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19p13.12-p13.11CNV Type: Deletion


Largest CNV size: 1400000 bp

Statistics Box:
Number of Reports: 4



Summary Information

A de novo deletion in this region was identified in a male patient with intellectual disability and autistic features.

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 case of microdeletion of 19p13 with intellectual disability, hypertrichosis, synophrys, and protruding front teeth.
Deletion

Minor Reports

Title
Author, Year
Report Class
CNV Type
Reciprocal Relationship between Head Size, an Autism Endophenotype, and Gene Dosage at 19p13.12 Points to AKAP8 and AKAP8L.
Deletion-Duplication
Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder
Deletion

Cases

Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
 jelsig_12_ID_discovery_cases
 First child of healthy, non-consanguineous parents with healthy younger sibling
 1
 Intellectual disability, autistic features, microcephaly, hearing impairment, and additional dysmorphic features
 15 yrs.
 Male
 1400000
 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
 783940
 0
 1
 1
 latypova_21_ASD/ADHD/DD/ID_discovery_cases
 Individuals with de novo deletions affecting the SIN3B gene (three of these individuals were from DECIPHER)
 5
 All five individuals presented with developmental delay and/or intellectual disability; one case was diagnosed with autism spectrum disorder, and two cases were diagnosed with ADHD.
 Range, 2 yrs. 6 mos.-20 yrs.
 60.00% Male
 1521825
 1
 0
 1
 nebel_15_DD/ID_discovery_cases
 Cases from DECIPHER and other publications with overlapping events at the 19p13.12 locus
 16
 Cases presented with at least one of the following phenotypes: developmental delay, intellectual disability, microcephaly, or macrocephaly
 N/A
 50.00% Male
 2570000
 3
 1
 4

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
 jelsig_12_ID_discovery_cases
  Caucasian/Denmark
 aCGH
  Agilent SurePrint G3 Human CGH Microarray 2x400K
 
 Agilent Genomic Workbench
 MLPA
 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
 latypova_21_ASD/ADHD/DD/ID_discovery_cases
  France, Belgium, United States, and United Kingdom
 CMA
  Agilent 60K, Agilent 180K (BCM v.8.1), ISCA v.2 60K
 
