9p23-p22.2CNV Type: Deletion
Largest CNV size: 8372721 bp
Statistics Box:
Number of Reports: 3
Number of Reports: 3
Summary Information
Deletions within this region were found 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
NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing
Duplication
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
8372721
3
0
3
schanze_18_DD/ID_discovery_cases
Individuals with overlapping microdeletions of the chromosomal 9p23-p22.2 region affecting the NFIB gene
10
All individuals presented with mild intellectual disability or learning disability and speech delay; three cases presented with ASD, one case presented with ADHD.
Range, 3 years 5 months-32 years
40.0% Male
4900000
3
0
3
wang_20_ID_discovery_cases
Patients recruited from the Department of Neurology, Affiliated Childrens Hospital of the Capital Institute of Pediatrics (Beijing, China) between Jan. 2016.01 and Dec. 2018.
95
All cases presented with intellectual disability (ID); 52 patients had ID with multiple congenital anomalies, and 14 patients had ID with autism spectrum disorder
Range, 1 yr. 1 mo.-16 yrs.
68.0% Male
6720003
0
1
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
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
schanze_18_DD/ID_discovery_cases
4 Caucasian, 6 not reported
aCGH, array SNP, solid phase hybridization
Affymetrix 6.0, Affymetrix CytoScan HD, Agilent 60K, BlueGnome CytoChip v1.1, Illumina Infinium II HumanHap610 BeadChip, OGT CytoSure ISCA v2 8x60k, OGT CytoSure ISCA v2 180K
Affymetrix Genotyping Console v.3.0.1, Affymetrix Genotyping Console v.4.1, Affymetrix ChAS v.1.2, A
MLPA
wang_20_ID_discovery_cases
Han Chinese
WGS
Illumina HiSeq 2000
Short Oligonucleotide Analysis Package (SOAP) v.2.21
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
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000110
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
9661633
18034356
8372724
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000986
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
11086096
17636671
6550576
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002791
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
11818291
17963882
6145592
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP13
7 yrs. 10 mos.
F
Intellectual disability
Birth/neonatal history: born after uneventful pregnancy at 41 weeks of gestation; weight 4030 g (+1.32 SD, 91st %ile), length 56 cm (+2.38 SD, 99th %ile), and OFC 37 cm (+1.22 SD, 89th %ile)at birth. Developmental milestones: initial developmental milestones reported normal; delayed speech and language development. Language and communication evaluation: speech improved with speech therapy (receptive language skills appears to be less delayed than expressive speech). Motor and musculoskeletal evaluation: muscular hypotonia, long fingers and toes, flat feet. Behavioral/psychiatric evaluation: attention deficit, temper tantrums, aggressive behavior. Brain imaging: complete agenesis of the corpus callosum, mildly decreased white matter volume, slightly enlarged cerebral ventricles. Additional medical history: recurrent infections (several pneumonias and frequent otitis media) during early childhood. Dysmorphic features: downslanting palpebral fissures, sparse lateral eyebrows, high and narrow nasal bridge, flat philtrum, thin upper lip vermillion, thick lower lip, small ears, slight retrognathia, left inverted nipple, bilateral sandal gaps. Growth parameters: macrocephaly; height 137 cm (+2.68 SD, >99th %ile), weight 43.9 kg (+3.82 SD, >99th %ile), OFC 57 cm (+4.39 SD, >99th %ile). Family history: first of two children of a non-consanguineous, healthy couple with unremarkable family history.
Mild intellectual disability (global IQ of 45 at age of 6 years 5 months using HAWIK)
14178769
16619011
2440243
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP14
10 yrs.
M
ASD and intellectual disability
Birth/neonatal history: born at 40 weeks of gestation; weight 3200 g (-0.58 SD, 28th %ile) and length 49 cm (-0.44 SD, 33rd %ile) at birth (OFC not determined); feeding difficulties and crying spells for several months. Developmental milestones: delayed speech and language development, motor delay. Motor and musculoskeletal evaluation: muscular hypotonia, distended abdomen with weak abdominal muscles. Behavioral/psychiatric evaluation: attention deficit, diagnosis of ASD, one psychotic episode at age of 8 years. Additional medical history: cryptorchidism. Dysmorphic features: trigonocephaly (surgically corrected), short and narrow palpebral fissures, sparse eyebrows, epicanthus, long philtrum, high narrow palate, small and low-set ears. Growth parameters: height 144 cm (+0.80 SD, 79th %ile), weight 41 kg (+0.99 SD, 84th %ile), OFC 54.5 cm (+1.19 SD, 88th %ile). Family history: second child of healthy, non-consanguineous Caucasian parents.
