9p23-p22.3CNV Type: Deletion
Largest CNV size: 1618988 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
A deletion within this region was identified in a patient with agenesis of the corpus callosum and developmental delay (Sajan et al., 2013).
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.
Deletion
Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders.
Deletion
NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
mazzonetto_24_ASD/DD/ID_discovery_cases
Patients from a total of 15 non-profit organizations and university centers located in different states of Brazil who were enrolled between July 2021 and June 2022 and referred with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorder (ASD), and/or multiple congenital anomalies.
1363
"95% of individuals in this cohort reported with the HPO phenotype ""Abnormality of the nervous system"" (HP:0000707); the HPO phenotypes ""Intellectual disability"" (HP:0001249; 36%), ""Global developmental delay"" (HP:0001263; 32%), and ""Autism"" (HP:0000717; 28%) were the most frequently reported phenotype subcategories within this subset of individuals."
63.17% Male
5200000
1
0
1
pfundt_16_NDD_discovery_cases
Subset of a cohort of 2,603 patients affected by genetic disorders for which exome seqeuncing was performed in a diagnostic setting
1215
Neurodevelopmental disorders
N/A
N/A
2027257
1
0
1
sajan_13_ACC/CBLH/PMG_discovery_cases
Individuals with severe congenital brain malformations [agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG)] and additional neurodevelopmental phenotypes
487
Diagnosis of agenesis of the corpus callosum (ACC), cerebellar hypoplasia (CBLH), and/or polymicrogyria (PMG); additional diagnoses of autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID) and/or seizures in some patients
N/A
N/A
1618988
1
0
1
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
1600000
7
0
7
yuan_23_ASD_discovery_cases
ASD probands from 353 pedigrees (338 simplex trios, 15 multiplex families) recruited from the Department of Child and Adolescent Psychiatry, Shanghai Mental Health Center (Shanghai, China).
369
Cases diagnosed with ASD using DSM-IV.
NA
NA
225816
0
1
1
Controls
No Control Data Available
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
mazzonetto_24_ASD/DD/ID_discovery_cases
Brazil
Low-pass WGS
Illumina NovaSeq 6000
SNP-FASST2 (HMM)
BioDiscovery NxClinical
pfundt_16_NDD_discovery_cases
N/A
WES
Solid5500xl, IlluminaHiSeq2000
CoNIFER
Array SNP (Affymetrix CytoScan HD)
sajan_13_ACC/CBLH/PMG_discovery_cases
81.31% Caucasian
Solid phase hybridization
Illumina InfiniumII HumanHap610
PennCNV
qPCR
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
FISH, MLPA, qPCR
yuan_23_ASD_discovery_cases
China
WES
Illumina HiSeq
NA
GATK v.4.2.0.0.
None
Controls
No Control Data Available
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530526
F
Developmental delay
Global developmental delay (HP:0001263), poor speech (HP:0002465), atypical behavior (HP:0000708), abnormal facial shape (HP:0001999)
9410001
14610000
5200000
GRCh38
Deletion
No
pfundt_16_NDD_discovery_cases-case90
N/A
N/A
NDD and mitochondrial oxidative phosphorylation disorder
Disease cohort: neurodevelopmental disorder / mitochondrial oxidative phosphorylation disorder. Description: FREM1 MOTA deletion; de novo
13406379
15433637
2027259
GRCh38
Deletion
Yes
sajan_13_ACC/CBLH/PMG_discovery_cases-case1127-0
N/A
N/A
ACC
Diagnosis of agenesis of the corpus callosum (ACC). ASD: no. Seizures: no.
Developmental delay: yes. Intellectual disability: no.
13044408
14663396
1618989
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP10a
20 yrs.
F
Intellectual disability
Birth/neonatal history: weight 4400 g (+2.13 SD, 98th %ile), length 58 cm (+3.1 SD, > 99th %ile), and OFC 39 cm (+1.92 SD, 97th %ile) at birth. Developmental milestones: delayed speech and language development, motor delay. Motor and musculoskeletal evaluation: muscular hypotonia. Behavioral/psychiatric evaluation: attention deficit short temper. Additional medical history: history of histiocytosis in skull (treated with radiotherapy and made a full recovery). Dysmorphic features: high forehead, anteverted nares, broad nasal tip. Growth parameters: microcephaly; height 165 cm (+0.27 SD, 61st %ile), weight 68.5 kg (+0.68 SD, 75th %ile), OFC 61 cm (+6.01 SD, >99th %ile).
Mild intellectual disability
13974416
14286260
311845
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP10b
3 yrs. 5 mos.
