Xq12-q13.3CNV Type: Duplication
Largest CNV size: 9427204 bp
Statistics Box:
Number of Reports: 2
Number of Reports: 2
Summary Information
A duplication in this region was found to closely segregate with disease in a family with males diagnosed with ASD and intellectual disability.
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...
Duplication
A novel X-linked disorder with developmental delay and autistic features.
Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
No Minor Reports
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
6861139
0
1
1
kaya_11_ASD_discovery_cases
Affected males from an extended pedigree in which autism/developmental delay segregated in an X-linked recessive manner
3
Two cases with diagnosis of ASD, one case with autistic traits and intellectual disability. Diagnosis of ASD based on usage of Turkish & Arabic versions of the Childhood Autism Rating Scale (CARS).
Range, 4-36 yrs.
100% Male
9427204
0
3
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
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
kaya_11_ASD_discovery_cases
Arabic
aCGH
Agilent 44K and 244A assays
Z-score
Agilent Feature Extraction, CGH Analytics 3.4.40
G-banded karyotyping, FISH
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
kaya_11_ASD_discovery_controls
NA
aCGH, array SNP
Agilent 44K, Agilent 244A, Affymetrix GeneChip 100K, Affymetrix 250/500K, Affymetrix 6.0, Affymetrix 2.7M
Affymetrix Genotyping Console v.3.0, Affymetrix ChAS
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-ISCA00004340
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
68382004
75243150
6861147
GRCh38
Duplication
Yes
kaya_11_ASD_discovery_cases-patient1
10 yrs.
M
ASD
Diagnosis of ASD according to DSM-IV and based on Turkish version of Childhood Autism Rating Scale (CARS); CARS total score of 40. Developmental milestones: severely delayed gross motor milestones (sat at 15 months, first walked at 48 months); significant speech delay (single words at 7 years, rarely used two word phrases). Behavioral/psychiatric characteristics: deficits in socio-emotional area such as lack of eye contact, joint attention, impairment in social response, severe impairment in imitative plays & abilities; unable to interact with peers, preferred to stay alone; no pretend play; unable to sustain reciprocal interaction; special interest in music; played with same toys repetitively. Adaptive function (as assessed by Turkish version of Vineland Adaptive Function Scale): communication, 2 yrs.; daily life skills, 3 yrs 4 mos.; socialization, 2 yrs.; motor domains, 3 yrs. Brain CT & MRI: mild signal changes bilaterally in dentate nuclei, tegmentum, cerebellar peduncle, & periaqueductal gray matter; mild ventricular enlargement & thinned corpus callosum at 7 yrs of age. MRS: normal creatine small lactate peak spectra. Epilepsy/seizures: hypsarrhythmia suggested by EEG, but no frank seizures; treatment with lamictal cleared these activities; flash VEP showed bilaterally prolonged P2 wave latency; flash ERG showed prolonged & lowered b latency on right side. Hypotonia, balance problems, poor muscle tone & strength, no pathological reflexes. Ophthalmological examination revealed sharp disc margins & plae discs. Reduced alkaline phosphatase (20% of normal) and elevated creatine kinase levels observed on three occasions. Markedly reduced pain sensation. Recurrent infections: history of four episodes of bronchopneumonia before the age of 4 yrs. Past medical history: low somatomedin C and IGF1 (responded well to growth hormone therapy); bilateral undescended testicles (responded to orchiopexy treatment). Dysmorphic features: microcephaly; slightly triangular face; flattened nasal bridge; bilateral epicanthic folds; bilateral nicked/crenellated ear lobes; pectus excavatum; partially fused 2nd, 3rd, and 4th fingers; fused 2nd and 3rd toes. Growth parameters: height, 123 cm (<5th %ile); weight, 24 kg (<5th %ile); head circumference, 49 cm (<5th %ile). Family history: younger brother with ASD and similar clinical/developmental cpurse (brother is more social).
Leiter-R IQ: 30 (severe delay in intellectual abilities)
65687555
75114785
9427231
GRCh38
Duplication
Yes
kaya_11_ASD_discovery_cases-patient2
4 yrs.
