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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:
RCV000754292.1

Allele description [Variation Report for Single allele]

Genes:
  • ARL14EPL:ADP ribosylation factor like GTPase 14 effector protein like [Gene - HGNC]
  • LOC129994384:ATAC-STARR-seq lymphoblastoid active region 22922 [Gene]
  • LOC129994385:ATAC-STARR-seq lymphoblastoid active region 22923 [Gene]
  • LOC129994388:ATAC-STARR-seq lymphoblastoid active region 22925 [Gene]
  • LOC129994390:ATAC-STARR-seq lymphoblastoid active region 22926 [Gene]
  • LOC129994391:ATAC-STARR-seq lymphoblastoid active region 22927 [Gene]
  • LOC129994393:ATAC-STARR-seq lymphoblastoid active region 22928 [Gene]
  • LOC129994394:ATAC-STARR-seq lymphoblastoid active region 22929 [Gene]
  • LOC129994395:ATAC-STARR-seq lymphoblastoid active region 22930 [Gene]
  • LOC129994396:ATAC-STARR-seq lymphoblastoid active region 22931 [Gene]
  • LOC129994397:ATAC-STARR-seq lymphoblastoid active region 22932 [Gene]
  • LOC129994398:ATAC-STARR-seq lymphoblastoid active region 22933 [Gene]
  • LOC129994399:ATAC-STARR-seq lymphoblastoid active region 22934 [Gene]
  • LOC129994402:ATAC-STARR-seq lymphoblastoid active region 22936 [Gene]
  • LOC129994405:ATAC-STARR-seq lymphoblastoid active region 22939 [Gene]
  • LOC129994406:ATAC-STARR-seq lymphoblastoid active region 22940 [Gene]
  • LOC129994407:ATAC-STARR-seq lymphoblastoid active region 22941 [Gene]
  • LOC129994408:ATAC-STARR-seq lymphoblastoid active region 22942 [Gene]
  • LOC129994409:ATAC-STARR-seq lymphoblastoid active region 22943 [Gene]
  • LOC129994410:ATAC-STARR-seq lymphoblastoid active region 22944 [Gene]
  • LOC129994412:ATAC-STARR-seq lymphoblastoid active region 22945 [Gene]
  • LOC129994415:ATAC-STARR-seq lymphoblastoid active region 22946 [Gene]
  • LOC129994416:ATAC-STARR-seq lymphoblastoid active region 22948 [Gene]
  • LOC129994417:ATAC-STARR-seq lymphoblastoid active region 22950 [Gene]
  • LOC129994418:ATAC-STARR-seq lymphoblastoid active region 22951 [Gene]
  • LOC129994419:ATAC-STARR-seq lymphoblastoid active region 22952 [Gene]
  • LOC129994420:ATAC-STARR-seq lymphoblastoid active region 22953 [Gene]
  • LOC129994421:ATAC-STARR-seq lymphoblastoid active region 22954 [Gene]
  • LOC129994422:ATAC-STARR-seq lymphoblastoid active region 22955 [Gene]
  • LOC129994423:ATAC-STARR-seq lymphoblastoid active region 22956 [Gene]
  • LOC129994383:ATAC-STARR-seq lymphoblastoid silent region 16244 [Gene]
  • LOC129994386:ATAC-STARR-seq lymphoblastoid silent region 16245 [Gene]
  • LOC129994387:ATAC-STARR-seq lymphoblastoid silent region 16246 [Gene]
  • LOC129994389:ATAC-STARR-seq lymphoblastoid silent region 16247 [Gene]
  • LOC129994392:ATAC-STARR-seq lymphoblastoid silent region 16248 [Gene]
  • LOC129994400:ATAC-STARR-seq lymphoblastoid silent region 16252 [Gene]
  • LOC129994401:ATAC-STARR-seq lymphoblastoid silent region 16254 [Gene]
  • LOC129994403:ATAC-STARR-seq lymphoblastoid silent region 16255 [Gene]
  • LOC129994404:ATAC-STARR-seq lymphoblastoid silent region 16256 [Gene]
  • LOC129994411:ATAC-STARR-seq lymphoblastoid silent region 16257 [Gene]
  • LOC129994413:ATAC-STARR-seq lymphoblastoid silent region 16258 [Gene]
  • LOC129994414:ATAC-STARR-seq lymphoblastoid silent region 16259 [Gene]
  • LOC126807482:BRD4-independent group 4 enhancer GRCh37_chr5:114404076-114405275 [Gene]
