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Single allele AND Autism

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:
RCV000754147.1

Allele description [Variation Report for Single allele]

Genes:
  • LOC106736480:15q13 proximal microdeletion recombination region [Gene]
  • LOC106736465:15q13.2 beta inversion distal recombination region [Gene]
  • LOC106736464:15q13.2 beta inversion proximal recombination region [Gene]
  • LOC106736468:15q13.2-13.3 gamma inversion proximal recombination region [Gene]
  • ARHGAP11B-DT:ARHGAP11B divergent transcript [Gene - HGNC]
  • 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]
  • LOC130056720:ATAC-STARR-seq lymphoblastoid active region 9163 [Gene]
  • LOC130056721:ATAC-STARR-seq lymphoblastoid active region 9164 [Gene]
  • LOC130056722:ATAC-STARR-seq lymphoblastoid active region 9165 [Gene]
  • LOC130056725:ATAC-STARR-seq lymphoblastoid active region 9166 [Gene]
  • LOC130056707:ATAC-STARR-seq lymphoblastoid silent region 6257 [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]
  • LOC130056719:ATAC-STARR-seq lymphoblastoid silent region 6262 [Gene]
  • LOC130056723:ATAC-STARR-seq lymphoblastoid silent region 6265 [Gene]
  • LOC130056724:ATAC-STARR-seq lymphoblastoid silent region 6266 [Gene]
  • LOC130056726:ATAC-STARR-seq lymphoblastoid silent region 6267 [Gene]
  • LOC130056727:ATAC-STARR-seq lymphoblastoid silent region 6268 [Gene]
  • ATP10A-DT:ATP10A divergent transcript [Gene - HGNC]
  • ATP10A:ATPase phospholipid transporting 10A (putative) [Gene - OMIM - HGNC]
  • LOC126862075:BRD4-independent group 4 enhancer GRCh37_chr15:24001764-24002963 [Gene]
  • LOC126862078:BRD4-independent group 4 enhancer GRCh37_chr15:26860170-26861369 [Gene]
  • LOC126862079:BRD4-independent group 4 enhancer GRCh37_chr15:27034764-27035963 [Gene]
  • LOC126862081:BRD4-independent group 4 enhancer GRCh37_chr15:27585914-27587113 [Gene]
  • LOC126862082:BRD4-independent group 4 enhancer GRCh37_chr15:27699000-27700199 [Gene]
  • LOC126862084:BRD4-independent group 4 enhancer GRCh37_chr15:27958849-27960048 [Gene]
  • LOC126862088:BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 [Gene]
  • LOC126862074:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:22990202-22991401 [Gene]
  • LOC126862076:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:25789643-25790842 [Gene]
  • LOC126862077:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:26791415-26792614 [Gene]
  • LOC126862080:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:27302839-27304038 [Gene]
  • LOC126862086:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:30052673-30053872 [Gene]
  • LOC126862087:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:30226175-30227374 [Gene]
  • CHRFAM7A:CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion [Gene - OMIM - HGNC]
  • FAN1:FANCD2 and FANCI associated nuclease 1 [Gene - OMIM - HGNC]
  • GABRG3-AS1:GABRG3 antisense RNA 1 [Gene - HGNC]
