1q42.13-q42.2CNV Type: Deletion
Largest CNV size: 2021892 bp
Statistics Box:
Number of Reports: 8
Number of Reports: 8
Summary Information
A maternally-inherited deletion in this region of chromosome 1 has been observed in two studies and contains DISC1, which has been identified by genetic association studies as an autism-associated gene.
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
A 1q42 deletion involving DISC1, DISC2, and TSNAX in an autism spectrum disorder.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Duplication
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.
Deletion
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
girirajan_13a_ASD_discovery_cases
1979 simplex cases from the Simons Simplex Collection (SSC), 579 multiplex cases from AGRE.
2588
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
NA
NA
2013543
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
1633747
0
3
3
krumm_13_ASD_discovery_cases
Probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Diagnosis of ASD. Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
81.265% Male
1780675
1
0
1
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
1780675
1
0
1
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
2021892
1
0
1
schmidt_24_ASD/DD/ID_discovery_cases
Patients who had undergone exome sequencing and were partially analyzed with next-generation phenotyping approaches enrolled in the TRANSLATE NAMSE prospective study at ten German university hospitals.
1577
The majority of children were assigned to the disease category neurodevelopmental disorders (n=702, 54%); patient phenotypes were also annotated with terms of the Human Phenotype Ontology (HPO) by the respective CRD physicians.
268 adults, 1309 children
3606171
1
0
1
wang_18_TS_discovery_cases
Probands from 789 trio families (582 simplex trios, 103 multi-generational trios, and 104 trios with insufficient parental phenotypic data) from TIC Genetics, TAAICG, UTC, and TSGENESEE cohorts
789
Probands diagnosed with Tourette syndrome
N/A
80.57% Male
4649957
1
0
1
williams_09_ASD_discovery_cases
3 year old male with ASD
1
Diagnosis of PDD-NOS
3
Male
2000000
1
0
1
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
krumm_13_ASD_discovery_controls
Unaffected siblings of ASD probands from quad families ascertained as part of the Simons Simplex Collection (SSC); CNVs detected using data from four previously published exome sequencing studies (O'Roak et al., 2011; Iossifov et al., 2012; O'Roak et al., 2012; Sanders et al., 2012)
411
Control (unaffected siblings of ASD probands). Social Responsiveness Scale (SRS) used as a quantitative measure of social deficits
N/A
46.47% Male
0
0
0
0
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
0
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
girirajan_13a_ASD_discovery_cases
NA
aCGH
Custom microarray with a high density of probes targeted to 1,367 regions with a susceptible genomic architecture
ADM-2
Agilent Genomic Workbench
aCGH (NimbleGen 135K array)
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
krumm_13_ASD_discovery_cases
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
sanders_11_ASD_discovery_cases
White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
Solid phase hybridization
Illumina 1M v1, Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
schmidt_24_ASD/DD/ID_discovery_cases
Germany
aCGH, Exome sequencing
Illumina HiSeq 2500 or NovaSeq 6000
ExomeDepth v1.1.10, ClinCNV v1.16.1
wang_18_TS_discovery_cases
N/A
WES
Agilent SureSelect v1.1, Nimblegen EZ v2, Nimblegen EZ v3, IDT xGen
CoNIFER
None
williams_09_ASD_discovery_cases
50% Caucasian, 50% Pakistani
aCGH
Human Genome CGH Microarray Kit 244A (Agilent 244K, G4411B)
ADM-2
Feature Extraction Software v 9.1.3, CGH Analytics 3.4.40
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
krumm_13_ASD_discovery_controls
N/A
WES
Whole exome sequencing platforms used in four recent publications (O'Roak et al., 2011; Sanders et al., 2012; O'Roak et al., 2012, and Iossifov et al., 2012)
DNACopy, CGHCall
CoNIFER
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
girirajan_13a_ASD_discovery_cases-12162.p1
N/A
N/A
ASD
Diagnosis of ASD based on meeting criteria on the Autism Diagnostic Observation Schedule (ADOS) and on the Autism Diagnostic Interview, Revised (ADI-R)
N/A
229985351
231998895
2013545
GRCh38
Deletion
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000706
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
230519755
231232066
712312
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005370
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
230489657
231243203
753547
GRCh38
Duplication
Yes
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005375
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
229883805
231517553
1633749
GRCh38
Duplication
Yes
krumm_13_ASD_discovery_cases-case12162.p1
N/A
M
ASD
ASD proband from SSC quad family 12162. SRS score of 77.
Full-scale IQ (FSIQ) score of 67.
230178217
231958892
1780676
GRCh38
Deletion
No (not tested)
krumm_15_ASD_discovery_cases-case12162.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
230178217
231958892
1780676
GRCh38
Deletion
Yes
sanders_11_ASD_discovery_cases-12162.p1
4.3
M
Autism
NA
Full-scale IQ, 67; non-verbal IQ, 68; verbal IQ, 75
229986307
232008200
2021894
GRCh38
Deletion
No
schmidt_24_ASD/DD/ID_discovery_cases-case889
Child
M
Developmental delay
Motor delay (HP:0001270), EEG abnormality (HP:0002353), epicanthus (HP:0000286), wide nasal bridge (HP:0000431).