Mild intellectual disability
13563538
18491754
4928217
GRCh38
Deletion
schanze_18_DD/ID_discovery_cases-subjectP15
17 yrs.
F
Learning disability
Birth/neonatal history: born at term after uneventful pregnancy, birth weight 3370 g (-0.11 SD, 46th %ile), length and OFC at birth not determined; slow feeding and recurrent infections in infancy. Developmental milestones: delayed speech and language development. Language and communication evaluation: articulation difficulties. Motor and musculoskeletal evaluation: muscular hypotonia, reduced muscle tone; mild radial deviation of the 4th distal phalanges, broad thumbs, 2nd toes longer than halluces, very short 4th and 5th metatarsals, mild shortening of the 4th and 5th metacarpals. Behavioral/psychiatric evaluation: attention deficit, episodes of challenging behavior. Cardiac evaluation: bicuspid aortic valve, systolic murmur, mild tricuspid valve regurgitation. Visual evaluation: bilateral esotropia, hypermetropia. Additional medical history: bilateral mid-ear effusions (treated with grommets), tonsillectomy. Dysmorphic features: significant epicanthal folds, short and narrow palpebral fissures, sparse lateral eyebrows, small ears with flat upper helices, low-set right ear, small nose, narrow nasal bridge, small mouth, everted lower lip, fetal finger pads, hypertrichosis of the lower back and lower legs, distended abdomen. Growth parameters: height 75th %ile, weight 50th-75th %ile, OFC 50th-75th %ile. Family history: only child of non-consanguineous Caucasian parents, four maternal and paternal healthy half-siblings; distal limb anomalies were similarly present in the patient's mother who was otherwise healthy and probably represent a familial form of Brachydactyly Type E.
Learning disability
13739631
18023841
4284211
GRCh38
Deletion
wang_20_ID_discovery_cases-case5
4 yrs. 6 mos.
M
Intellectual disability
Abnormality of the palmar creases, laryngomalacia, muscular hypertonia, facial abnormality
Intellectual disability
10060000
16780002
6720003
GRCh38
Duplication
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000110
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
AKAP8P1,RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,RN7SL720P,RPS29P33,SAMM50P1,PABPC1P11,IMP3P1,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,SNAPC3,PTPRD-AS2,LURAP1L-AS1,MPDZ,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,CNTLN,SH3GL2,ZDHHC21,CCDC171,ADAMTSL1,PTPRD,BNC2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000986
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,RN7SL720P,RPS29P33,SAMM50P1,PABPC1P11,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,SNAPC3,LURAP1L-AS1,MPDZ,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,CNTLN,SH3GL2,ZDHHC21,CCDC171,BNC2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00002791
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
De novo
Unknown
Unknown
RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,RN7SL720P,RPS29P33,SAMM50P1,PABPC1P11,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,SNAPC3,LURAP1L-AS1,MPDZ,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,CNTLN,SH3GL2,ZDHHC21,CCDC171,ADAMTSL1,BNC2
schanze_18_DD/ID_discovery_cases-subjectP13
MLPA
De novo
Simplex
Segregated
CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,SNAPC3,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,ZDHHC21,CCDC171,BNC2
schanze_18_DD/ID_discovery_cases-subjectP14
De novo
Simplex
Segregated
PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,RN7SL720P,RPS29P33,SAMM50P1,PABPC1P11,LINC00583,RPL3P11,SNAPC3,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,CNTLN,SH3GL2,ZDHHC21,CCDC171,ADAMTSL1,BNC2
schanze_18_DD/ID_discovery_cases-subjectP15
De novo
Simplex
Segregated
PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,RN7SL720P,RPS29P33,SAMM50P1,PABPC1P11,LINC00583,RPL3P11,SNAPC3,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,CNTLN,SH3GL2,ZDHHC21,CCDC171,ADAMTSL1,BNC2
wang_20_ID_discovery_cases-case5
Unknown
Unknown
Unknown
AKAP8P1,RNU2-47P,RN7SL849P,PRDX1P1,PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,RN7SL98P,FTH1P12,RNU6-246P,HMGN2P16,RNU6-14P,BNC2-AS1,LSM1P1,IMP3P1,JKAMPP1,TYRP1,LURAP1L,LINC01235,LINC00583,RPL3P11,SNAPC3,PTPRD-AS2,LURAP1L-AS1,MPDZ,NFIB,FREM1,CLCN3P1,TTC39B,PSIP1,C9orf92,ZDHHC21,CCDC171,PTPRD,BNC2
Controls
No Control Data Available
No Animal Model Data Available