MTX1P1,SCAMP3,PKLR,ADAR,PYGO2,CKS1B,FLAD1,ZBTB7B,DCST2,DCST1,DPM3,KRTCAP2,THBS3,GBAP1,GBA,FAM189B,CLK2,HCN3,KCNN3,PMVK,ADAM15,MUC1
 

Controls

No Control Data Available
No Animal Model Data Available
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