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NC_000001.11:g.(?_145430995)_(148427734_?)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:
RCV000754127.1

Allele description [Variation Report for NC_000001.11:g.(?_145430995)_(148427734_?)del]

NC_000001.11:g.(?_145430995)_(148427734_?)del

Genes:
  • LOC129931325:ATAC-STARR-seq lymphoblastoid active region 1609 [Gene]
  • LOC129931328:ATAC-STARR-seq lymphoblastoid active region 1610 [Gene]
  • LOC129931329:ATAC-STARR-seq lymphoblastoid active region 1611 [Gene]
  • LOC129931330:ATAC-STARR-seq lymphoblastoid active region 1612 [Gene]
  • LOC129931331:ATAC-STARR-seq lymphoblastoid active region 1613 [Gene]
  • LOC129931332:ATAC-STARR-seq lymphoblastoid active region 1614 [Gene]
  • LOC129931338:ATAC-STARR-seq lymphoblastoid active region 1616 [Gene]
  • LOC129931339:ATAC-STARR-seq lymphoblastoid active region 1617 [Gene]
  • LOC129931342:ATAC-STARR-seq lymphoblastoid active region 1621 [Gene]
  • LOC129931343:ATAC-STARR-seq lymphoblastoid active region 1622 [Gene]
  • LOC129931344:ATAC-STARR-seq lymphoblastoid active region 1626 [Gene]
  • LOC129931345:ATAC-STARR-seq lymphoblastoid active region 1627 [Gene]
  • LOC129931346:ATAC-STARR-seq lymphoblastoid active region 1628 [Gene]
  • LOC129931349:ATAC-STARR-seq lymphoblastoid active region 1629 [Gene]
  • LOC129931358:ATAC-STARR-seq lymphoblastoid active region 1635 [Gene]
  • LOC129931359:ATAC-STARR-seq lymphoblastoid active region 1637 [Gene]
  • LOC129931360:ATAC-STARR-seq lymphoblastoid active region 1638 [Gene]
  • LOC129931361:ATAC-STARR-seq lymphoblastoid active region 1639 [Gene]
  • LOC129931362:ATAC-STARR-seq lymphoblastoid active region 1640 [Gene]
  • LOC129931363:ATAC-STARR-seq lymphoblastoid active region 1641 [Gene]
  • LOC129931326:ATAC-STARR-seq lymphoblastoid silent region 1262 [Gene]
  • LOC129931327:ATAC-STARR-seq lymphoblastoid silent region 1263 [Gene]
  • LOC129931333:ATAC-STARR-seq lymphoblastoid silent region 1264 [Gene]
  • LOC129931334:ATAC-STARR-seq lymphoblastoid silent region 1265 [Gene]
  • LOC129931335:ATAC-STARR-seq lymphoblastoid silent region 1266 [Gene]
  • LOC129931336:ATAC-STARR-seq lymphoblastoid silent region 1267 [Gene]
  • LOC129931337:ATAC-STARR-seq lymphoblastoid silent region 1268 [Gene]
  • LOC129931340:ATAC-STARR-seq lymphoblastoid silent region 1269 [Gene]
  • LOC129931341:ATAC-STARR-seq lymphoblastoid silent region 1270 [Gene]
  • LOC129931347:ATAC-STARR-seq lymphoblastoid silent region 1271 [Gene]
  • LOC129931348:ATAC-STARR-seq lymphoblastoid silent region 1272 [Gene]
  • LOC129931350:ATAC-STARR-seq lymphoblastoid silent region 1273 [Gene]
  • LOC129931351:ATAC-STARR-seq lymphoblastoid silent region 1276 [Gene]
  • LOC129931352:ATAC-STARR-seq lymphoblastoid silent region 1277 [Gene]
  • LOC129931353:ATAC-STARR-seq lymphoblastoid silent region 1278 [Gene]
  • LOC129931354:ATAC-STARR-seq lymphoblastoid silent region 1279 [Gene]
