NC_000015.10:g.(?_22681827)_(23226874_?)del AND Schizophrenia

Germline classification:: 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:: RCV000754152.1

Allele description [Variation Report for NC_000015.10:g.(?_22681827)_(23226874_?)del]

NC_000015.10:g.(?_22681827)_(23226874_?)del

Genes:

LOC130056712:ATAC-STARR-seq lymphoblastoid active region 9154 [Gene]
LOC130056713:ATAC-STARR-seq lymphoblastoid active region 9155 [Gene]
LOC130056714:ATAC-STARR-seq lymphoblastoid active region 9156 [Gene]
LOC130056715:ATAC-STARR-seq lymphoblastoid active region 9157 [Gene]
LOC130056716:ATAC-STARR-seq lymphoblastoid active region 9158 [Gene]
LOC130056717:ATAC-STARR-seq lymphoblastoid active region 9159 [Gene]
LOC130056718:ATAC-STARR-seq lymphoblastoid active region 9160 [Gene]
LOC130056708:ATAC-STARR-seq lymphoblastoid silent region 6258 [Gene]
LOC130056709:ATAC-STARR-seq lymphoblastoid silent region 6259 [Gene]
LOC130056710:ATAC-STARR-seq lymphoblastoid silent region 6260 [Gene]
LOC130056711:ATAC-STARR-seq lymphoblastoid silent region 6261 [Gene]
LOC126862074:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:22990202-22991401 [Gene]
NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
NIPA2:NIPA magnesium transporter 2 [Gene - OMIM - HGNC]
LOC112272576:Sharpr-MPRA regulatory region 3977 [Gene]
LOC112272575:Sharpr-MPRA regulatory region 8478 [Gene]
CYFIP1:cytoplasmic FMR1 interacting protein 1 [Gene - OMIM - HGNC]
GOLGA6L1:golgin A6 family like 1 [Gene - HGNC]
MIR4509-1:microRNA 4509-1 [Gene - HGNC]
TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
LOC283683:uncharacterized LOC283683 [Gene]

Variant type:

Deletion

Cytogenetic location:

15q11.2

Genomic location:

Chr15: 22681827 - 23226874 (on Assembly GRCh38)

Preferred name:

NC_000015.10:g.(?_22681827)_(23226874_?)del

HGVS:

NC_000015.10:g.(?_22681827)_(23226874_?)del

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
SCV000777955	Department of Psychiatry, Nagoya University	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	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

SCV000777955

Department of Psychiatry, Nagoya University

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

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, SCV000777955.1

#	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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Relating variation to medicine