Single allele 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:: RCV000754186.1

Allele description [Variation Report for Single allele]

Genes:

LOC130058760:ATAC-STARR-seq lymphoblastoid active region 10658 [Gene]
LOC130058761:ATAC-STARR-seq lymphoblastoid active region 10659 [Gene]
LOC130058762:ATAC-STARR-seq lymphoblastoid active region 10660 [Gene]
LOC130058763:ATAC-STARR-seq lymphoblastoid active region 10661 [Gene]
LOC130058764:ATAC-STARR-seq lymphoblastoid active region 10662 [Gene]
LOC130058765:ATAC-STARR-seq lymphoblastoid active region 10663 [Gene]
LOC130058766:ATAC-STARR-seq lymphoblastoid active region 10664 [Gene]
LOC130058769:ATAC-STARR-seq lymphoblastoid active region 10665 [Gene]
LOC130058770:ATAC-STARR-seq lymphoblastoid active region 10667 [Gene]
LOC130058772:ATAC-STARR-seq lymphoblastoid active region 10668 [Gene]
LOC130058773:ATAC-STARR-seq lymphoblastoid active region 10669 [Gene]
LOC130058774:ATAC-STARR-seq lymphoblastoid active region 10670 [Gene]
LOC130058775:ATAC-STARR-seq lymphoblastoid active region 10671 [Gene]
LOC130058777:ATAC-STARR-seq lymphoblastoid active region 10672 [Gene]
LOC130058778:ATAC-STARR-seq lymphoblastoid active region 10673 [Gene]
LOC130058780:ATAC-STARR-seq lymphoblastoid active region 10674 [Gene]
LOC130058781:ATAC-STARR-seq lymphoblastoid active region 10675 [Gene]
LOC130058783:ATAC-STARR-seq lymphoblastoid active region 10676 [Gene]
LOC130058787:ATAC-STARR-seq lymphoblastoid active region 10677 [Gene]
LOC130058790:ATAC-STARR-seq lymphoblastoid active region 10679 [Gene]
LOC130058792:ATAC-STARR-seq lymphoblastoid active region 10680 [Gene]
LOC130058793:ATAC-STARR-seq lymphoblastoid active region 10682 [Gene]
LOC130058794:ATAC-STARR-seq lymphoblastoid active region 10683 [Gene]
LOC130058799:ATAC-STARR-seq lymphoblastoid active region 10684 [Gene]
LOC130058802:ATAC-STARR-seq lymphoblastoid active region 10686 [Gene]
LOC130058803:ATAC-STARR-seq lymphoblastoid active region 10687 [Gene]
LOC130058808:ATAC-STARR-seq lymphoblastoid active region 10688 [Gene]
LOC130058810:ATAC-STARR-seq lymphoblastoid active region 10689 [Gene]
LOC130058812:ATAC-STARR-seq lymphoblastoid active region 10690 [Gene]
LOC130058814:ATAC-STARR-seq lymphoblastoid active region 10691 [Gene]
LOC130058815:ATAC-STARR-seq lymphoblastoid active region 10692 [Gene]
LOC130058816:ATAC-STARR-seq lymphoblastoid active region 10693 [Gene]
LOC130058767:ATAC-STARR-seq lymphoblastoid silent region 7329 [Gene]
LOC130058768:ATAC-STARR-seq lymphoblastoid silent region 7330 [Gene]
LOC130058771:ATAC-STARR-seq lymphoblastoid silent region 7331 [Gene]
LOC130058776:ATAC-STARR-seq lymphoblastoid silent region 7332 [Gene]
LOC130058779:ATAC-STARR-seq lymphoblastoid silent region 7333 [Gene]
LOC130058782:ATAC-STARR-seq lymphoblastoid silent region 7334 [Gene]
LOC130058784:ATAC-STARR-seq lymphoblastoid silent region 7335 [Gene]
LOC130058785:ATAC-STARR-seq lymphoblastoid silent region 7336 [Gene]
LOC130058786:ATAC-STARR-seq lymphoblastoid silent region 7337 [Gene]
LOC130058788:ATAC-STARR-seq lymphoblastoid silent region 7338 [Gene]
LOC130058789:ATAC-STARR-seq lymphoblastoid silent region 7339 [Gene]
LOC130058791:ATAC-STARR-seq lymphoblastoid silent region 7340 [Gene]
LOC130058795:ATAC-STARR-seq lymphoblastoid silent region 7341 [Gene]
LOC130058796:ATAC-STARR-seq lymphoblastoid silent region 7342 [Gene]
LOC130058797:ATAC-STARR-seq lymphoblastoid silent region 7343 [Gene]
LOC130058798:ATAC-STARR-seq lymphoblastoid silent region 7344 [Gene]
LOC130058800:ATAC-STARR-seq lymphoblastoid silent region 7345 [Gene]
LOC130058801:ATAC-STARR-seq lymphoblastoid silent region 7346 [Gene]
LOC130058804:ATAC-STARR-seq lymphoblastoid silent region 7347 [Gene]