M
ASD
Diagnosis of autism based on Turkish version of Childhood Autism Rating Scale (CARS); CARS total score of 44. Diagnosed with West syndrome in first year, which was controlled by steroids. Developmental milestones: unable to walk, severe motor developmental delay, severe psychomotor retardation; no meaningful words, no response to calling name or to smiling. Display of midline hand stereotypies. Adaptive function (as assessed by Turkish version of Vineland Adaptive Function Scale): communication, 10 months; daily life skills, 8 months; socialization, 6 months; motor domain, 8 months. Epilepsy/seizures: EEG showed severe hypsarrhythmia accompanying myoclonic seizures; no seizures after 3rd year, currently EEG is normal. Recurrent infections: hospitalized twice with bronchopneumonia. Elevated creatine kinase levels confirmed several times. Brain CT: normal at 1 yr. Family history: older brother with autism and similar clinical/developmental course, but who is less social.
Leiter-R IQ: 36.
65687555
75114785
9427231
GRCh38
Duplication
Yes
kaya_11_ASD_discovery_cases-patient3
36 yrs.
M
Intellectual disability
Detailed psychiatric examination not performed due to patient's lack of cooperation. Behavioral/psychiatric characteristics: antisocal, uncooperative, periods of agitation, panic attacks, excessive eating followed by vomiting, bulimia nervosa that has resulted in severe weight decline (60 kg to 22 kg). Developmental milestones: slow physical and psychological development. Gradually advancing muscle atrophy since 15 yrs.; muscle weakness. Brain MRI: thinned corpus callosum, bilaterally enlarged lateral ventricles. Cachectic on physical examination. Dysmorphic features: hypertelorism, bilateral cleft of ear lobes, pectus excavatum. Family history: neurologically normal 25-yr-old brother; great-grandmother with Alzheimer's and Parkinson diseases.
Mild-to-moderate intellectual disability (ID)
65687555
75114785
9427231
GRCh38
Duplication
Yes
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-ISCA00004340
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