  • HERC2:HECT and RLD domain containing E3 ubiquitin protein ligase 2 [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]
  • MAGEL2:MAGE family member L2 [Gene - OMIM - HGNC]
  • LOC126862083:MED14-independent group 3 enhancer GRCh37_chr15:27939287-27940486 [Gene]
  • LOC126862089:MED14-independent group 3 enhancer GRCh37_chr15:31442413-31443612 [Gene]
  • LOC129390675:MPRA-validated peak2277 silencer [Gene]
  • LOC129390676:MPRA-validated peak2278 silencer [Gene]
  • LOC129390677:MPRA-validated peak2281 silencer [Gene]
  • LOC129390678:MPRA-validated peak2283 silencer [Gene]
  • LOC129390679:MPRA-validated peak2284 silencer [Gene]
  • LOC129390680:MPRA-validated peak2285 silencer [Gene]
  • NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
  • NIPA2:NIPA magnesium transporter 2 [Gene - OMIM - HGNC]
  • NSMCE3:NSE3 homolog, SMC5-SMC6 complex component [Gene - OMIM - HGNC]
  • LOC132090298:Neanderthal introgressed variant-containing enhancer experimental_39258 [Gene]
  • LOC132090299:Neanderthal introgressed variant-containing enhancer experimental_39278 [Gene]
  • OCA2:OCA2 melanosomal transmembrane protein [Gene - OMIM - HGNC]
  • OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
  • LOC126862085:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:30010173-30011372 [Gene]
  • PWAR1:Prader Willi/Angelman region RNA 1 [Gene - OMIM - HGNC]
  • PWAR4:Prader Willi/Angelman region RNA 4 [Gene - HGNC]
  • PWAR5:Prader Willi/Angelman region RNA 5 [Gene - OMIM - HGNC]
  • PWAR6:Prader Willi/Angelman region RNA 6 [Gene - HGNC]
  • PWARSN:Prader Willi/Angelman region RNA, SNRPN neighbor [Gene - HGNC]
  • PWRN1:Prader-Willi region non-protein coding RNA 1 [Gene - OMIM - HGNC]
  • PWRN2:Prader-Willi region non-protein coding RNA 2 [Gene - OMIM - HGNC]
  • PWRN3:Prader-Willi region non-protein coding RNA 3 [Gene - HGNC]
  • PWRN4:Prader-Willi region non-protein coding RNA 4 [Gene - HGNC]
  • ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
  • SNURF:SNRPN upstream open reading frame [Gene - HGNC]
  • LOC125078053:Sharpr-MPRA regulatory region 11410 [Gene]
  • LOC125078052:Sharpr-MPRA regulatory region 13292 [Gene]
  • LOC112272581:Sharpr-MPRA regulatory region 3573 [Gene]
  • LOC112272576:Sharpr-MPRA regulatory region 3977 [Gene]
  • LOC112272580:Sharpr-MPRA regulatory region 4259 [Gene]
  • LOC112272582:Sharpr-MPRA regulatory region 5138 [Gene]
  • LOC125078049:Sharpr-MPRA regulatory region 5301 [Gene]
  • LOC125078046:Sharpr-MPRA regulatory region 5757 [Gene]
  • LOC125078047:Sharpr-MPRA regulatory region 718 [Gene]
  • LOC121847940:Sharpr-MPRA regulatory region 7323 [Gene]
  • LOC121847941:Sharpr-MPRA regulatory region 8183 [Gene]
  • LOC112272575:Sharpr-MPRA regulatory region 8478 [Gene]
  • LOC112272579:Sharpr-MPRA regulatory region 849 [Gene]
  • LOC125078051:Sharpr-MPRA regulatory region 8593 [Gene]
  • LOC112272578:Sharpr-MPRA regulatory region 9168 [Gene]
  • LOC125078048:Sharpr-MPRA regulatory region 9219 [Gene]
  • LOC110121498:VISTA enhancer hs2231 [Gene]