  • LOC126807487:BRD4-independent group 4 enhancer GRCh37_chr5:116277759-116278958 [Gene]
  • LOC126807485:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:115823690-115824889 [Gene]
  • COMMD10:COMM domain containing 10 [Gene - OMIM - HGNC]
  • LOC126807481:MED14-independent group 3 enhancer GRCh37_chr5:114368052-114369251 [Gene]
  • LOC126807486:MED14-independent group 3 enhancer GRCh37_chr5:115853599-115854798 [Gene]
  • LOC126807488:MED14-independent group 3 enhancer GRCh37_chr5:117814027-117815226 [Gene]
  • LOC129389348:MPRA-validated peak5426 silencer [Gene]
  • LOC129389349:MPRA-validated peak5429 silencer [Gene]
  • LOC129389350:MPRA-validated peak5430 silencer [Gene]
  • LOC132089162:Neanderthal introgressed variant-containing enhancer experimental_80810 [Gene]
  • LOC126807483:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:114795999-114797198 [Gene]
  • LOC126807484:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:115265650-115266849 [Gene]
  • SEMA6A-AS1:SEMA6A antisense RNA 1 [Gene - HGNC]
  • SEMA6A-AS2:SEMA6A antisense RNA 2 [Gene - HGNC]
  • LOC123497956:Sharpr-MPRA regulatory region 14872 [Gene]
  • LOC121725216:Sharpr-MPRA regulatory region 5951 [Gene]
  • LOC112997554:Sharpr-MPRA regulatory region 6 [Gene]
  • LOC121079958:Sharpr-MPRA regulatory region 8609 [Gene]
  • LOC121725215:Sharpr-MPRA regulatory region 9285 [Gene]
  • LOC123497955:Sharpr-MPRA regulatory region 9424 [Gene]
  • TICAM2-AS1:TICAM2 antisense RNA 1 [Gene - HGNC]
  • TICAM2:TIR domain containing adaptor molecule 2 [Gene - OMIM - HGNC]
  • TMED7-TICAM2:TMED7-TICAM2 readthrough [Gene - HGNC]
  • AP3S1:adaptor related protein complex 3 subunit sigma 1 [Gene - OMIM - HGNC]
  • ATG12:autophagy related 12 [Gene - OMIM - HGNC]
  • CCDC112:coiled-coil domain containing 112 [Gene - HGNC]
  • CDO1:cysteine dioxygenase type 1 [Gene - OMIM - HGNC]
  • FEM1C:fem-1 homolog C [Gene - OMIM - HGNC]
  • LVRN:laeverin [Gene - OMIM - HGNC]
  • LINCADL:lincRNA adipogenesis and lipogenesis associated [Gene - HGNC]
  • LINC01957:long intergenic non-protein coding RNA 1957 [Gene - HGNC]
  • LINC02147:long intergenic non-protein coding RNA 2147 [Gene - HGNC]
  • LINC02148:long intergenic non-protein coding RNA 2148 [Gene - HGNC]
  • LINC02208:long intergenic non-protein coding RNA 2208 [Gene - HGNC]
  • LINC02214:long intergenic non-protein coding RNA 2214 [Gene - HGNC]
  • LINC02215:long intergenic non-protein coding RNA 2215 [Gene - HGNC]
  • LINC02216:long intergenic non-protein coding RNA 2216 [Gene - HGNC]
  • LINC00992:long intergenic non-protein coding RNA 992 [Gene - HGNC]
  • MIR12130:microRNA 12130 [Gene - HGNC]
  • KCNN2:potassium calcium-activated channel subfamily N member 2 [Gene - OMIM - HGNC]
  • PGGT1B:protein geranylgeranyltransferase type I subunit beta [Gene - OMIM - HGNC]
  • SEMA6A:semaphorin 6A [Gene - OMIM - HGNC]
  • TMED7:transmembrane p24 trafficking protein 7 [Gene - OMIM - HGNC]
  • TRIM36:tripartite motif containing 36 [Gene - OMIM - HGNC]
  • LOC101927078:uncharacterized LOC101927078 [Gene]
  • LOC101927190:uncharacterized LOC101927190 [Gene]
  • LOC102467217:uncharacterized LOC102467217 [Gene]
Variant type:
Duplication
Cytogenetic location:
5q22.3-23.1
Genomic location:
Chr5: 114046360 - 118610426 (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
SCV000778095Department 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, SCV000778095.1

#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