RNU6-245P,RPL31P63,COX6CP12,ACTR3P2,SERBP1P1,PJA1,HMGN1P35,CYCSP43,RNA5SP506,CNOT7P1,MIR676,OTUD6A,MTCYBP31,MTND4P31,IGBP1-AS2,IGBP1-AS1,RN7SL581P,RNA5SP507,P2RY4,RAB41,RNY4P23,GDPD2,RNU4-81P,DLG3-AS1,SNORD3E,RPS23P8,NUTF2P7,RNU1-56P,SOCS5P4,FOXO4,IL2RG,INGX,CXCR3,LINC00891,CXorf49,CXorf49B,RNU6-1078P,RPS26P11,RTL5,RN7SL388P,RNU2-68P,RNU1-112P,FAM236B,FAM236D,FAM236C,FAM236A,PABPC1L2B-AS1,PABPC1L2B,PABPC1L2A,NAP1L6,NAP1L2,TOMM20P4,YWHAZP8,RNU6-1044P,MORF4L1P6,RPL7P53,SEPHS1P4,RPSAP14,UHRF2P1,DDX3P2,MKRN5P,ATP5MDP1,MIR421,MIR374B,MIR374C,RN7SL648P,MIR545,MIR374A,ZCCHC13,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RNU6-330P,BUD31P2,RNU6-562P,YIPF6,EFNB1,FAM155B,AWAT2,IGBP1,DGAT2L6,AWAT1,ARR3,PDZD11,DLG3,SLC7A3,SNX12,CXorf65,MED12,NLGN3,GJB1,ZMYM3,NONO,GCNA,RPS4X,CITED1,PHKA1-AS1,DMRTC1B,FAM226B,CDX4,XIST,FXYD6P3,DDX3P1,RAB11FIP1P1,RLIM,STARD8,EDA,KIF4A,TEX11,TAF1,OGT,NHSL2,PIN4,ERCC6L,PHKA1,DMRTC1,MAP2K4P1,CHIC1,TSIX,JPX,FTX,BMP2KL,NEXMIF,ABCB7,OPHN1,LINC00269,ITGB1BP2,HDAC8,SLC16A2
kaya_11_ASD_discovery_cases-patient1
G-banded karyotyping, FISH
Maternal
Multiplex
Segregated
NANOGP9,ETF1P3,MIR223,EIF4BP9,PKMP2,RNU6-394P,BMI1P1,RNU6-1225P,AKIRIN1P2,RNU6-245P,RPL31P63,COX6CP12,ACTR3P2,SERBP1P1,PJA1,HMGN1P35,CYCSP43,RNA5SP506,CNOT7P1,MIR676,OTUD6A,MTCYBP31,MTND4P31,IGBP1-AS2,IGBP1-AS1,RN7SL581P,RNA5SP507,P2RY4,RAB41,RNY4P23,GDPD2,RNU4-81P,DLG3-AS1,SNORD3E,RPS23P8,NUTF2P7,RNU1-56P,SOCS5P4,FOXO4,IL2RG,INGX,CXCR3,LINC00891,CXorf49,CXorf49B,RNU6-1078P,RPS26P11,RTL5,RN7SL388P,RNU2-68P,RNU1-112P,FAM236B,FAM236D,FAM236C,FAM236A,PABPC1L2B-AS1,PABPC1L2B,PABPC1L2A,NAP1L6,NAP1L2,TOMM20P4,YWHAZP8,RNU6-1044P,MORF4L1P6,RPL7P53,SEPHS1P4,RPSAP14,UHRF2P1,DDX3P2,MKRN5P,ATP5MDP1,MIR421,MIR374B,MIR374C,RN7SL648P,MIR545,MIR374A,ZCCHC13,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RNU6-330P,VSIG4,EDA2R,YIPF6,EFNB1,FAM155B,AWAT2,IGBP1,DGAT2L6,AWAT1,ARR3,PDZD11,DLG3,SLC7A3,SNX12,CXorf65,MED12,NLGN3,GJB1,ZMYM3,NONO,GCNA,RPS4X,CITED1,PHKA1-AS1,DMRTC1B,FAM226B,CDX4,XIST,FXYD6P3,DDX3P1,RAB11FIP1P1,RLIM,MSN,HEPH,AR,STARD8,EDA,KIF4A,TEX11,TAF1,OGT,NHSL2,PIN4,ERCC6L,PHKA1,DMRTC1,MAP2K4P1,CHIC1,TSIX,JPX,FTX,BMP2KL,NEXMIF,ABCB7,OPHN1,LINC00269,ITGB1BP2,HDAC8,SLC16A2
478 up- or down-regulated genes (compared to controls)
kaya_11_ASD_discovery_cases-patient2
G-banded karyotyping, FISH
Maternal
Multiplex
Segregated
