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GRCh38/hg38 15q11.2-13.3(chr15:23319714-32607357)x3 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 12, 2011
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:
RCV000051112.6

Allele description [Variation Report for GRCh38/hg38 15q11.2-13.3(chr15:23319714-32607357)x3]

GRCh38/hg38 15q11.2-13.3(chr15:23319714-32607357)x3

Genes:
  • LOC106736481:15q13 distal microdeletion recombination region [Gene]
  • 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]
  • LOC106736469:15q13.2-13.3 gamma inversion distal recombination region [Gene]
  • LOC106736468:15q13.2-13.3 gamma inversion proximal recombination region [Gene]
  • ARHGAP11A-DT:ARHGAP11A divergent transcript [Gene - HGNC]
  • ARHGAP11B-DT:ARHGAP11B divergent transcript [Gene - HGNC]
  • 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]
  • 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]
  • 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]
  • LOC129390681:MPRA-validated peak2289 silencer [Gene]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • GOLGA8K:golgin A8 family member K [Gene - HGNC]
  • GOLGA8M:golgin A8 family member M [Gene - HGNC]
  • GOLGA8N:golgin A8 family member N [Gene - HGNC]
  • GOLGA8O:golgin A8 family member O [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]
  • LINC02256:long intergenic non-protein coding RNA 2256 [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]
  • MIR4509-2: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]
  • UBE3A:ubiquitin protein ligase E3A [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
15q11.2-13.3
Genomic location:
Preferred name:
GRCh38/hg38 15q11.2-13.3(chr15:23319714-32607357)x3
HGVS:
  • NC_000015.10:g.(?_23319714)_(32607357_?)dup
  • NC_000015.8:g.(?_20249886)_(30686850_?)dup
  • NC_000015.9:g.(?_22698522)_(32899558_?)dup
Note:
N.B.: Remap data for this variant included multiple placements, suggesting it falls within a region of the genome that significantly changed between assemblies. We present the highest-scoring remap placement here; however the variant's location should be interpreted with caution.
Links:
dbVar: nssv576967; dbVar: nsv529660
Observations:
1

Condition(s)

Name:
See cases [See the Variation display for details]
Identifiers:

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000078452ISCA site 4

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]
PMID:
21844811
PMCID:
PMC3661946

Details of each submission

From ISCA site 4, SCV000078452.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024