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3p14.2-p14.1CNV Type: Deletion


Largest CNV size: 6666112 bp

Statistics Box:
Number of Reports: 7



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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Decipher

            Decipher Symbol

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
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion
A 3p interstitial deletion in two monozygotic twin brothers and an 18-year-old man: further characterization and review.
Deletion
Excess of rare, inherited truncating mutations in autism.
Deletion
3p14 De Novo Interstitial Microdeletion in a Patient with Intellectual Disability and Autistic Features with Language Impairment: A Comparison with...
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
3p interstitial deletion including PRICKLE2 in identical twins with autistic features.
Deletion
NA
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 de_la_hoz_15_ID_discovery_cases
 First-born child of healthy non-consanguineous parents with no family history of congenital abnormalities or intellectual disability presenting with intellectual disability and autistic features
 1
 Intellectual disability (IQ of 40 at age of 7 years) and autistic features (lack of social smile, poor eye contact, stereotypic movements)
 11 yrs.
 Female
 8000000
 1
 0
 1
 girirajan_13a_ASD_discovery_cases
 1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
 2588
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 NA
 NA
 5633749
 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
 6666112
 1
 0
 1
 krumm_15_ASD_discovery_cases
 Probands from the Simons Simplex Collection
 2377
 Diagnosis of ASD
 N/A
 N/A
 4765842
 1
 0
 1
 larson_17_ASD_discovery_cases
  NA NA
 Participants with a dual diagnosis of ASD and psychosis that were recruited from clinical services in the public and independent sectors in the United Kingdom, as well as from charities and an Asperger's syndrome social networking website (study took place from January 2011 and April 2014)
 116
 All cases with a dual diagnosis of ASD and psychosis (affective, schizophrenic, and atypical)
 N/A
 N/A
 1107454
 1
 0
 1
 okumura_14_DD/ID_discovery_cases
 Male monozygotic twins born to healthy non-consanguineous parents with no family history of congenital anomalies or intellectual deficits
 2
 Severe developmental delay/intellectual disability and autistic features (poor eye contact, lack of social smile, stereotyped behaviors, preference for solitary play)
 4 yrs. 1 mo.
 Male
 6880000
 2
 0
 2
 schwaibold_13_ID/DD/ASD_discovery_cases
 Three patients (two monozygotic twin brothers, one unrelated 18-year-old man) with 3p interstitial deletions and similar phenotypes
 3
 All three cases display severe intellectual disability (ID), psychomotor delay, autistic features, and mild facial dysmorphisms
 Range, 2 yrs. 10 mos.-18 yrs.
 Male
 4760000
 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
 krumm_15_ASD_discovery_controls
 Unaffected siblings from quad families from the Simons Simplex Collection
 1786
 Control
 N/A
 N/A
 0
 0
 0
 0
 larson_17_ASD_discovery_controls
  NA NA
 Entries listed in the Database of Genomic Variants (up to October 2017)
 N/A
 Control
 N/A
 N/A
 1107454
 0
 0
 0

Cases

Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
 de_la_hoz_15_ID_discovery_cases
  Spain
 aCGH
  Perkin Elmer CGX Oligo Array 8x60K
 
 Agilent Feature Extraction v11.0.1.1, Agilent CytoGenomics v2.7, Signature Genomics Genoglyphix
 qRT-PCR
 girirajan_13a_ASD_discovery_cases
  NA
 aCGH
  Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
 ADM-2
 Agilent Genomic Workbench
 aCGH (NimbleGen 135K array)
 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
 krumm_15_ASD_discovery_cases
  N/A
 WES
 
 CoNIFER, XHMM
 
 Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
 larson_17_ASD_discovery_cases
  United Kingdom
 Array SNP
  Affymetrix CytoScan HD 2.8M, Affymetrix Cytogenetics
 SNP-FASST2 Segmentation
 Nexus Copy Number 7 (BioDiscovery), Affymetrix ChAS
 None
 okumura_14_DD/ID_discovery_cases
  Japanese
 aCGH
  Agilent SurePrint G3 Human
 
 
 None
 schwaibold_13_ID/DD/ASD_discovery_cases
  Germany
 aCGH
  Agilent SurePrint G3 4x180K
 
 Feature Extraction v9.1, Cytogenomics 2.0 (Agilent)
 qPCR

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
 
  krumm_15_ASD_discovery_controls
  N/A
  WES
 
  CoNIFER, XHMM
 
  None
  larson_17_ASD_discovery_controls
  N/A
  N/A
  N/A
 
 
 