NANOGP9,ETF1P3,MIR223,EIF4BP9,PKMP2,RNU6-394P,BMI1P1,RNU6-1225P,AKIRIN1P2,RNU6-245P,RPL31P63,COX6CP12,ACTR3P2,SERBP1P1,PJA1,HMGN1P35,CYCSP43,RNA5SP506,CNOT7P1,MIR676,OTUD6A,MTCYBP31,MTND4P31,IGBP1-AS2,IGBP1-AS1,RN7SL581P,RNA5SP507,P2RY4,RAB41,RNY4P23,GDPD2,RNU4-81P,DLG3-AS1,SNORD3E,RPS23P8,NUTF2P7,RNU1-56P,SOCS5P4,FOXO4,IL2RG,INGX,CXCR3,LINC00891,CXorf49,CXorf49B,RNU6-1078P,RPS26P11,RTL5,RN7SL388P,RNU2-68P,RNU1-112P,FAM236B,FAM236D,FAM236C,FAM236A,PABPC1L2B-AS1,PABPC1L2B,PABPC1L2A,NAP1L6,NAP1L2,TOMM20P4,YWHAZP8,RNU6-1044P,MORF4L1P6,RPL7P53,SEPHS1P4,RPSAP14,UHRF2P1,DDX3P2,MKRN5P,ATP5MDP1,MIR421,MIR374B,MIR374C,RN7SL648P,MIR545,MIR374A,ZCCHC13,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RNU6-330P,VSIG4,EDA2R,YIPF6,EFNB1,FAM155B,AWAT2,IGBP1,DGAT2L6,AWAT1,ARR3,PDZD11,DLG3,SLC7A3,SNX12,CXorf65,MED12,NLGN3,GJB1,ZMYM3,NONO,GCNA,RPS4X,CITED1,PHKA1-AS1,DMRTC1B,FAM226B,CDX4,XIST,FXYD6P3,DDX3P1,RAB11FIP1P1,RLIM,MSN,HEPH,AR,STARD8,EDA,KIF4A,TEX11,TAF1,OGT,NHSL2,PIN4,ERCC6L,PHKA1,DMRTC1,MAP2K4P1,CHIC1,TSIX,JPX,FTX,BMP2KL,NEXMIF,ABCB7,OPHN1,LINC00269,ITGB1BP2,HDAC8,SLC16A2
478 up- or down-regulated genes (compared to controls)
kaya_11_ASD_discovery_cases-patient3
G-banded karyotyping, FISH
Maternal
Simplex
Possibly segregated (genetic testing on normal sibling NA)
NANOGP9,ETF1P3,MIR223,EIF4BP9,PKMP2,RNU6-394P,BMI1P1,RNU6-1225P,AKIRIN1P2,RNU6-245P,RPL31P63,COX6CP12,ACTR3P2,SERBP1P1,PJA1,HMGN1P35,CYCSP43,RNA5SP506,CNOT7P1,MIR676,OTUD6A,MTCYBP31,MTND4P31,IGBP1-AS2,IGBP1-AS1,RN7SL581P,RNA5SP507,P2RY4,RAB41,RNY4P23,GDPD2,RNU4-81P,DLG3-AS1,SNORD3E,RPS23P8,NUTF2P7,RNU1-56P,SOCS5P4,FOXO4,IL2RG,INGX,CXCR3,LINC00891,CXorf49,CXorf49B,RNU6-1078P,RPS26P11,RTL5,RN7SL388P,RNU2-68P,RNU1-112P,FAM236B,FAM236D,FAM236C,FAM236A,PABPC1L2B-AS1,PABPC1L2B,PABPC1L2A,NAP1L6,NAP1L2,TOMM20P4,YWHAZP8,RNU6-1044P,MORF4L1P6,RPL7P53,SEPHS1P4,RPSAP14,UHRF2P1,DDX3P2,MKRN5P,ATP5MDP1,MIR421,MIR374B,MIR374C,RN7SL648P,MIR545,MIR374A,ZCCHC13,RN7SL790P,THAP12P1,RPS7P14,HNRNPA1P25,PABPC1P3,RNU6-330P,VSIG4,EDA2R,YIPF6,EFNB1,FAM155B,AWAT2,IGBP1,DGAT2L6,AWAT1,ARR3,PDZD11,DLG3,SLC7A3,SNX12,CXorf65,MED12,NLGN3,GJB1,ZMYM3,NONO,GCNA,RPS4X,CITED1,PHKA1-AS1,DMRTC1B,FAM226B,CDX4,XIST,FXYD6P3,DDX3P1,RAB11FIP1P1,RLIM,MSN,HEPH,AR,STARD8,EDA,KIF4A,TEX11,TAF1,OGT,NHSL2,PIN4,ERCC6L,PHKA1,DMRTC1,MAP2K4P1,CHIC1,TSIX,JPX,FTX,BMP2KL,NEXMIF,ABCB7,OPHN1,LINC00269,ITGB1BP2,HDAC8,SLC16A2
478 up- or down-regulated genes (compared to controls)
Controls
No Control Data Available
No Animal Model Data Available