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GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1 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:
RCV000148061.5

Allele description [Variation Report for GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1]

GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1

Genes:
  • 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]
  • 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]
  • 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]
  • 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]
  • GABRG3-AS1:GABRG3 antisense RNA 1 [Gene - HGNC]
  • HERC2:HECT and RLD domain containing E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
  • MAGEL2:MAGE family member L2 [Gene - OMIM - HGNC]
  • LOC126862083:MED14-independent group 3 enhancer GRCh37_chr15:27939287-27940486 [Gene]
  • LOC129390675:MPRA-validated peak2277 silencer [Gene]
  • LOC129390676:MPRA-validated peak2278 silencer [Gene]
  • NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
  • NIPA2:NIPA magnesium transporter 2 [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]
  • 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]
  • SNURF:SNRPN upstream open reading frame [Gene - HGNC]
  • LOC112272576:Sharpr-MPRA regulatory region 3977 [Gene]
  • LOC112272580:Sharpr-MPRA regulatory region 4259 [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]
  • LOC112272575:Sharpr-MPRA regulatory region 8478 [Gene]
  • LOC112272579:Sharpr-MPRA regulatory region 849 [Gene]
  • LOC112272578:Sharpr-MPRA regulatory region 9168 [Gene]
  • LOC125078048:Sharpr-MPRA regulatory region 9219 [Gene]
  • CYFIP1:cytoplasmic FMR1 interacting protein 1 [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]
  • GOLGA6L26:golgin A6 family like 26 [Gene - HGNC]
  • GOLGA6L2:golgin A6 family like 2 [Gene - HGNC]
  • GOLGA8F:golgin A8 family member F [Gene - HGNC]
  • GOLGA8S:golgin A8 family member S [Gene - HGNC]
  • IPW:imprinted in Prader-Willi syndrome [Gene - OMIM - HGNC]
  • LINC02250:long intergenic non-protein coding RNA 2250 [Gene - HGNC]
  • LINC02346:long intergenic non-protein coding RNA 2346 [Gene - HGNC]
  • LINC00929:long intergenic non-protein coding RNA 929 [Gene - HGNC]
  • MKRN3:makorin ring finger protein 3 [Gene - OMIM - HGNC]
  • LOC128772394:melanoma risk locus-associated MPRA allelic enhancer 15:28365618 [Gene]
  • MIR4508:microRNA 4508 [Gene - HGNC]
  • MIR4509-1:microRNA 4509-1 [Gene - HGNC]
  • MIR4509-2:microRNA 4509-2 [Gene - HGNC]
  • MIR4715:microRNA 4715 [Gene - HGNC]
  • NDN:necdin, MAGE family member [Gene - OMIM - HGNC]
  • NPAP1:nuclear pore associated protein 1 [Gene - OMIM - HGNC]
  • 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]
  • TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
  • UBE3A:ubiquitin protein ligase E3A [Gene - OMIM - HGNC]
  • LOC283683:uncharacterized LOC283683 [Gene]
Variant type:
copy number loss
Cytogenetic location:
15q11.2-13.1
Genomic location:
Preferred name:
GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1
HGVS:
  • NC_000015.10:g.(?_22358243)_(28481444_?)del
  • NC_000015.8:g.(?_20249886)_(26829558_?)del
  • NC_000015.9:g.(?_22698522)_(29030517_?)del
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: nssv579682; dbVar: nsv1067603
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000190815ISCA site 17

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 17, SCV000190815.3

#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