F
Intellectual disability
Birth/neonatal history: born by normal delivery; weight 3400 g (-0.05 SD, 48th %ile) and OFC 37 cm (+1.22 SD, 89th %ile) at birth; no neonatal problems. Developmental milestones: normal early milestones; delayed speech and language development, motor delay. Motor and musculoskeletal evaluation: muscular hypotonia. Cardiac evaluation: patent ductus arteriosus. Additional medical history: bilateral inguinal hernias, blocked tear ducts. Dysmorphic features: anteverted nares, high forehead. Growth parameters: macrocephaly; height 92 cm (-0.68 SD, 25th %ile), weight 18.9 kg (+2.36 SD, 99th %ile), OFC 55.5 cm (+4.60 SD, >99th %ile).
Mild intellectual disability
13974416
14286260
311845
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP11
8 yrs. 4 mos.
M
Intellectual disability
Birth/neonatal history: born eutrophic after uneventful pregnancy at 39 weeks of gestation; weight 2750 g (-1.30 SD, 10th %ile), length 49 cm (-0.44 SD, 33th %ile), and OFC 34 cm (-0.83 SD, 20th %ile) at birth; neonatal feeding difficulties. Developmental milestones: delayed speech and language development (no longer impaired by 8 years). Motor and musculoskeletal evaluation: brachydactyly. Behavioral/psychiatric evaluation: pervasive developmental disorder, attention deficit, anxiety, heteroaggression. Dysmorphic features: downslanting palpebral fissures, deep-set eyes, blepharophimosis, broad nasal tip, thin upper lip vermillion, small ears with lobule, finger pads, transverse palmar crease. Growth parameters: height 131.5 cm (+0.62 SD, 73rd %ile), weight 25.5 kg (-0.04 SD, 48th %ile), OFC 52.5 cm (+0.15 SD, 56th %ile). Family history: moteher had a personal and familial history of breakdown.
Mild intellectual disability
13106807
14639973
1533167
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP12
32 yrs.
M
ASD, ADHD, and learning disability
Birth/neonatal history: weight, length, and OFC at birth not determined. Developmental milestones: delayed speech and language development, motor delay. Motor and musculoskeletal evaluation: difficulties with balance, abnormal upper and lower limb reflexes, abnormal extraocular movements. Behavioral/psychiatric evaluation: attention deficit, ASD, impulse control problems, trouble gauging emotions, diagnosis of ADHD. Epilepsy/seizures: no (seizures suspected at one point, but EEG was unrevealing, and he had no recurrence). Brain imaging: complete agenesis of the corpus callosum, moderately decreased white matter volume, bilateral probst bundles, associated parallel orientation of the lateral ventricles, colpocephaly, prominence of the third ventricle. Additional medical history: insensitivity to pain, temperature dysregulation with associated hyperhydrosis, elevated blood pressure. Growth parameters: macrocephaly; height 177.8 cm (-0.17 SD, 57th %ile), weight not determined, OFC 61.5 cm (+4.46 SD, >99th %ile). Family history: unknown (adopted at birth).
Learning disability (full scale IQ 88, verbal IQ 95, performance IQ 79 at 22 years)
13044408
14663396
1618989
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP8a
6 yrs.
F
Learning disability
Birth/neonatal history: weight, length, and OFC at birth not determined. Developmental milestones: delayed speech and language development, motor development noted as delayed at 4 years of age. Behavioral/psychiatric evaluation: attention deficit, reactive attachment disorder, passive and pleasing behavior. Cardiac evaluation: small ventricular septal defect, systolic heart murmur. Dysmorphic features: everted lower lip, small alae nasi, fetal fingerpads on thumbs. Growth parameters: macrocephaly; height 122.6 cm (+1.46 SD, 93rd %ile), weight 26.2 kg (+1.32 SD, 91th %ile), OFC 55.6 cm (+3.35 SD, >99th %ile). Family history: biological mother has learning difficulties but was not tested genetically.
Learning disability
14098660
14324148
225489
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP8b
8 yrs.
F
ASD and intellectual disability
Birth/neonatal history: birth weight of 3470 g (-0.1 SD, 54th %ile); length and OFC at birth not determined. Developmental milestones: markedly delayed speech and language development, slight motor delay. Behavioral/psychiatric evaluation: case fulfilled criteria for ASD at age of 4 years; attention deficit, autistic features, social difficulties. Brain imaging: slightly asymmetric hemispheres (asymmetric cranium, slightly larger left hemisphere). Cardiac evaluation: narrow pulmonary artery (normalized at 2 years), cardiac murmur ascribed to mild supravalvular pulmonary stenosis. Dysmorphic features: small ears with attached ear lobules, retrognathia, everted lower lip, small alae nasi, fetal fingerpads on thumbs. Growth parameters: macrocephaly; height 131 cm (+0.56 SD, 71st %ile), weight 28.9 kg (+0.49 SD, 69th %ile), OFC 55.2 cm (+2.71 SD, >99th %ile). Family history: biological mother has learning difficulties but was not tested genetically.