  • LOC129931355:ATAC-STARR-seq lymphoblastoid silent region 1280 [Gene]
  • LOC129931356:ATAC-STARR-seq lymphoblastoid silent region 1281 [Gene]
  • LOC129931357:ATAC-STARR-seq lymphoblastoid silent region 1282 [Gene]
  • BCL9:BCL9 transcription coactivator [Gene - OMIM - HGNC]
  • LOC108254679:BRD4-independent group 4 enhancer GRCh37_chr1:145455010-145456209 [Gene]
  • LOC126805854:BRD4-independent group 4 enhancer GRCh37_chr1:146764440-146765639 [Gene]
  • CD160:CD160 molecule [Gene - OMIM - HGNC]
  • LOC126805850:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:145584188-145585387 [Gene]
  • LOC126805849:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:145727451-145728650 [Gene]
  • LOC126805852:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:146501494-146502693 [Gene]
  • GPR89A:G protein-coupled receptor 89A [Gene - OMIM - HGNC]
  • GPR89B:G protein-coupled receptor 89B [Gene - OMIM - HGNC]
  • LOC111556113:HNF4 motif-containing MPRA enhancer 9 [Gene]
  • LIX1L-AS1:LIX1L antisense RNA 1 [Gene - HGNC]
  • LOC126805851:MED14-independent group 3 enhancer GRCh37_chr1:145507474-145508673 [Gene]
  • LOC129388601:MPRA-validated peak399 silencer [Gene]
  • LOC129388602:MPRA-validated peak400 silencer [Gene]
  • LOC129388603:MPRA-validated peak402 silencer [Gene]
  • LOC129388604:MPRA-validated peak403 silencer [Gene]
  • NBPF10:NBPF member 10 [Gene - OMIM - HGNC]
  • NBPF11:NBPF member 11 [Gene - OMIM - HGNC]
  • NBPF12:NBPF member 12 [Gene - OMIM - HGNC]
  • LOC126805853:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:146633127-146634326 [Gene]
  • PDZK1:PDZ domain containing 1 [Gene - OMIM - HGNC]
  • RBM8A:RNA binding motif protein 8A [Gene - OMIM - HGNC]
  • POLR3C:RNA polymerase III subunit C [Gene - OMIM - HGNC]
  • POLR3GL:RNA polymerase III subunit GL [Gene - OMIM - HGNC]
  • RNVU1-1:RNA, variant U1 small nuclear 1 [Gene - HGNC]
  • RNVU1-31:RNA, variant U1 small nuclear 31 [Gene - HGNC]
  • RNVU1-3:RNA, variant U1 small nuclear 3 [Gene - HGNC]
  • RNVU1-6:RNA, variant U1 small nuclear 6 [Gene - HGNC]
  • RNVU1-7:RNA, variant U1 small nuclear 7 [Gene - HGNC]
  • RNVU1-8:RNA, variant U1 small nuclear 8 [Gene - HGNC]
  • LOC121725052:Sharpr-MPRA regulatory region 10305 [Gene]
  • LOC122128420:Sharpr-MPRA regulatory region 3144 [Gene]
  • LOC112577490:Sharpr-MPRA regulatory region 3868 [Gene]
  • LOC122128419:Sharpr-MPRA regulatory region 4010 [Gene]
  • LOC121725051:Sharpr-MPRA regulatory region 5908 [Gene]
  • LOC121725053:Sharpr-MPRA regulatory region 879 [Gene]
  • LOC110121261:VISTA enhancer hs2126 [Gene]
  • ACP6:acid phosphatase 6, lysophosphatidic [Gene - OMIM - HGNC]
  • ANKRD34A:ankyrin repeat domain 34A [Gene - HGNC]
  • ANKRD35:ankyrin repeat domain 35 [Gene - HGNC]
  • CHD1L:chromodomain helicase DNA binding protein 1 like [Gene - OMIM - HGNC]
  • LOC106783502:conserved acetylation island sequence C12 enhancer [Gene]
  • FMO5:flavin containing dimethylaniline monoxygenase 5 [Gene - OMIM - HGNC]