  • APBA2:amyloid beta precursor protein binding family A member 2 [Gene - OMIM - HGNC]
  • CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
  • CYFIP1:cytoplasmic FMR1 interacting protein 1 [Gene - OMIM - HGNC]
  • LOC106736477:distal CHRNA7 low-copy repeat recombination region [Gene]
  • ENTREP2:endosomal transmembrane epsin interactor 2 [Gene - OMIM - HGNC]
  • GABRA5:gamma-aminobutyric acid type A receptor subunit alpha5 [Gene - OMIM - HGNC]
  • GABRB3:gamma-aminobutyric acid type A receptor subunit beta3 [Gene - OMIM - HGNC]
  • GABRG3:gamma-aminobutyric acid type A receptor subunit gamma3 [Gene - OMIM - HGNC]
  • GOLGA6L1:golgin A6 family like 1 [Gene - HGNC]
  • GOLGA6L22:golgin A6 family like 22 [Gene - HGNC]
  • GOLGA6L24:golgin A6 family like 24 [Gene - HGNC]
  • GOLGA6L25:golgin A6 family like 25 [Gene - HGNC]
  • GOLGA6L26:golgin A6 family like 26 [Gene - HGNC]
  • GOLGA6L2:golgin A6 family like 2 [Gene - HGNC]
  • GOLGA6L7:golgin A6 family like 7 [Gene - HGNC]
  • GOLGA8F:golgin A8 family member F [Gene - HGNC]
  • GOLGA8G:golgin A8 family member G [Gene - HGNC]
  • GOLGA8H:golgin A8 family member H [Gene - HGNC]
  • GOLGA8J:golgin A8 family member J [Gene - HGNC]
  • GOLGA8M:golgin A8 family member M [Gene - HGNC]
  • GOLGA8Q:golgin A8 family member Q [Gene - HGNC]
  • GOLGA8R:golgin A8 family member R [Gene - HGNC]
  • GOLGA8S:golgin A8 family member S [Gene - HGNC]
  • GOLGA8T:golgin A8 family member T [Gene - HGNC]
  • IPW:imprinted in Prader-Willi syndrome [Gene - OMIM - HGNC]
  • LINC02249:long intergenic non-protein coding RNA 2249 [Gene - HGNC]
  • LINC02250:long intergenic non-protein coding RNA 2250 [Gene - HGNC]
  • LINC02346:long intergenic non-protein coding RNA 2346 [Gene - HGNC]
  • LINC02352:long intergenic non-protein coding RNA 2352 [Gene - HGNC]
  • LINC03034:long intergenic non-protein coding RNA 3034 [Gene - HGNC]
  • LINC00929:long intergenic non-protein coding RNA 929 [Gene - HGNC]
  • LCIIAR:lung cancer immune cell infiltration associated lncRNA [Gene - HGNC]
  • MKRN3:makorin ring finger protein 3 [Gene - OMIM - HGNC]
  • LOC128772394:melanoma risk locus-associated MPRA allelic enhancer 15:28365618 [Gene]
  • MIR211:microRNA 211 [Gene - OMIM - HGNC]
  • MIR4508:microRNA 4508 [Gene - HGNC]
  • MIR4509-1:microRNA 4509-1 [Gene - HGNC]
  • MIR4509-2:microRNA 4509-2 [Gene - HGNC]
  • MIR4509-3:microRNA 4509-3 [Gene - HGNC]
  • MIR4715:microRNA 4715 [Gene - HGNC]
  • MTMR10:myotubularin related protein 10 [Gene - HGNC]
  • NDN:necdin, MAGE family member [Gene - OMIM - HGNC]
  • LOC106783506:nonconserved acetylation island sequence 49 enhancer [Gene]
  • NPAP1:nuclear pore associated protein 1 [Gene - OMIM - HGNC]
  • LOC106736476:proximal CHRNA7 low-copy repeat recombination region [Gene]
  • SNRPN:small nuclear ribonucleoprotein polypeptide N [Gene - OMIM - HGNC]
  • SNHG14:small nucleolar RNA host gene 14 [Gene - OMIM - HGNC]
  • SNORD107:small nucleolar RNA, C/D box 107 [Gene - HGNC]