 
 None
 nebel_15_DD/ID_discovery_cases
  N/A
 N/A
  N/A
 
 
 N/A

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
  jelsig_12_ID_discovery_cases-case1
 15 yrs.
 M
 Intellectual disability + autistic features
 Birth/neonatal history: pregnancy followed due to reduced fetal movements; delivered at 41 weeks gestation by emergency C-section due to weak heart sounds; birth weight in 3rd %ile and birth length in 25th %ile. Developmental milestones: delayed language development; mildly delayed motor milestones (sitting at 7 months, unsupported walking at 20 months). Motor and musculoskeletal evaluation: hypermobile joints with dislocations of both right and left patellae. Behavioral/psychiatric evaluation: autistic behaviors evident at early age. Brain imaging: skull X-ray at 16 months showed early closure of emtopic suture and late closure of anterior fonanelle; normal CNS MRI. Auditory evaluation: bilateral sensorineural hearing impairment with a mild conductive element, narrow external ear canals. Recurrent infections: recurrent middle ear infections and placement of ventilation tubes before age of 11 years; several recent moderate infections with fever. Other medical concerns and comorbidities: entered puberty at 10-11 years of age; recent episodes of throbocytopenia and mild neutropenia; daily shaving needed from 13 years of age. Dysmorphic features: broad eyebrows, synophrys, hypertelorism, downslanting palpebral fissures, small epicanthal folds, strabismus, hypermetropia, protuberant external ears, mild syndactyly of 2nd and 3rd toes bilaterally, high palate, protruding front teeth, low set ears, dental crowding leading to extraction of several teeth, hypertrichosis on arms, hands, and thorax. Growth parameters: microcephaly (head circumference -3 SD) noted at age of 2 years and 9 months. Family history: healthy non-consanguineous parents; healthy younger sibling.
 Intellectual disability (ID)
 15068026
 16517883
  1449858
 GRCh38
 Deletion
 Yes
  kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005039
 NA
 NA
 Developmental delay/intellectual disability/ASD
 Clinical profile NA
 Cognitive profile NA
 16065434
 16849373
  783940
 GRCh38
 Duplication
 Yes
  latypova_21_ASD/ADHD/DD/ID_discovery_cases-case2
 11 yrs.
 F
 ADHD, developmental delay, and intellectual disability
 Developmental delay (development equivalent to 24 months when evaluated at 49 months with Brunet Lezine scale), delayed ability to walk (2 years 8 months), speech delay (expressive language delay with first words at 3 years), ADHD, dysmorphic features (low frontal hairline, bilateral epicanthus, thick eyebrows, synophrys, downturned corners of the mouth, brachydactyly), bilateral fifth finger clinodactyly, genu recurvatum, ventricular septal defect, bifid uvula, strabismus (esotropia), ataxia, small for gestational age (birth weight <3rd %ile), birth length less than 3rd percentile, recurrent bronchitis until 3 years of age, delayed ability to sit (1 years), temper tantrums as a toddler, hyperactivity, amblyopia, mild hypermetropia (DECIPHER ID 262142).
 Intellectual disability (WISC IQ 41)
 15867794
 17389618
  1521825
 GRCh38
 Deletion
 No
  nebel_15_DD/ID_discovery_cases-case13
 N/A
 M
 Intellectual disability and microcephaly
 Case originally described in Jelsig et al., 2012. Microcephaly
 Intellectual disability
 15069189
 16509189
  1440001
 GRCh38
 Deletion
 N/A
  nebel_15_DD/ID_discovery_cases-case14
 N/A
 F
 Intellectual disability and macrocephaly
 DECIPHER ID 250827. Macrocephaly
 Intellectual disability
 15069189
 16349189
  1280001
 GRCh38
 Duplication
 N/A
  nebel_15_DD/ID_discovery_cases-case15
 N/A
 M
 Intellectual disability and microcephaly
 DECIPHER ID 255839. Microcephaly
 Intellectual disability
 15079189
 16509189
  1430001
 GRCh38
 Deletion
 N/A
  nebel_15_DD/ID_discovery_cases-case6
 N/A
 F
 Intellectual disability and microcephaly
 Case originally described in Engels et al., 2007/Bonaglia et al., 2010. Microcephaly
 Intellectual disability
 13989188
 16559189
  2570002
 GRCh38
 Deletion
 N/A

Controls

No Control Data Available

Cases

Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
 jelsig_12_ID_discovery_cases-case1
 MLPA
 
 De novo
 Simplex
 Possibly segregated
 SYDE1,OR10B1P,RNU6-782P,MIR6795,EPHX3,MIR1470,RASAL3,RPL23AP2,CYP4F10P,OR10H3,ZNF861P,LINC01764,UCA1,CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,OR1I1,ILVBL,NOTCH3,BRD4,AKAP8,AKAP8L,WIZ,PGLYRP2,CYP4F22,CYP4F23P,CYP4F8,CYP4F3,CYP4F12,CYP4F24P,OR10H5,OR10H1,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,CALR3,LINC01835,CYP4F9P,RAB8A,EPS15L1,C19orf44,OR10H2
 
 kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005039
 FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
 
 Unknown
 Unknown
 Unknown
 LINC01855,KLF2,RN7SL146P,TPM4,HSH2D,CIB3,FAM32A,AP1M1,CALR3,CHERP,SLC35E1,MED26,TMEM38A,SIN3B,RAB8A,EPS15L1,C19orf44,SMIM7,NWD1
 
 latypova_21_ASD/ADHD/DD/ID_discovery_cases-case2
 
 
 De novo
 
 
 CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,RN7SL146P,RN7SL835P,RN7SL823P,OCEL1,GTPBP3,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,KLF2-DT,CALR3,CHERP,SLC35E1,MED26,TMEM38A,SIN3B,F2RL3,HAUS8,USE1,NR2F6,USHBP1,BABAM1,ANKLE1,DDA1,ANO8,PLVAP,CYP4F9P,RAB8A,EPS15L1,C19orf44,SMIM7,CPAMD8,MYO9B,ABHD8,MRPL34,NWD1
 