Cases

Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
  de_la_hoz_15_ID_discovery_cases-case1
 11 yrs.
 F
 Intellectual disability and autistic features
 Birth/neonatal history: unremarkable pregnancy; born at term (39 weeks gestation) by normal delivery; birth weight of 2400 g (<3rd %ile), head circumference of 33.5 cm (<25th %ile); Apgar scores of 7 and 10 at 1 and 5 minutes; no remarkable observations in perinatal period. Developmental milestones: first evaluated at age of 6 months due to poor response to stimuli and lack of social smile, clinical examination at this time revealed significant motor developmental delay; able to walk despite motor clumsiness without support at 20 months; speech difficulties with marked expressive language disorder and global learning problems. Language and communication evaluation: speech difficulties at age of 11 years. Motor and musculoskeletal evaluation: significantly improved motor skills at age of 11 years. Behavioral/psychiatric evaluation: autistic features including stereotypic movements and difficulties with eye contact; social interaction difficulties at 11 years. Brain imaging: no abnormalities on brain MRI at age of 9 years. Dysmorphic features: long face, prominent chin, broad forehead, broad large mouth with widely spaced upper front teeth, slightly large and detached ears. Growth parameters: growing proportionately with age. Family history: first-born child of healthy non-consanguineous parents with no family history of congenital abnormalities or intellectual disability.
 Severe intellectual disability. Received cognitive stimulation therapy from the age of 12 months; psychometric assessment revealed an IQ of 40 at 7 years of age; learning disability at age of 11 years.
 60475583
 68466302
  7990720
 GRCh38
 Deletion
 Yes
  girirajan_13a_ASD_discovery_cases-13830.p1
 N/A
 N/A
 ASD
 Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
 N/A
 60807942
 66269322
  5461381
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000795
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 61970847
 68465832
  6494986
 GRCh38
 Deletion
 Yes
  krumm_15_ASD_discovery_cases-case13830.p1
 N/A
 Male
 ASD
 Proband from the Simons Simplex Collection (SSC). Family type: Quad
 
