19p13.12-p13.11CNV Type: Deletion
Largest CNV size: 1400000 bp
Statistics Box:
Number of Reports: 5
Number of Reports: 5
Summary Information
A de novo deletion in this region was identified in a male patient with intellectual disability and autistic features.
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 case of microdeletion of 19p13 with intellectual disability, hypertrichosis, synophrys, and protruding front teeth.
Deletion
Understanding the new BRD4-related syndrome: Clinical and genomic delineation with an international cohort study
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
jouret_22_DD/ID_discovery_cases
Individuals with de novo deletions affecting the BRD4 gene (from an initial cohort of 14 patients with BRD4 variation) organized in an international collaborative project with the European Reference Network Ithaca (www. ern-ithaca.eu), reinforced by the collaboration of the French Cytogenetic Society network (ACLF).
6
Two cases were medically terminated fetuses (due to multiple congenital anomalies); the remaining four cases all presented with developmental delay (DD), with one case also presenting with intellectual disability (ID).
Range, fetus-20 yrs.
50% Male
2154508
3
0
3
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
jouret_22_DD/ID_discovery_cases
NA
CMA
CGH 4x44K, 6x60K, 8x60K, 4x180K, Agilent microarrays
NA
NA
qPCR, FISH
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
jouret_22_DD/ID_discovery_cases-case1
3 yrs. 9 mos.
M
Developmental delay and learning disability
Birth/neonatal history: intrauterine growth retardation. Developmental milestones: initial global developmental delay. Additional medical history: nasogastric tube feeding, giant hiatal hernia. Dysmorphic features: synophrys, arched and sparse eyebrows, downslanting palpebral fissures, short nose, anteverted nares, strabismus, large ears, low forehead, frontal upsweep of hair, prominent incisors. Growth parameters: microcephaly (-6 SD).
Learning disability
14861728
16146300
1284573
GRCh38
Deletion
Yes
jouret_22_DD/ID_discovery_cases-case2
10 wks.
M
Developmental delay
Birth/neonatal history: intrauterine growth retardation. Developmental milestones: initial global developmental delay. Brain imaging: hypoplasia of the corpus callosum. Additional medical history: central swallowing difficulties. Dysmorphic features: strabismus, large and low-set ears, preauricular enchondroma. Growth parameters: microcephaly (-3 SD).
14374974
16529481
2154508
GRCh38
Deletion
Yes
jouret_22_DD/ID_discovery_cases-case5
20 yrs.
M
Developmental delay and intellectual disability
Developmental milestones: initial global developmental delay. Motor and musculoskeletal evaluation: narrow and sloping shoulders. Behavioral/psychiatric evaluation: hypersexualized behavior, trichotillomania. Additional medical history: severe gastroesophageal reflux, , pulmonary atresia, ventricular septal defect, late-onset puberty. Dysmorphic features: synophrys, arched and sparse eyebrows, short nose, large ears. Growth parameters: microcephaly (-4 SD).
Intellectual disability
14258736
16146156
1887421
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
jouret_22_DD/ID_discovery_cases-case1
qPCR, FISH
De novo
OR10H1,OR7A15P,OR10H3,OR10H2,AKAP8L,OR7A3P,OR7A17,OR7C2,OR7A11P,CYP4F11,WIZ,RASAL3,CYP4F12,EPHX3,OR1AB1P,OR7A18P,SYDE1,HSH2D,LINC00661,PGLYRP2,OR1I1,CYP4F22,CCDC105,OR10H4,LINC00905,OR10H5,CYP4F24P,OR7A2P,OR7A1P,OR10B1P,RPL23AP2,CYP4F10P,UCA1,CYP4F3,NOTCH3,RAB8A,MIR1470,ZNF861P,CYP4F36P,CYP4F23P,SNX33P1,MIR6795,CLEC4OP,CYP4F9P,LINC01855,LINC01764,SLC1A6,TPM4,RNU6-782P,CYP4F2,ILVBL-AS1,ILVBL,CYP4F8,AKAP8,CASP14,BRD4
jouret_22_DD/ID_discovery_cases-case2
qPCR, FISH
De novo
ADGRE5,OR7A8P,OR10H1,OR7A15P,OR10H3,OR10H2,AKAP8L,OR7A3P,OR7A17,OR7C1,OR7A5,OR7C2,OR7A11P,ADGRE2,CYP4F11,WIZ,EPS15L1,RASAL3,CYP4F12,EPHX3,ZNF333,OR1AB1P,C19orf44,OR7A18P,SYDE1,ADGRE3,HSH2D,LINC00661,PGLYRP2,OR1I1,CIB3,CYP4F22,CCDC105,OR10H4,CALR3,LINC00905,DNAJB1,OR10H5,CYP4F24P,CLEC17A,OR7A10,OR7A2P,OR7A1P,OR10B1P,RPL23AP2,CYP4F10P,MIR639,UCA1,SNRPGP15,CYP4F3,NOTCH3,RAB8A,NDUFB7,MIR1470,ZNF861P,ITGB1P1,CYP4F36P,CYP4F23P,SNX33P1,PKN1,PTGER1,MIR6795,CLEC4OP,CYP4F9P,LINC01855,LINC01764,SLC1A6,TPM4,RN7SL842P,RN7SL337P,RNU6-782P,CYP4F2,AP1M1,ILVBL-AS1,KLF2-DT,TECR,DDX39A,ILVBL,KLF2,CHERP,GIPC1,CYP4F8,AKAP8,FAM32A,CASP14,BRD4
jouret_22_DD/ID_discovery_cases-case5
qPCR, FISH
De novo
ADGRE5,OR7A8P,OR10H1,OR7A15P,OR10H3,OR10H2,AKAP8L,OR7A3P,OR7A17,OR7C1,OR7A5,OR7C2,OR7A11P,ADGRE2,CYP4F11,WIZ,RASAL3,CYP4F12,EPHX3,ZNF333,OR1AB1P,OR7A18P,SYDE1,ADGRE3,HSH2D,LINC00661,PGLYRP2,OR1I1,CYP4F22,CCDC105,OR10H4,LINC00905,DNAJB1,OR10H5,CYP4F24P,CLEC17A,OR7A10,OR7A2P,OR7A1P,OR10B1P,RPL23AP2,CYP4F10P,MIR639,UCA1,SNRPGP15,CYP4F3,NOTCH3,RAB8A,NDUFB7,MIR1470,ZNF861P,ITGB1P1,CYP4F36P,CYP4F23P,SNX33P1,PKN1,PTGER1,LINC01842,MIR6795,CLEC4OP,CYP4F9P,LINC01855,LINC01764,LINC01841,SLC1A6,TPM4,RN7SL842P,RN7SL337P,RNU6-782P,CYP4F2,ILVBL-AS1,TECR,DDX39A,ILVBL,GIPC1,CYP4F8,AKAP8,CASP14,BRD4
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