LOC130058805:ATAC-STARR-seq lymphoblastoid silent region 7348 [Gene]
LOC130058806:ATAC-STARR-seq lymphoblastoid silent region 7349 [Gene]
LOC130058807:ATAC-STARR-seq lymphoblastoid silent region 7350 [Gene]
LOC130058809:ATAC-STARR-seq lymphoblastoid silent region 7351 [Gene]
LOC130058811:ATAC-STARR-seq lymphoblastoid silent region 7352 [Gene]
LOC130058813:ATAC-STARR-seq lymphoblastoid silent region 7356 [Gene]
LOC130058817:ATAC-STARR-seq lymphoblastoid silent region 7357 [Gene]
LOC130058818:ATAC-STARR-seq lymphoblastoid silent region 7358 [Gene]
CDIPTOSP:CDIP transferase opposite strand, pseudogene [Gene - HGNC]
CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
CORO1A-AS1:CORO1A antisense RNA 1 [Gene - HGNC]
LOC116276452:CRISPRi-validated cis-regulatory element chr16.2261 [Gene]
HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
INO80E:INO80 complex subunit E [Gene - HGNC]
LOC129390783:MPRA-validated peak2562 silencer [Gene]
MVP-DT:MVP divergent transcript [Gene - HGNC]
MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
LOC125146440:Sharpr-MPRA regulatory region 10200 [Gene]
LOC125146439:Sharpr-MPRA regulatory region 12104 [Gene]
LOC112352679:Sharpr-MPRA regulatory region 12377 [Gene]
LOC121847977:Sharpr-MPRA regulatory region 13449 [Gene]
LOC121847976:Sharpr-MPRA regulatory region 1439 [Gene]
LOC112352680:Sharpr-MPRA regulatory region 6067 [Gene]
LOC121587540:Sharpr-MPRA regulatory region 8247 [Gene]
LOC125146441:Sharpr-MPRA regulatory region 9068 [Gene]
TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
TAOK2:TAO kinase 2 [Gene - OMIM - HGNC]
TLCD3B:TLC domain containing 3B [Gene - OMIM - HGNC]
YPEL3-DT:YPEL3 divergent transcript [Gene - HGNC]
ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
ASPHD1:aspartate beta-hydroxylase domain containing 1 [Gene - HGNC]
C16orf54:chromosome 16 open reading frame 54 [Gene - HGNC]
C16orf92:chromosome 16 open reading frame 92 [Gene - OMIM - HGNC]
CORO1A:coronin 1A [Gene - OMIM - HGNC]
DOC2A:double C2 domain alpha [Gene - OMIM - HGNC]
GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
KIF22:kinesin family member 22 [Gene - OMIM - HGNC]
MVP:major vault protein [Gene - OMIM - HGNC]
MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
KCTD13:potassium channel tetramerization domain containing 13 [Gene - OMIM - HGNC]
PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
QPRT:quinolinate phosphoribosyltransferase [Gene - OMIM - HGNC]
SEZ6L2:seizure related 6 homolog like 2 [Gene - OMIM - HGNC]
SPN:sialophorin [Gene - OMIM - HGNC]
TMEM219:transmembrane protein 219 [Gene - OMIM - HGNC]
LOC112694756:uncharaterized LOC112694756 [Gene]
YPEL3:yippee like 3 [Gene - OMIM - HGNC]
ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p11.2

Genomic location:

Chr16: 29614026 - 30184960 (on Assembly GRCh38)

Condition(s)

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

Recent activity

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RecName: Full=Cytochrome b; AltName: Full=Complex III subunit 3; AltName: Full=C...
RecName: Full=Cytochrome b; AltName: Full=Complex III subunit 3; AltName: Full=Complex III subunit III; AltName: Full=Cytochrome b-c1 complex subunit 3; AltName: Full=Ubiquinol-cytochrome-c reductase complex cytochrome b subunit
gi|14194558|sp|O48041.1|CYB_CHIAG

Protein
RecName: Full=Neurotrophin-3; Short=NT-3; Flags: Precursor
RecName: Full=Neurotrophin-3; Short=NT-3; Flags: Precursor
gi|123887546|sp|Q1KN23.1|NTF3_CHISR

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000777989	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

SCV000777989

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, SCV000777989.1

#	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

ClinVar

Relating variation to medicine