1p21.3-p13.3CNV Type: Deletion
Largest CNV size: 13365909 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
Deletions within this region were identified in three cases 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
Minor Reports
Title
Author, Year
Report Class
CNV Type
The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population.
Deletion
Two New Cases of 1p21.3 Deletions and an Unbalanced Translocation t(8;12) among Individuals with Syndromic Obesity.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
Retrospective chart review of patients (n=584) with a neurocognitive phenotype (mainly referred from pediatric neurology clinics) seen by a single clinical geneticist from September 2007 to July 2013
584
Inclusion criteria: presence of a neurocognitive phenotype (i.e., syndromic and non-syndromic cases of developmental delay, autism, intellectual disability, and epilepsy) with a normal karyotype
N/A
N/A
11190001
1
0
1
d'angelo_15_ID_discovery_cases
Female patients referred to analysis for obesity and intellectual disability that presented with 1p21.3 microdeletions affecting DPYD and MIR137
2
Both individuals presented with intellectual disability, obesity, and postnatal macrocephaly; one case presented with pervasive developmental disorder
Range, 8 yrs. 8 mos.-15 yrs.
Female
12000000
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
13365909
3
0
3
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
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases
Saudi Arabia
Array SNP
Affymetrix 6.0, Affymetrix Cyto-V2, Affymetrix CytoScan HD
HMM
Affymetrix GeneChip Command Console v.1.2, Affymetrix ChAS version Cyto 2.0.0.195
None
d'angelo_15_ID_discovery_cases
Brazil
aCGH
OGT CytoSure ISCA 4x180K
ADM-2
Agilent Feature Extraction, Agilent Genomic Workbench
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
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
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case08DG00312
N/A
M
Developmental delay
Global developmental delay, remarkable shyness, with subtle dysmorphic features and obesity. Non-consanguineous parents.
Global developmental delay
96064444
107177378
11112935
GRCh38
Deletion
No
d'angelo_15_ID_discovery_cases-case2
8 yrs. 8 mos.
F
Intellectual disability and pervasive developmental disorder
Birth/neonatal history: born at 39 weeks of gestation after uneventful pregnancy; birth weight 4500 (97th %ile), birth length 52 cm (75th %ile); rapid weight gain during the first weeks of life (put on a calorie-restricted diet at 3 months of age). Developmental milestones: psychomotor delay (walked at 20 months), severe language delay (first words at age of 2 years). Motor and musculoskeletal evaluation: large hands (> 97th %ile). Behavioral/psychiatric evaluation: pervasive developmental disorder; marked hyperphagia. Additional medical history: precocious puberty; advanced bone age; low plasmatic iron level (40 micrograms/dl; normal range 50-150 micrograms/dl). Growth parameters: obesity, postnatal macrocephaly; weight of 46 kg (> 97th %ile), height of 123 cm (90th-95th %ile), OFC of 54.5 cm (> 98th %ile), and BMI 30.4 (> 95th %ile) at age of 6 years; weight of 65 kg (> 97th %ile), height of 140 cm (90th-95th %ile), and BMI of 33.2 (> 95th %ile) at most recent examination. Family history: born to unrelated healthy parents (parental samples not available for testing).
Intellectual disability
95230888
107213257
11982370
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002262
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
97410602
110670510
13259909
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005311
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
98557000
107949047
9392048
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005366
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
98557000
107949047
9392048
