Single allele AND Schizophrenia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 20, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000754162.1

Allele description [Variation Report for Single allele]

Genes:

LOC106736480:15q13 proximal microdeletion recombination region [Gene]
LOC106736465:15q13.2 beta inversion distal recombination region [Gene]
LOC106736468:15q13.2-13.3 gamma inversion proximal recombination region [Gene]
ARHGAP11B-DT:ARHGAP11B divergent transcript [Gene - HGNC]
LOC130056726:ATAC-STARR-seq lymphoblastoid silent region 6267 [Gene]
LOC130056727:ATAC-STARR-seq lymphoblastoid silent region 6268 [Gene]
LOC126862088:BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 [Gene]
FAN1:FANCD2 and FANCI associated nuclease 1 [Gene - OMIM - HGNC]
KLF13:KLF transcription factor 13 [Gene - OMIM - HGNC]
LOC127829159:KLF13 promoter region [Gene]
LOC128899998:KLF13-II enhancer [Gene]
LOC128899999:KLF13-III enhancer [Gene]
LOC126862089:MED14-independent group 3 enhancer GRCh37_chr15:31442413-31443612 [Gene]
LOC129390679:MPRA-validated peak2284 silencer [Gene]
LOC129390680:MPRA-validated peak2285 silencer [Gene]
LOC129390681:MPRA-validated peak2289 silencer [Gene]
OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
LOC125078053:Sharpr-MPRA regulatory region 11410 [Gene]
LOC112272582:Sharpr-MPRA regulatory region 5138 [Gene]
LOC121847941:Sharpr-MPRA regulatory region 8183 [Gene]
LOC110121498:VISTA enhancer hs2231 [Gene]
CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
LOC106736477:distal CHRNA7 low-copy repeat recombination region [Gene]
GOLGA8H:golgin A8 family member H [Gene - HGNC]
GOLGA8Q:golgin A8 family member Q [Gene - HGNC]
LINC02352:long intergenic non-protein coding RNA 2352 [Gene - HGNC]
LINC03034:long intergenic non-protein coding RNA 3034 [Gene - HGNC]
MIR211:microRNA 211 [Gene - OMIM - HGNC]
MTMR10:myotubularin related protein 10 [Gene - HGNC]
LOC106783506:nonconserved acetylation island sequence 49 enhancer [Gene]
LOC106736476:proximal CHRNA7 low-copy repeat recombination region [Gene]
TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

15q13.2-13.3

Genomic location:

Chr15: 30506022 - 32161746 (on Assembly GRCh38)

Condition(s)

Name:: Schizophrenia (SCZD)
Identifiers:: MONDO: MONDO:0005090; MeSH: D012559; MedGen: C0036341; OMIM: 181500; Human Phenotype Ontology: HP:0100753

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000777965	Department of Psychiatry, Nagoya University	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Likely pathogenic (Mar 20, 2018)	germline	research	PubMed (2) [See all records that cite these PMIDs] 21681106, 30208311

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000777965

Department of Psychiatry, Nagoya University

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Likely pathogenic
(Mar 20, 2018)

germline

research

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee.

Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a.

PubMed [citation]

PMID:: 21681106

Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.

Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, et al.

Cell Rep. 2018 Sep 11;24(11):2838-2856. doi: 10.1016/j.celrep.2018.08.022.

PubMed [citation]

PMID:: 30208311

Details of each submission

From Department of Psychiatry, Nagoya University, SCV000777965.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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