  • GJA5:gap junction protein alpha 5 [Gene - OMIM - HGNC]
  • GJA8:gap junction protein alpha 8 [Gene - OMIM - HGNC]
  • HJV:hemojuvelin BMP co-receptor [Gene - OMIM - HGNC]
  • ITGA10:integrin subunit alpha 10 [Gene - OMIM - HGNC]
  • LIX1L:limb and CNS expressed 1 like [Gene - HGNC]
  • LINC01719:long intergenic non-protein coding RNA 1719 [Gene - HGNC]
  • LINC01731:long intergenic non-protein coding RNA 1731 [Gene - HGNC]
  • LINC02805:long intergenic non-protein coding RNA 2805 [Gene - HGNC]
  • LINC02806:long intergenic non-protein coding RNA 2806 [Gene - HGNC]
  • LINC00624:long intergenic non-protein coding RNA 624 [Gene - HGNC]
  • MIR5087:microRNA 5087 [Gene - HGNC]
  • MIR6077:microRNA 6077 [Gene - HGNC]
  • MIR6736:microRNA 6736 [Gene - HGNC]
  • NOTCH2NLA:notch 2 N-terminal like A [Gene - OMIM - HGNC]
  • NUDT17:nudix hydrolase 17 [Gene - HGNC]
  • PPIAL4H:peptidylprolyl isomerase A like 4H [Gene - HGNC]
  • PEX11B:peroxisomal biogenesis factor 11 beta [Gene - OMIM - HGNC]
  • PIAS3:protein inhibitor of activated STAT 3 [Gene - OMIM - HGNC]
  • PRKAB2:protein kinase AMP-activated non-catalytic subunit beta 2 [Gene - OMIM - HGNC]
  • RNF115:ring finger protein 115 [Gene - OMIM - HGNC]
  • TRN-GTT24-1:tRNA-Asn (anticodon GTT) 24-1 [Gene - HGNC]
  • TRN-GTT9-1:tRNA-Asn (anticodon GTT) 9-1 [Gene - HGNC]
  • TRN-GTT9-2:tRNA-Asn (anticodon GTT) 9-2 [Gene - HGNC]
  • TRQ-CTG3-1:tRNA-Gln (anticodon CTG) 3-1 [Gene - HGNC]
  • TRQ-CTG3-2:tRNA-Gln (anticodon CTG) 3-2 [Gene - HGNC]
  • TRQ-CTG4-1:tRNA-Gln (anticodon CTG) 4-1 [Gene - HGNC]
  • TRQ-CTG7-1:tRNA-Gln (anticodon CTG) 7-1 [Gene - HGNC]
  • TRE-CTC1-1:tRNA-Glu (anticodon CTC) 1-1 [Gene - HGNC]
  • TRG-TCC2-1:tRNA-Gly (anticodon TCC) 2-1 [Gene - HGNC]
  • TRH-GTG1-1:tRNA-His (anticodon GTG) 1-1 [Gene - HGNC]
  • TRH-GTG1-2:tRNA-His (anticodon GTG) 1-2 [Gene - HGNC]
  • TRH-GTG1-3:tRNA-His (anticodon GTG) 1-3 [Gene - HGNC]
  • TRH-GTG1-4:tRNA-His (anticodon GTG) 1-4 [Gene - HGNC]
  • TRK-CTT2-1:tRNA-Lys (anticodon CTT) 2-1 [Gene - HGNC]
  • TXNIP:thioredoxin interacting protein [Gene - OMIM - HGNC]
  • LOC101927468:uncharacterized LOC101927468 [Gene]
  • CH17-408M7.1:uncharacterized LOC102724558 [Gene]
  • LOC128071544:uncharacterized LOC128071544 [Gene]
Variant type:
Deletion
Cytogenetic location:
1q21.1-21.2
Genomic location:
Chr1: 145430995 - 148427734 (on Assembly GRCh38)
Preferred name:
NC_000001.11:g.(?_145430995)_(148427734_?)del
HGVS:
NC_000001.11:g.(?_145430995)_(148427734_?)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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000777930Department of Psychiatry, Nagoya University
criteria provided, single submitter

(ACMG CNV Guidelines, 2011)		Pathogenic
(Mar 20, 2018) 		germlineresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch

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, SCV000777930.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024