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Single allele AND Autism

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:
RCV000754277.1

Allele description [Variation Report for Single allele]

Genes:
  • BDH1:3-hydroxybutyrate dehydrogenase 1 [Gene - OMIM - HGNC]
  • LOC129938257:ATAC-STARR-seq lymphoblastoid active region 21064 [Gene]
  • LOC129938264:ATAC-STARR-seq lymphoblastoid active region 21065 [Gene]
  • LOC129938267:ATAC-STARR-seq lymphoblastoid active region 21066 [Gene]
  • LOC129938268:ATAC-STARR-seq lymphoblastoid active region 21067 [Gene]
  • LOC129938269:ATAC-STARR-seq lymphoblastoid active region 21068 [Gene]
  • LOC129938270:ATAC-STARR-seq lymphoblastoid active region 21069 [Gene]
  • LOC129938272:ATAC-STARR-seq lymphoblastoid active region 21070 [Gene]
  • LOC129938273:ATAC-STARR-seq lymphoblastoid active region 21071 [Gene]
  • LOC129938274:ATAC-STARR-seq lymphoblastoid active region 21072 [Gene]
  • LOC129938275:ATAC-STARR-seq lymphoblastoid active region 21076 [Gene]
  • LOC129938276:ATAC-STARR-seq lymphoblastoid active region 21077 [Gene]
  • LOC129938279:ATAC-STARR-seq lymphoblastoid active region 21081 [Gene]
  • LOC129938280:ATAC-STARR-seq lymphoblastoid active region 21082 [Gene]
  • LOC129938281:ATAC-STARR-seq lymphoblastoid active region 21083 [Gene]
  • LOC129938283:ATAC-STARR-seq lymphoblastoid active region 21086 [Gene]
  • LOC129938285:ATAC-STARR-seq lymphoblastoid active region 21087 [Gene]
  • LOC129938288:ATAC-STARR-seq lymphoblastoid active region 21090 [Gene]
  • LOC129938289:ATAC-STARR-seq lymphoblastoid active region 21091 [Gene]
  • LOC129938290:ATAC-STARR-seq lymphoblastoid active region 21092 [Gene]
  • LOC129938292:ATAC-STARR-seq lymphoblastoid active region 21095 [Gene]
  • LOC129938295:ATAC-STARR-seq lymphoblastoid active region 21096 [Gene]
  • LOC129938298:ATAC-STARR-seq lymphoblastoid active region 21097 [Gene]
  • LOC129938299:ATAC-STARR-seq lymphoblastoid active region 21098 [Gene]
  • LOC129938300:ATAC-STARR-seq lymphoblastoid active region 21099 [Gene]
  • LOC129938301:ATAC-STARR-seq lymphoblastoid active region 21100 [Gene]
  • LOC129938302:ATAC-STARR-seq lymphoblastoid active region 21101 [Gene]
  • LOC129938305:ATAC-STARR-seq lymphoblastoid active region 21106 [Gene]
  • LOC129938309:ATAC-STARR-seq lymphoblastoid active region 21107 [Gene]
  • LOC129938314:ATAC-STARR-seq lymphoblastoid active region 21108 [Gene]
  • LOC129938315:ATAC-STARR-seq lymphoblastoid active region 21111 [Gene]
  • LOC129938256:ATAC-STARR-seq lymphoblastoid silent region 15047 [Gene]
  • LOC129938258:ATAC-STARR-seq lymphoblastoid silent region 15048 [Gene]
  • LOC129938259:ATAC-STARR-seq lymphoblastoid silent region 15049 [Gene]
  • LOC129938260:ATAC-STARR-seq lymphoblastoid silent region 15050 [Gene]
  • LOC129938261:ATAC-STARR-seq lymphoblastoid silent region 15051 [Gene]
  • LOC129938262:ATAC-STARR-seq lymphoblastoid silent region 15052 [Gene]
  • LOC129938263:ATAC-STARR-seq lymphoblastoid silent region 15053 [Gene]