  • SNORD108:small nucleolar RNA, C/D box 108 [Gene - HGNC]
  • SNORD109A:small nucleolar RNA, C/D box 109A [Gene - HGNC]
  • SNORD109B:small nucleolar RNA, C/D box 109B [Gene - HGNC]
  • SNORD115-10:small nucleolar RNA, C/D box 115-10 [Gene - HGNC]
  • SNORD115-11:small nucleolar RNA, C/D box 115-11 [Gene - HGNC]
  • SNORD115-12:small nucleolar RNA, C/D box 115-12 [Gene - HGNC]
  • SNORD115-13:small nucleolar RNA, C/D box 115-13 [Gene - HGNC]
  • SNORD115-14:small nucleolar RNA, C/D box 115-14 [Gene - HGNC]
  • SNORD115-15:small nucleolar RNA, C/D box 115-15 [Gene - HGNC]
  • SNORD115-16:small nucleolar RNA, C/D box 115-16 [Gene - HGNC]
  • SNORD115-17:small nucleolar RNA, C/D box 115-17 [Gene - HGNC]
  • SNORD115-18:small nucleolar RNA, C/D box 115-18 [Gene - HGNC]
  • SNORD115-19:small nucleolar RNA, C/D box 115-19 [Gene - HGNC]
  • SNORD115-1:small nucleolar RNA, C/D box 115-1 [Gene - OMIM - HGNC]
  • SNORD115-20:small nucleolar RNA, C/D box 115-20 [Gene - HGNC]
  • SNORD115-21:small nucleolar RNA, C/D box 115-21 [Gene - HGNC]
  • SNORD115-22:small nucleolar RNA, C/D box 115-22 [Gene - HGNC]
  • SNORD115-23:small nucleolar RNA, C/D box 115-23 [Gene - HGNC]
  • SNORD115-24:small nucleolar RNA, C/D box 115-24 [Gene - HGNC]
  • SNORD115-25:small nucleolar RNA, C/D box 115-25 [Gene - HGNC]
  • SNORD115-26:small nucleolar RNA, C/D box 115-26 [Gene - HGNC]
  • SNORD115-27:small nucleolar RNA, C/D box 115-27 [Gene - HGNC]
  • SNORD115-28:small nucleolar RNA, C/D box 115-28 [Gene - HGNC]
  • SNORD115-29:small nucleolar RNA, C/D box 115-29 [Gene - HGNC]
  • SNORD115-2:small nucleolar RNA, C/D box 115-2 [Gene - HGNC]
  • SNORD115-30:small nucleolar RNA, C/D box 115-30 [Gene - HGNC]
  • SNORD115-31:small nucleolar RNA, C/D box 115-31 [Gene - HGNC]
  • SNORD115-32:small nucleolar RNA, C/D box 115-32 [Gene - HGNC]
  • SNORD115-33:small nucleolar RNA, C/D box 115-33 [Gene - HGNC]
  • SNORD115-34:small nucleolar RNA, C/D box 115-34 [Gene - HGNC]
  • SNORD115-35:small nucleolar RNA, C/D box 115-35 [Gene - HGNC]
  • SNORD115-36:small nucleolar RNA, C/D box 115-36 [Gene - HGNC]
  • SNORD115-37:small nucleolar RNA, C/D box 115-37 [Gene - HGNC]
  • SNORD115-38:small nucleolar RNA, C/D box 115-38 [Gene - HGNC]
  • SNORD115-39:small nucleolar RNA, C/D box 115-39 [Gene - HGNC]
  • SNORD115-3:small nucleolar RNA, C/D box 115-3 [Gene - HGNC]
  • SNORD115-40:small nucleolar RNA, C/D box 115-40 [Gene - HGNC]
  • SNORD115-41:small nucleolar RNA, C/D box 115-41 [Gene - HGNC]
  • SNORD115-42:small nucleolar RNA, C/D box 115-42 [Gene - HGNC]
  • SNORD115-43:small nucleolar RNA, C/D box 115-43 [Gene - HGNC]
  • SNORD115-44:small nucleolar RNA, C/D box 115-44 [Gene - HGNC]
  • SNORD115-45:small nucleolar RNA, C/D box 115-45 [Gene - HGNC]
  • SNORD115-46:small nucleolar RNA, C/D box 115-46 [Gene - HGNC]
  • SNORD115-47:small nucleolar RNA, C/D box 115-47 [Gene - HGNC]
  • SNORD115-48:small nucleolar RNA, C/D box 115-48 [Gene - HGNC]
  • SNORD115-4:small nucleolar RNA, C/D box 115-4 [Gene - HGNC]