 nebel_15_DD/ID_discovery_cases-case13
 CNV validation N/A
 
 De novo
 
 
 SYDE1,OR10B1P,RNU6-782P,MIR6795,EPHX3,MIR1470,RASAL3,RPL23AP2,CYP4F10P,OR10H3,ZNF861P,LINC01764,UCA1,CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,OR1I1,ILVBL,NOTCH3,BRD4,AKAP8,AKAP8L,WIZ,PGLYRP2,CYP4F22,CYP4F23P,CYP4F8,CYP4F3,CYP4F12,CYP4F24P,OR10H5,OR10H1,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,CALR3,LINC01835,CYP4F9P,RAB8A,EPS15L1,C19orf44,OR10H2
 
 nebel_15_DD/ID_discovery_cases-case14
 CNV validation N/A
 
 De novo
 
 
 SYDE1,OR10B1P,RNU6-782P,MIR6795,EPHX3,MIR1470,RASAL3,RPL23AP2,CYP4F10P,OR10H3,ZNF861P,LINC01764,UCA1,CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,OR1I1,ILVBL,NOTCH3,BRD4,AKAP8,AKAP8L,WIZ,PGLYRP2,CYP4F22,CYP4F23P,CYP4F8,CYP4F3,CYP4F12,CYP4F24P,OR10H5,OR10H1,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,LINC01835,CYP4F9P,RAB8A,OR10H2
 
 nebel_15_DD/ID_discovery_cases-case15
 CNV validation N/A
 
 De novo
 
 
 SYDE1,OR10B1P,RNU6-782P,MIR6795,EPHX3,MIR1470,RASAL3,RPL23AP2,CYP4F10P,OR10H3,ZNF861P,LINC01764,UCA1,CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,OR1I1,ILVBL,NOTCH3,BRD4,AKAP8,AKAP8L,WIZ,PGLYRP2,CYP4F22,CYP4F23P,CYP4F8,CYP4F3,CYP4F12,CYP4F24P,OR10H5,OR10H1,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,CALR3,LINC01835,CYP4F9P,RAB8A,EPS15L1,C19orf44,OR10H2
 
 nebel_15_DD/ID_discovery_cases-case6
 CNV validation N/A
 
 Unknown
 
 
 RLN3,EEF1DP1,MIR1199,C19orf67,RN7SL231P,PTGER1,SNRPGP15,MIR639,NDUFB7,RN7SL337P,RN7SL842P,OR7A8P,OR7A2P,OR7A17,OR7A18P,OR7A3P,OR7A11P,OR7A15P,CCDC105,SYDE1,OR10B1P,RNU6-782P,MIR6795,EPHX3,MIR1470,RASAL3,RPL23AP2,CYP4F10P,OR10H3,ZNF861P,LINC01764,UCA1,CYP4F36P,OR10H4,SNX33P1,OR1AB1P,LINC01855,KLF2,RN7SL146P,RFX1,IL27RA,PALM3,MISP3,SAMD1,PRKACA,ASF1B,LINC01841,LINC01842,ADGRE5,PKN1,GIPC1,DNAJB1,CLEC17A,ZNF333,ADGRE2,OR7A5,OR7A10,OR7A1P,SLC1A6,CASP14,OR1I1,ILVBL,NOTCH3,BRD4,AKAP8,AKAP8L,WIZ,PGLYRP2,CYP4F22,CYP4F23P,CYP4F8,CYP4F3,CYP4F12,CYP4F24P,OR10H5,OR10H1,CYP4F2,CYP4F11,LINC00661,LINC00905,TPM4,HSH2D,CIB3,FAM32A,AP1M1,CALR3,CHERP,SLC35E1,ADGRL1,DDX39A,TECR,OR7C1,OR7C2,LINC01835,CYP4F9P,RAB8A,EPS15L1,C19orf44,ADGRE3,OR10H2
 

Controls

No Control Data Available
No Animal Model Data Available
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