  • LOC129938265:ATAC-STARR-seq lymphoblastoid silent region 15054 [Gene]
  • LOC129938266:ATAC-STARR-seq lymphoblastoid silent region 15055 [Gene]
  • LOC129938271:ATAC-STARR-seq lymphoblastoid silent region 15056 [Gene]
  • LOC129938277:ATAC-STARR-seq lymphoblastoid silent region 15057 [Gene]
  • LOC129938278:ATAC-STARR-seq lymphoblastoid silent region 15058 [Gene]
  • LOC129938282:ATAC-STARR-seq lymphoblastoid silent region 15059 [Gene]
  • LOC129938284:ATAC-STARR-seq lymphoblastoid silent region 15060 [Gene]
  • LOC129938286:ATAC-STARR-seq lymphoblastoid silent region 15063 [Gene]
  • LOC129938287:ATAC-STARR-seq lymphoblastoid silent region 15064 [Gene]
  • LOC129938291:ATAC-STARR-seq lymphoblastoid silent region 15065 [Gene]
  • LOC129938293:ATAC-STARR-seq lymphoblastoid silent region 15066 [Gene]
  • LOC129938294:ATAC-STARR-seq lymphoblastoid silent region 15067 [Gene]
  • LOC129938296:ATAC-STARR-seq lymphoblastoid silent region 15069 [Gene]
  • LOC129938297:ATAC-STARR-seq lymphoblastoid silent region 15070 [Gene]
  • LOC129938303:ATAC-STARR-seq lymphoblastoid silent region 15072 [Gene]
  • LOC129938304:ATAC-STARR-seq lymphoblastoid silent region 15073 [Gene]
  • LOC129938306:ATAC-STARR-seq lymphoblastoid silent region 15080 [Gene]
  • LOC129938307:ATAC-STARR-seq lymphoblastoid silent region 15081 [Gene]
  • LOC129938308:ATAC-STARR-seq lymphoblastoid silent region 15082 [Gene]
  • LOC129938310:ATAC-STARR-seq lymphoblastoid silent region 15083 [Gene]
  • LOC129938311:ATAC-STARR-seq lymphoblastoid silent region 15084 [Gene]
  • LOC129938312:ATAC-STARR-seq lymphoblastoid silent region 15086 [Gene]
  • LOC129938313:ATAC-STARR-seq lymphoblastoid silent region 15087 [Gene]
  • LOC129938316:ATAC-STARR-seq lymphoblastoid silent region 15088 [Gene]
  • LOC126806932:BRD4-independent group 4 enhancer GRCh37_chr3:195973646-195974845 [Gene]
  • LOC112935924:BRD4-independent group 4 enhancer GRCh37_chr3:196064783-196065982 [Gene]
  • LOC126806934:BRD4-independent group 4 enhancer GRCh37_chr3:196293567-196294766 [Gene]
  • LOC121048736:BRD4-independent group 4 enhancer GRCh37_chr3:196758105-196759304 [Gene]
  • LOC126806935:BRD4-independent group 4 enhancer GRCh37_chr3:197136564-197137763 [Gene]
  • LOC126806936:BRD4-independent group 4 enhancer GRCh37_chr3:197205169-197206368 [Gene]
  • LOC115995537:CRISPRi-validated cis-regulatory element chr3.5812 [Gene]
  • LOC115995538:CRISPRi-validated cis-regulatory element chr3.5817 [Gene]
  • DLG1-AS1:DLG1 antisense RNA 1 [Gene - HGNC]
  • FBXO45:F-box protein 45 [Gene - OMIM - HGNC]
  • LOC123464504:H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:197216831-197217376 and GRCh37_chr3:197217377-197217922 [Gene]
  • LOC126806933:MED14-independent group 3 enhancer GRCh37_chr3:196289997-196291196 [Gene]
  • MELTF-AS1:MELTF antisense RNA 1 [Gene - HGNC]
  • LOC129389196:MPRA-validated peak4992 silencer [Gene]
  • LOC129389197:MPRA-validated peak4993 silencer [Gene]
  • NCBP2AS2:NCBP2 antisense 2 (head to head) [Gene - HGNC]
  • NCBP2-AS1:NCBP2 antisense RNA 1 [Gene - HGNC]