  • SNORD115-5:small nucleolar RNA, C/D box 115-5 [Gene - HGNC]
  • SNORD115-6:small nucleolar RNA, C/D box 115-6 [Gene - HGNC]
  • SNORD115-7:small nucleolar RNA, C/D box 115-7 [Gene - HGNC]
  • SNORD115-8:small nucleolar RNA, C/D box 115-8 [Gene - HGNC]
  • SNORD115-9:small nucleolar RNA, C/D box 115-9 [Gene - HGNC]
  • SNORD116-10:small nucleolar RNA, C/D box 116-10 [Gene - HGNC]
  • SNORD116-11:small nucleolar RNA, C/D box 116-11 [Gene - HGNC]
  • SNORD116-12:small nucleolar RNA, C/D box 116-12 [Gene - HGNC]
  • SNORD116-13:small nucleolar RNA, C/D box 116-13 [Gene - HGNC]
  • SNORD116-14:small nucleolar RNA, C/D box 116-14 [Gene - HGNC]
  • SNORD116-15:small nucleolar RNA, C/D box 116-15 [Gene - HGNC]
  • SNORD116-16:small nucleolar RNA, C/D box 116-16 [Gene - HGNC]
  • SNORD116-17:small nucleolar RNA, C/D box 116-17 [Gene - HGNC]
  • SNORD116-18:small nucleolar RNA, C/D box 116-18 [Gene - HGNC]
  • SNORD116-19:small nucleolar RNA, C/D box 116-19 [Gene - HGNC]
  • SNORD116-1:small nucleolar RNA, C/D box 116-1 [Gene - OMIM - HGNC]
  • SNORD116-20:small nucleolar RNA, C/D box 116-20 [Gene - HGNC]
  • SNORD116-21:small nucleolar RNA, C/D box 116-21 [Gene - HGNC]
  • SNORD116-22:small nucleolar RNA, C/D box 116-22 [Gene - HGNC]
  • SNORD116-23:small nucleolar RNA, C/D box 116-23 [Gene - HGNC]
  • SNORD116-24:small nucleolar RNA, C/D box 116-24 [Gene - HGNC]
  • SNORD116-25:small nucleolar RNA, C/D box 116-25 [Gene - HGNC]
  • SNORD116-26:small nucleolar RNA, C/D box 116-26 [Gene - HGNC]
  • SNORD116-27:small nucleolar RNA, C/D box 116-27 [Gene - HGNC]
  • SNORD116-28:small nucleolar RNA, C/D box 116-28 [Gene - HGNC]
  • SNORD116-29:small nucleolar RNA, C/D box 116-29 [Gene - HGNC]
  • SNORD116-2:small nucleolar RNA, C/D box 116-2 [Gene - HGNC]
  • SNORD116-30:small nucleolar RNA, C/D box 116-30 [Gene - HGNC]
  • SNORD116-3:small nucleolar RNA, C/D box 116-3 [Gene - HGNC]
  • SNORD116-4:small nucleolar RNA, C/D box 116-4 [Gene - HGNC]
  • SNORD116-5:small nucleolar RNA, C/D box 116-5 [Gene - HGNC]
  • SNORD116-6:small nucleolar RNA, C/D box 116-6 [Gene - HGNC]
  • SNORD116-7:small nucleolar RNA, C/D box 116-7 [Gene - HGNC]
  • SNORD116-8:small nucleolar RNA, C/D box 116-8 [Gene - HGNC]
  • SNORD116-9:small nucleolar RNA, C/D box 116-9 [Gene - HGNC]
  • SNORD64:small nucleolar RNA, C/D box 64 [Gene - HGNC]
  • TRE-TTC2-2:tRNA-Glu (anticodon TTC) 2-2 [Gene - HGNC]
  • TJP1:tight junction protein 1 [Gene - OMIM - HGNC]
  • TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]
  • TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
  • UBE3A:ubiquitin protein ligase E3A [Gene - OMIM - HGNC]
  • LOC283683:uncharacterized LOC283683 [Gene]
Variant type:
Duplication
Cytogenetic location:
15q11.2-13.3
Genomic location:
Chr15: 22420897 - 32130343 (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
SCV000777950Department 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, SCV000777950.1

#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: Jun 9, 2024