227815717
231421887
3606171
GRCh38
Deletion
No
wang_18_TS_discovery_cases-case1061707514
N/A
N/A
Tourette syndrome
Tourette syndrome proband from phase 1 cohort; no additional clinical information available
228458477
233160388
4701912
GRCh38
Deletion
No
williams_10_ASD_discovery_cases-case1
3
M
ASD/PDD-NOS
Impairments in communication & social interactions, composite social-emotional domain scores with borderline deficient range; does not demonstrate restricted repetitive and stereotyped patterns of behavior and activities; motor delays, composite motor scores within deficient range; no dysmorphic features; slightly increased tone & decreased flexibility in lower bilateral extremities
Composite congitive score within borderline deficient range, language delay, composite language scores with deficient range
229976081
232010073
2033993
GRCh38
Deletion
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
girirajan_13a_ASD_discovery_cases-12162.p1
aCGH (NimbleGen 135K array)
Paternal
Simplex
Unknown
LINC01736,LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,COG2,TSNAX-DISC1,DISC1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00000706
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC01737,RNA5SP79,RN7SL837P,MIR1182,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,TTC13,TRIM67,COG2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005370
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
LINC01737,RNA5SP79,RN7SL837P,MIR1182,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,TTC13,TRIM67,COG2
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005375
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Maternal
Unknown
Unknown
LINC01736,LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,LINC01682,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,COG2
krumm_13_ASD_discovery_cases-case12162.p1
Maternal
Simplex
Segregated
LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,COG2,TSNAX-DISC1,DISC1
krumm_15_ASD_discovery_cases-case12162.p1
Illumina 1MDuo
Maternal
Simplex
Segregated
LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,COG2,TSNAX-DISC1,DISC1
sanders_11_ASD_discovery_cases-12162.p1
Maternal
Simplex (quad-proband matched)
Segregated
LINC01736,LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,COG2,TSNAX-DISC1,DISC1
schmidt_24_ASD/DD/ID_discovery_cases-case889
De novo
ACTA1,ARF1,AGT,TAF5L,TRIM17,NUP133,EGLN1,RHOU,GJC2,ARV1,PGBD5,TTC13,C1orf35,SPRTN,OBSCN,TRIM11,C1orf198,WNT3A,H2AW,C1orf131,MRPL55,H2BU1,CCSAP,EXOC8,RNF187,TRIM67-AS1,IBA57,GALNT2,FTH1P2,GUK1,PRSS38,H2BU2P,FAM89A,CIAO2AP2,RPL23AP15,TRIM67,IBA57-DT,OBSCN-AS1,DUSP5P1,CICP26,HMGB1P26,TMEM78,BTNL10,RNA5S9,RNA5S10,RNA5S8,RNA5S2,RNA5S6,RNA5S15,RNA5S16,RNA5S14,RNA5S13,RNA5S1,RNA5S4,RNA5S5,RNA5S3,RNA5S17,RNA5S7,RNA5S11,RNA5S12,ISCA1P2,MIR1182,MIR3620,LINC02809,MIR4666A,RNA5SP80,RNA5SP18,RNA5SP79,MIR5008,RNA5SP78,RNA5SP19,RNA5SP162,HMGN2P19,LINC01736,LINC01737,LINC01682,RAB4A,MIR6742,LINC02815,RN7SKP276,SEPTIN14P17,RNU6-180P,RN7SL837P,RNU4-21P,LINC02814,WNT9A,GNPAT,H3-4,URB2,COG2,CAPN9,ABCB10
wang_18_TS_discovery_cases-case1061707514
CNV validation not attempted
De novo
MIR4666A,HIST3H2BA,BTNL10,RNA5SP19,RNA5SP162,RNA5S1,RNA5S2,RNA5S3,RNA5S4,RNA5S5,RNA5S6,RNA5S7,RNA5S8,RNA5S9,RNA5S10,RNA5S11,RNA5S12,RNA5S13,RNA5S14,RNA5S15,RNA5S16,RNA5S17,RNA5SP18,DUSP5P1,FTH1P2,ISCA1P2,TMEM78,SPHAR,RNU6-180P,RN7SKP276,ACTA1,RNU4-21P,RNA5SP78,HMGN2P19,HMGB1P26,LINC01736,LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,RN7SL299P,RNU6-1211P,MAP10,RNU1-74P,RNF187,RHOU,RAB4A,CCSAP,ABCB10,TAF5L,LINC01682,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,LINC01745,LINC01744,NTPCR,HIST3H2BB,NUP133,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,SIPA1L2,PCNX2,URB2,COG2,TSNAX-DISC1,DISC1
williams_10_ASD_discovery_cases-case1
FISH
Maternal
Simplex
NA
LINC01736,LINC01737,RNA5SP79,RN7SL837P,MIR1182,RNA5SP80,EXOC8,SNRPD2P2,RNU5A-5P,AGT,CAPN9,C1orf198,ARV1,FAM89A,C1orf131,GNPAT,EGLN1,TSNAX,DISC1-IT1,GALNT2,PGBD5,TTC13,TRIM67,SPRTN,LINC00582,COG2,TSNAX-DISC1,DISC1
Controls
No Control Data Available
No Animal Model Data Available