  • LOC111828515:OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:197268447-197269042 [Gene]
  • LOC121725167:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:197121050-197122249 [Gene]
  • SENP5:SUMO specific peptidase 5 [Gene - OMIM - HGNC]
  • LOC123464501:Sharpr-MPRA regulatory region 11589 [Gene]
  • LOC123464503:Sharpr-MPRA regulatory region 1192 [Gene]
  • LOC123464502:Sharpr-MPRA regulatory region 2091 [Gene]
  • LOC123464500:Sharpr-MPRA regulatory region 363 [Gene]
  • LOC123464499:Sharpr-MPRA regulatory region 4041 [Gene]
  • LOC123464505:Sharpr-MPRA regulatory region 5776 [Gene]
  • LOC123464498:Sharpr-MPRA regulatory region 7098 [Gene]
  • TM4SF19-AS1:TM4SF19 antisense RNA 1 [Gene - HGNC]
  • TM4SF19-DYNLT2B:TM4SF19-DYNLT2B readthrough (NMD candidate) [Gene - HGNC]
  • UBXN7:UBX domain protein 7 [Gene - OMIM - HGNC]
  • UBXN7-AS1:UBXN7 antisense RNA 1 [Gene - HGNC]
  • WDR53:WD repeat domain 53 [Gene - OMIM - HGNC]
  • CEP19:centrosomal protein 19 [Gene - OMIM - HGNC]
  • DLG1:discs large MAGUK scaffold protein 1 [Gene - OMIM - HGNC]
  • DYNLT2B:dynein light chain Tctex-type 2B [Gene - OMIM - HGNC]
  • LOC112268458:keratinocyte proline-rich protein [Gene]
  • LINC01063:long intergenic non-protein coding RNA 1063 [Gene - HGNC]
  • LINC02012:long intergenic non-protein coding RNA 2012 [Gene - HGNC]
  • LINC00885:long intergenic non-protein coding RNA 885 [Gene - HGNC]
  • MELTF:melanotransferrin [Gene - OMIM - HGNC]
  • MIR4797:microRNA 4797 [Gene - HGNC]
  • NRROS:negative regulator of reactive oxygen species [Gene - OMIM - HGNC]
  • NCBP2:nuclear cap binding protein subunit 2 [Gene - OMIM - HGNC]
  • PAK2:p21 (RAC1) activated kinase 2 [Gene - OMIM - HGNC]
  • PCYT1A:phosphate cytidylyltransferase 1A, choline [Gene - OMIM - HGNC]
  • PIGX:phosphatidylinositol glycan anchor biosynthesis class X [Gene - OMIM - HGNC]
  • PIGZ:phosphatidylinositol glycan anchor biosynthesis class Z [Gene - OMIM - HGNC]
  • RNF168:ring finger protein 168 [Gene - OMIM - HGNC]
  • SMCO1:single-pass membrane protein with coiled-coil domains 1 [Gene - HGNC]
  • SLC51A:solute carrier family 51 member A [Gene - OMIM - HGNC]
  • TFRC:transferrin receptor [Gene - OMIM - HGNC]
  • TM4SF19:transmembrane 4 L six family member 19 [Gene - OMIM - HGNC]
  • LOC105374308:uncharacterized LOC105374308 [Gene]
  • ZDHHC19:zinc finger DHHC-type palmitoyltransferase 19 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
3q29
Genomic location:
Chr3: 195939900 - 197632041 (on Assembly GRCh38)

Condition(s)

Name:
Autism (AUTS)
Synonyms:
Autistic disorder; Autistic disorder of childhood onset
Identifiers:
MONDO: MONDO:0005260; MeSH: D001321; MedGen: C0004352; OMIM: 209850; Human Phenotype Ontology: HP:0000717

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000778080Department of Psychiatry, Nagoya University
criteria provided, single submitter

(ACMG CNV Guidelines, 2011)		Likely 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, SCV000778080.1

#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: Sep 1, 2024