 61562287
 66263379
  4701093
 GRCh38
 Deletion
 Yes
  larson_17_ASD_discovery_cases-case6
  NA NA
 N/A
 F
 ASD and psychosis
 Female, learning disabilities, psychosis onset mid teens, diagnosis of psychosis NOS, FDR history of depression. CNV not reported in DGV.
 Learning disabilities
 63346147
 64453601
  1107455
 GRCh38
 Deletion
 No
  okumura_14_DD/ID_discovery_cases-case1
 4 yrs. 1 mo.
 M
 Developmental delay/intellectual disability and autistic features
 Referred to outpatient neurology clinic at 7 months of age due to developmental delay. Birth/neonatal history: fetal growth retardation; born at 35 weeks gestation by emergency C-section due to premature rupture of membranes; birth weight of 2096 g (10th %ile), length of 43.0 cm (10th %ile), and head circumference of 34.0 cm (90th %ile); Apgar scores of 8 and 10 at 1 and 5 minutes; mild respiratory distress requiring oxygen supplementation at 7 days; otherwise unremarkable postnatal course. Developmental milestones: sitting at 12 months, walking without support at 43 months; expressive language at 49 months of age. Langauge and communication evaluation: speech delay (no expressive language until 49 months of age). Motor and musculoskeletal evaluation: mild hypotonia. Behavioral/psychiatric evaluation: autistic features (poor eye contact, no social smile, stereotyped behaviors (including staring at a simple object, head-banging, shuddering-like movement, rubbing head on the floor, and repeating simple movements such as hand flapping), and preference for solitary play beyond 4 years of age. Brain imaging: unremarkable cranial MRI at 12 months of age. Dysmorphic features: upswept frontal hair, low-set posterior rotated ears, arched downslanting eyebrow, prominent forehead, epicanthic folds, micrognathia, hypertelorism, broad nasal bridge, short philtrum, camptodactyly of the bilateral 5th fingers. Growth parameters: short stature; height of 91.5 cm (-2.3 SD) and weight of 11.5 kg (-2.1 SD) at age of 49 months. Family history: monozygotic twin with similar phenotype; born to healthy non-consanguineous parents with no family history of congenital anomalies or intellectual deficits.
 Severe developmental delay/intellectual disability; development quotient of 33 (as measured by Kyoto Scale of Psychological Development 2001 at the age of 23 months)
 60472496
 67385119
  6880000
 Unknown
 Deletion
 No
  okumura_14_DD/ID_discovery_cases-case2
 4 yrs. 1 mo.
 M
 Developmental delay/intellectual disability and autistic features
 Referred to outpatient neurology clinic at 7 months of age due to developmental delay. Birth/neonatal history: fetal growth retardation; born at 35 weeks gestation by emergency C-section due to premature rupture of membranes; birth weight of 1530 g (<3rd %ile), length of 39.0 cm (<3rd %ile), and head circumference of 28.7 cm (3rd %ile); Apgar score of 8 and 9 at 1 and 5 minutes; mild respiratory insufficiency requiring oxygen supplementation and IV aminophylline; feeding difficulty that gradually worsened with bilous vomiting; diangosed with intestinal malrotation and transferred to NICU of surgical treatment at 5 days of age (repaired using Ladd procedure, no surgical complications noted); discharged from hospital at age of 34 days. Developmental milestones: sitting at 14 months, walking without support at 49 months; expressive language at 49 months of age. Langauge and communication evaluation: speech delay (no expressive language until 49 months of age). Motor and musculoskeletal evaluation: mild hypotonia. Behavioral/psychiatric evaluation: autistic features (poor eye contact, no social smile, stereotyped behaviors (including staring at a simple object, head-banging, shuddering-like movement, rubbing head on the floor, and repeating simple movements such as hand flapping), and preference for solitary play beyond 4 years of age. Brain imaging: cranial ultrasound revealed dilation of lateral ventricles and flat anterior fontanelle; serial MRI scans revealed nonprogressive mild ventricular dilation throughout clinical course. Additional medical history: slowly progressive ventriculomegaly observed, endoscopic third ventriculostomy performed at 12 months of age. Dysmorphic features: upswept frontal hair, low-set posterior rotated ears, arched downslanting eyebrow, prominent forehead, epicanthic folds, micrognathia, hypertelorism, broad nasal bridge, short philtrum, camptodactyly of the bilateral 5th fingers. Growth parameters: short stature; height of 84.3 cm (-4.2 SD) and weight of 10.4 kg (-2.6 SD) at age of 49 months. Family history: monozygotic twin with similar phenotype; born to healthy non-consanguineous parents with no family history of congenital anomalies or intellectual deficits.
 Severe developmental delay/intellectual disability; development quotient of 34 (as measured by Kyoto Scale of Psychological Development 2001 at the age of 23 months)
 60472496
 67385119
  6880000
 Unknown
 Deletion
 No
  schwaibold_13_ID/DD/ASD_discovery_cases-case3
 18 yrs.
 M
 Intellectual disability and autistic features
 Birth/neonatal history: pregnancy complicated by renal colic of mother at 16th gestational week and several violent assaults by father; spontaneous birth in 43rd gestational week (20 days after due date); birth weight 10th-25th %ile, birth length 10th-25th %ile, OFC 3rd %ile; very agitated and easily frightened as an infant. Developmental milestones: sitting at 15 months, walking at 3 years (gait on tiptoes). Language and communication evaluation: expressive language never developed; uttered sounds or made gestures to express himself; understanfding was better than active speech and could follow simple orders at age of 12 years; received speech therapy (in part due to severe hypersalivation and dismissive sensitivity to orofacial contact). Motor and musculoskeletal evaluation: gait on tiptoes; physiotherapy due to high muscle tone in lower limbs. Behavioral/psychiatric evaluation: demonstrated prolonged stages of screaming up to early adolescence; displayed autistic features, but started to develop eye contact and had friendly behavior in adolescence. EEG: abnormal beta activity assessed as unspecific sign at age of 7 years 9 months. Other features: severe hypersalivation, dismissive sensitivity to orofacial contact in adolescence; sleep disturbances which improved under medication and with further development; still needed diapers at night at age of 18 (seldom wet himself during day). Dysmorphic features: broad & mostly opened mouth with prominent chin and widely spaced teeth (partly with broken ends as case liked chewing hard things), long and slender face with deep-set eyes and flat occiput, fair skin and hair. Brain imaging: brain MRIs at ages of 4 years and 10 years revealed defect in temporal lobe (anamnestically). Family history: second child of non-consanguineous parents; healthy half-sister; history of father unknown (father not available for evaluation).
 Intellectual disability; attended therapeutic school from age of 7 years, received occupational and speech therapy
 59457445
 64176436
  4718992
 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
 de_la_hoz_15_ID_discovery_cases-case1
 qRT-PCR
 
