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GRCh38/hg38 15q11.2-13.1(chr15:23411789-28275167)x1 AND See cases

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Aug 12, 2011
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000148164.3

Allele description [Variation Report for GRCh38/hg38 15q11.2-13.1(chr15:23411789-28275167)x1]

GRCh38/hg38 15q11.2-13.1(chr15:23411789-28275167)x1

Genes:
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • LOC112272579:Sharpr-MPRA regulatory region 849 [Gene]
  • LOC112272578:Sharpr-MPRA regulatory region 9168 [Gene]
  • LOC125078048:Sharpr-MPRA regulatory region 9219 [Gene]
  • 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]
  • GOLGA6L2:golgin A6 family like 2 [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]
  • 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]
  • UBE3A:ubiquitin protein ligase E3A [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
15q11.2-13.1
Genomic location:
Preferred name:
GRCh38/hg38 15q11.2-13.1(chr15:23411789-28275167)x1
HGVS:
  • NC_000015.10:g.(?_23411789)_(28275167_?)del
  • NC_000015.8:g.(?_21208377)_(26193908_?)del
  • NC_000015.9:g.(?_23656936)_(28520313_?)del
Links:
dbVar: nssv579697; dbVar: nssv579699; dbVar: nssv579701; dbVar: nssv579702; dbVar: nssv579703; dbVar: nsv1067605
Observations:
5

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
SCV000190760ISCA site 14

See additional submitters

criteria provided, single submitter

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

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

SCV000190761ISCA 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 providedde novoyes1not providednot providednot providednot providedclinical testing
not providednot providedyes4not 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 14, SCV000190760.2

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

From ISCA site 4, SCV000190761.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
2not provided1not providednot providedclinical testing PubMed (1)
3not provided1not providednot providedclinical testing PubMed (1)
4not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided
2unknownyesnot providednot providedDiscovery1not providednot providednot provided
3unknownyesnot providednot providedDiscovery1not providednot providednot provided
4unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024