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
al-qattan_14_DD/ID/ASD/ADHD/EP_discovery_cases-case08DG00312
Unknown
Unknown
Unknown
RNU1-130P,UBE2WP1,EEF1A1P11,RN7SL831P,NDUFS5P2,RPL7P9,RN7SKP270,SEC63P1,RPL26P9,DPYD-AS2,MIR2682,MIR137,NFU1P2,HMGB3P10,RNU4-75P,RNU6-750P,RNU6-1318P,RPL23AP90,BRI3P1,MIR553,BCAS2P2,GPR88,S1PR1,PPIAP7,RNU6-965P,RPSAP19,RNU6-352P,DNAJA1P5,SOD2P1,RN7SKP285,ACTG1P4,AMY2A,AMYP1,AMY1C,FTLP17,CDK4P1,SEPT2P1,MTATP6P14,MTCO1P14,PRMT6,DPYD-IT1,LINC01776,PLPPR4,PALMD,MFSD14A,SASS6,LRRC39,DBT,RTCA-AS1,LINC01349,VCAM1,EXTL2,HNRNPA1P68,DPH5,LINC01307,AMY2B,AMY1A,AMY1B,LINC01676,LINC01677,LINC01787,PTBP2,DPYD-AS1,MIR137HG,SNX7,PLPPR5,LINC01708,FRRS1,AGL,SLC35A3,TRMT13,RTCA,CDC14A,SLC30A7,OLFM3,COL11A1,RNPC3,LINC01661,NTNG1,DPYD,LINC01709
d'angelo_15_ID_discovery_cases-case2
Unknown
LINC01760,LINC01650,LINC01761,RNU1-130P,UBE2WP1,EEF1A1P11,RN7SL831P,NDUFS5P2,RPL7P9,RN7SKP270,SEC63P1,RPL26P9,DPYD-AS2,MIR2682,MIR137,NFU1P2,HMGB3P10,RNU4-75P,RNU6-750P,RNU6-1318P,RPL23AP90,BRI3P1,MIR553,BCAS2P2,GPR88,S1PR1,PPIAP7,RNU6-965P,RPSAP19,RNU6-352P,DNAJA1P5,SOD2P1,RN7SKP285,ACTG1P4,AMY2A,AMYP1,AMY1C,FTLP17,CDK4P1,SEPT2P1,MTATP6P14,MTCO1P14,PRMT6,RWDD3,DPYD-IT1,LINC01776,PLPPR4,PALMD,MFSD14A,SASS6,LRRC39,DBT,RTCA-AS1,LINC01349,VCAM1,EXTL2,HNRNPA1P68,DPH5,LINC01307,AMY2B,AMY1A,AMY1B,LINC01676,LINC01677,TMEM56-RWDD3,LINC01787,PTBP2,DPYD-AS1,MIR137HG,SNX7,PLPPR5,LINC01708,FRRS1,AGL,SLC35A3,TRMT13,RTCA,CDC14A,SLC30A7,OLFM3,COL11A1,RNPC3,LINC01661,NTNG1,DPYD,LINC01709
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002262
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
SEC63P1,RPL26P9,DPYD-AS2,MIR2682,MIR137,NFU1P2,HMGB3P10,RNU4-75P,RNU6-750P,RNU6-1318P,RPL23AP90,BRI3P1,MIR553,BCAS2P2,GPR88,S1PR1,PPIAP7,RNU6-965P,RPSAP19,RNU6-352P,DNAJA1P5,SOD2P1,RN7SKP285,ACTG1P4,AMY2A,AMYP1,AMY1C,FTLP17,CDK4P1,SEPT2P1,MTATP6P14,MTCO1P14,PRMT6,MIR7852,ST13P21,PRPF38B,SPATA42,RANP5,TMEM167B,SCARNA2,C1orf194,ATXN7L2,AMIGO1,RNU6V,MIR197,RPL7P8,NDUFA5P10,UBL4B,LINC02586,LAMTOR5,PROK1,CYMP,CYMP-AS1,KCNA10,DPYD-IT1,LINC01776,PLPPR4,PALMD,MFSD14A,SASS6,LRRC39,DBT,RTCA-AS1,LINC01349,VCAM1,EXTL2,HNRNPA1P68,DPH5,LINC01307,AMY2B,AMY1A,AMY1B,LINC01676,LINC01677,VAV3-AS1,NBPF4,SLC25A24P1,NBPF6,FAM102B,FNDC7,AKNAD1,CLCC1,WDR47,TAF13,SARS,CELSR2,PSRC1,MYBPHL,PSMA5,SYPL2,CYB561D1,GPR61,GNAT2,AMPD2,GSTM4,GSTM5,GSTM3,EPS8L3,CSF1,AHCYL1,STRIP1,ALX3,SLC6A17,RBM15-AS1,RBM15,SLC16A4,MIR137HG,SNX7,PLPPR5,LINC01708,FRRS1,AGL,SLC35A3,TRMT13,RTCA,CDC14A,SLC30A7,OLFM3,COL11A1,RNPC3,LINC01661,NTNG1,VAV3,SLC25A24,NBPF5P,SLC25A24P2,HENMT1,STXBP3,GPSM2,KIAA1324,SORT1,GNAI3,GSTM2,GSTM1,LINC01768,KCNC4,LAMTOR5-AS1,KCNA2,DPYD,LINC01709,LINC01397
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005311
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
HMGB3P10,RNU4-75P,RNU6-750P,RNU6-1318P,RPL23AP90,BRI3P1,MIR553,BCAS2P2,GPR88,S1PR1,PPIAP7,RNU6-965P,RPSAP19,RNU6-352P,DNAJA1P5,SOD2P1,RN7SKP285,ACTG1P4,AMY2A,AMYP1,AMY1C,FTLP17,CDK4P1,SEPT2P1,MTATP6P14,MTCO1P14,PRMT6,MIR7852,PLPPR4,PALMD,MFSD14A,SASS6,LRRC39,DBT,RTCA-AS1,LINC01349,VCAM1,EXTL2,HNRNPA1P68,DPH5,LINC01307,AMY2B,AMY1A,AMY1B,LINC01676,LINC01677,SNX7,PLPPR5,LINC01708,FRRS1,AGL,SLC35A3,TRMT13,RTCA,CDC14A,SLC30A7,OLFM3,COL11A1,RNPC3,LINC01661,NTNG1,VAV3,LINC01709
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005366
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
HMGB3P10,RNU4-75P,RNU6-750P,RNU6-1318P,RPL23AP90,BRI3P1,MIR553,BCAS2P2,GPR88,S1PR1,PPIAP7,RNU6-965P,RPSAP19,RNU6-352P,DNAJA1P5,SOD2P1,RN7SKP285,ACTG1P4,AMY2A,AMYP1,AMY1C,FTLP17,CDK4P1,SEPT2P1,MTATP6P14,MTCO1P14,PRMT6,MIR7852,PLPPR4,PALMD,MFSD14A,SASS6,LRRC39,DBT,RTCA-AS1,LINC01349,VCAM1,EXTL2,HNRNPA1P68,DPH5,LINC01307,AMY2B,AMY1A,AMY1B,LINC01676,LINC01677,SNX7,PLPPR5,LINC01708,FRRS1,AGL,SLC35A3,TRMT13,RTCA,CDC14A,SLC30A7,OLFM3,COL11A1,RNPC3,LINC01661,NTNG1,VAV3,LINC01709
Controls
No Control Data Available
No Animal Model Data Available