 De novo
 Simplex
 Segregated
 MIR548BB,PPIAP70,PPIAP71,RPL10AP6,RNU2-10P,RN7SL863P,RNU6-139P,KRT8P35,UBL5P3,RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,RNU6-739P,ILF2P1,RPL17P17,RNU6-787P,RN7SL482P,RPL21P41,MIR4272,NDUFB4P1,COPS8P2,PTPRG-AS1,C3orf14,FEZF2,SNTN,THOC7,PSMD6,PSMD6-AS1,PRICKLE2-AS3,ADAMTS9-AS1,LINC02040,MAGI1-AS1,KBTBD8,CADPS,LINC00698,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,ADAMTS9,MAGI1,MAGI1-IT1,SLC25A26,LRIG1,SUCLG2,SUCLG2-AS1,FHIT,PTPRG,ATXN7,ADAMTS9-AS2,FAM19A1
 
 girirajan_13a_ASD_discovery_cases-13830.p1
 aCGH (NimbleGen 135K array)
 
 De novo
 Simplex
 Possibly segregated
 RPL10AP6,RNU2-10P,RN7SL863P,RNU6-139P,KRT8P35,UBL5P3,RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,RNU6-739P,ILF2P1,RPL17P17,PTPRG-AS1,C3orf14,FEZF2,SNTN,THOC7,PSMD6,PSMD6-AS1,PRICKLE2-AS3,ADAMTS9-AS1,LINC02040,MAGI1-AS1,CADPS,LINC00698,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,ADAMTS9,MAGI1,MAGI1-IT1,SLC25A26,FHIT,PTPRG,ATXN7,ADAMTS9-AS2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000795
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 De novo
 Unknown
 Unknown
 RNU2-10P,RN7SL863P,RNU6-139P,KRT8P35,UBL5P3,RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,RNU6-739P,ILF2P1,RPL17P17,RNU6-787P,RN7SL482P,RPL21P41,MIR4272,NDUFB4P1,COPS8P2,PTPRG-AS1,C3orf14,FEZF2,SNTN,THOC7,PSMD6,PSMD6-AS1,PRICKLE2-AS3,ADAMTS9-AS1,LINC02040,MAGI1-AS1,KBTBD8,CADPS,LINC00698,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,ADAMTS9,MAGI1,MAGI1-IT1,SLC25A26,LRIG1,SUCLG2,SUCLG2-AS1,PTPRG,ATXN7,ADAMTS9-AS2,FAM19A1
 
 krumm_15_ASD_discovery_cases-case13830.p1
 Omni2.5-4v1
 
 De novo
 Simplex
 Segregated
 RPL10AP6,RNU2-10P,RN7SL863P,RNU6-139P,KRT8P35,UBL5P3,RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,RNU6-739P,ILF2P1,RPL17P17,PTPRG-AS1,C3orf14,FEZF2,SNTN,THOC7,PSMD6,PSMD6-AS1,PRICKLE2-AS3,ADAMTS9-AS1,LINC02040,MAGI1-AS1,CADPS,LINC00698,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,ADAMTS9,MAGI1,MAGI1-IT1,SLC25A26,PTPRG,ATXN7,ADAMTS9-AS2
 
 larson_17_ASD_discovery_cases-case6
 
 
 Unknown
 
 Unknown
 RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,SNTN,THOC7,PSMD6,PSMD6-AS1,PRICKLE2-AS3,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,ATXN7
 
 okumura_14_DD/ID_discovery_cases-case1
 
 
 De novo
 Multiplex (monozygotic twins)
 Segregated
 FHIT, PTPRG, C3orf14, FEZF2, CADPS, SYNPR, SNTN, C3orf49, THOC7, ATXN7, PSMD6, PRICKLE2, ADAMTS9, MAGI1, SLC25A26, LRIG1, KBTBD8
 
 okumura_14_DD/ID_discovery_cases-case2
 
 
 De novo
 Multiplex (monozygotic twins)
 Segregated
 FHIT, PTPRG, C3orf14, FEZF2, CADPS, SYNPR, SNTN, C3orf49, THOC7, ATXN7, PSMD6, PRICKLE2, ADAMTS9, MAGI1, SLC25A26, LRIG1, KBTBD8
 
 schwaibold_13_ID/DD/ASD_discovery_cases-case3
 qPCR
 
 Unknown (not maternal)
 Unknown (possible simplex)
 Unknown
 MIR548BB,PPIAP70,PPIAP71,RPL10AP6,RNU2-10P,RN7SL863P,RNU6-139P,KRT8P35,UBL5P3,RNA5SP134,THOC7-AS1,SCAANT1,PSMD6-AS2,LINC00994,PRICKLE2-AS2,PRDX3P4,PTPRG-AS1,C3orf14,FEZF2,SNTN,THOC7,PSMD6,PSMD6-AS1,CADPS,LINC00698,SYNPR,SYNPR-AS1,C3orf49,PRICKLE2-AS1,PRICKLE2,FHIT,PTPRG,ATXN7
 

Controls

No Control Data Available
No Animal Model Data Available
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