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Xq12-q13.3CNV Type: Duplication


Largest CNV size: 9427204 bp

Statistics Box:
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

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USCS Symbol             NCBI Symbol

Decipher

            Decipher Symbol

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
 kaya_11_ASD_discovery_controls
 Controls
 250
 Control
 NA
 NA
 9427204
 0
 0
 0

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
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