3p14.2-p14.1CNV Type: Deletion
Largest CNV size: 6666112 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
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
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
3p14 De Novo Interstitial Microdeletion in a Patient with Intellectual Disability and Autistic Features with Language Impairment: A Comparison with...
Deletion
Minor Reports
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
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
streata_22_ASD/DD/ID_discovery_cases
Patients evaluated for global developmental delay and/or intellectual disability in pediatric, child neurology, or medical genetics departments throughout Romania who were referred to the Regional Centre for Medical Genetics for genetic testing between 2015 and 2022.
371
All cases presented with global developmental delay (DD) and/or intellectual disability (ID); a subset of cases also presented with autism spectrum disorder (ASD).
Range, 6 mos.-40 yrs. (median age, 5.5 yrs.)
63.07% Male
4158923
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
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
streata_22_ASD/DD/ID_discovery_cases
Romania
aCGH
Agilent SurePrint G3 ISCA v.2 8x60K, Agilent 4x180K, OGT CytoSure ISCA v.2 8x60K
NA
Agilent CytoGenomics, OGT CytoSure Interpret
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
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
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
streata_22_ASD/DD/ID_discovery_cases-case214
NA
F
Developmental delay and intellectual disability
Global developmental delay, speech and/or language delay or impairment, congenital anomalies, facial dysmorphism.
Severe intellectual disability
62160193
66319115
4158923
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
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
streata_22_ASD/DD/ID_discovery_cases-case214
Unknown
FEZF2,C3orf14,ADAMTS9,THOC7,SNTN,C3orf49,SYNPR,SLC25A26,MAGI1-IT1,PRICKLE2,LINC00698,UBL5P3,RPL17P17,LINC00994,KRT8P35,PRDX3P4,ILF2P1,PTPRG-AS1,ADAMTS9-AS2,PSMD6-AS2,PRICKLE2-AS1,SCAANT1,SYNPR-AS1,MAGI1-AS1,PRICKLE2-AS2,THOC7-AS1,PRICKLE2-AS3,PTPRG,ATXN7,PRICKLE2-DT,ADAMTS9-AS1,LINC02040,RNU6-787P,RNU6-739P,RN7SL863P,RNA5SP134,RNU6-139P,PSMD6-AS1,CADPS,PSMD6,MAGI1
Controls
No Control Data Available
No Animal Model Data Available