Borderline mild intellectual disability
14098660
14324148
225489
GRCh38
Deletion
Yes
schanze_18_DD/ID_discovery_cases-subjectP9
7 yrs.
M
Learning disability
Birth/neonatal history: pregnancy marked by gestational diabetes, hydramnios, and decreased fetal movements; born at 37 weeks by caesarean section due to breech presentation; weight 3500 g (-0.10 SD, 46th %ile), length 50 cm (-0.06 SD, 48th %ile), and OFC 37 cm (+0.68 SD, 75th %ile) at birth. Developmental milestones: delayed speech and language development (first words at 2 years, first sentences at 5 years), motor delay (walking at 3 years). Motor and musculoskeletal evaluation: muscular hypotonia, diffuse articular hyperlaxity, scoliosis. Behavioral/psychiatric evaluation: attention deficit, sleep disturbance. Additional medical history: chronic constipation, velvet skin. Dysmorphic features: long and flat face, upslanting palpebral fissures, malar hypoplasia, open mouth appearance, high arched palate. Growth parameters: macrocephaly; height 131 cm (+1.70 SD, 96th %ile), weight 22 kg (-0.41 SD, 34th %ile), OFC 55 cm (+2.17 SD, 99th %ile).
Learning disability
14102176
14386039
283864
GRCh38
Deletion
Yes
yuan_23_ASD_discovery_cases-qma01955d000
NA
NA
ASD
Case diagnosed with ASD according to DSM-IV criteria.
14087948
14313763
225816
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
mazzonetto_24_ASD/DD/ID_discovery_cases-caseDECIPHER530526
Unknown
ATP5PDP3,LURAP1L,PES1P2,LINC01235,AKAP8P1,IMP3P1,JKAMPP1,LINC00583,NFIB,RPL3P11,CDCA4P1,PTPRD,RN7SL5P,LURAP1L-AS1,PRDX1P1,TYRP1,RN7SL849P,RNU2-47P,MPDZ
pfundt_16_NDD_discovery_cases-case90
Array SNP (Affymetrix CytoScan HD)
De novo
PES1P2,ATP5PDP3,CDCA4P1,CER1,RNU6-1260P,LDHAP4,RNU6-559P,RPL7P33,RNU6-319P,LINC01235,LINC00583,RPL3P11,SNAPC3,NFIB,FREM1,CLCN3P1,TTC39B,ZDHHC21
sajan_13_ACC/CBLH/PMG_discovery_cases-case1127-0
qPCR
Unknown
Unknown
Unknown
PES1P2,ATP5PDP3,CDCA4P1,LINC01235,LINC00583,RPL3P11,MPDZ,NFIB,ZDHHC21
schanze_18_DD/ID_discovery_cases-subjectP10a
MLPA
De novo
Multi-generational
Segregated
PES1P2,ATP5PDP3,RPL3P11,NFIB
schanze_18_DD/ID_discovery_cases-subjectP10b
MLPA
Maternal
Maternal
Multi-generational
Segregated
PES1P2,ATP5PDP3,RPL3P11,NFIB
schanze_18_DD/ID_discovery_cases-subjectP11
qPCR
De novo
PES1P2,ATP5PDP3,CDCA4P1,LINC01235,LINC00583,RPL3P11,MPDZ,NFIB,ZDHHC21
schanze_18_DD/ID_discovery_cases-subjectP12
qPCR
Unknown
Unknown
PES1P2,ATP5PDP3,CDCA4P1,LINC01235,LINC00583,RPL3P11,MPDZ,NFIB,ZDHHC21
schanze_18_DD/ID_discovery_cases-subjectP8a
MLPA
Familial
Multiplex
Possibly segregated
NFIB
schanze_18_DD/ID_discovery_cases-subjectP8b
MLPA
Familial
Multiplex
Possibly segregated
NFIB
schanze_18_DD/ID_discovery_cases-subjectP9
FISH
De novo
NFIB
yuan_23_ASD_discovery_cases-qma01955d000
De novo
NFIB
Controls
No Control Data Available
No Animal Model Data Available