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GRCh38/hg38 15q21.1-21.2(chr15:47460844-52494222)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 18, 2011
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000135639.7

Allele description [Variation Report for GRCh38/hg38 15q21.1-21.2(chr15:47460844-52494222)x1]

GRCh38/hg38 15q21.1-21.2(chr15:47460844-52494222)x1

Genes:
  • LOC130057010:ATAC-STARR-seq lymphoblastoid active region 9370 [Gene]
  • LOC130057011:ATAC-STARR-seq lymphoblastoid active region 9371 [Gene]
  • LOC130057012:ATAC-STARR-seq lymphoblastoid active region 9372 [Gene]
  • LOC130057013:ATAC-STARR-seq lymphoblastoid active region 9373 [Gene]
  • LOC130057014:ATAC-STARR-seq lymphoblastoid active region 9374 [Gene]
  • LOC130057018:ATAC-STARR-seq lymphoblastoid active region 9375 [Gene]
  • LOC130057023:ATAC-STARR-seq lymphoblastoid active region 9377 [Gene]
  • LOC130057024:ATAC-STARR-seq lymphoblastoid active region 9378 [Gene]
  • LOC130057025:ATAC-STARR-seq lymphoblastoid active region 9379 [Gene]
  • LOC130057026:ATAC-STARR-seq lymphoblastoid active region 9380 [Gene]
  • LOC130057027:ATAC-STARR-seq lymphoblastoid active region 9381 [Gene]
  • LOC130057028:ATAC-STARR-seq lymphoblastoid active region 9382 [Gene]
  • LOC130057029:ATAC-STARR-seq lymphoblastoid active region 9383 [Gene]
  • LOC130057030:ATAC-STARR-seq lymphoblastoid active region 9384 [Gene]
  • LOC130057032:ATAC-STARR-seq lymphoblastoid active region 9387 [Gene]
  • LOC130057033:ATAC-STARR-seq lymphoblastoid active region 9388 [Gene]
  • LOC130057034:ATAC-STARR-seq lymphoblastoid active region 9389 [Gene]
  • LOC130057035:ATAC-STARR-seq lymphoblastoid active region 9390 [Gene]
  • LOC130057038:ATAC-STARR-seq lymphoblastoid active region 9391 [Gene]
  • LOC130057041:ATAC-STARR-seq lymphoblastoid active region 9392 [Gene]
  • LOC130057042:ATAC-STARR-seq lymphoblastoid active region 9393 [Gene]
  • LOC130057043:ATAC-STARR-seq lymphoblastoid active region 9394 [Gene]
  • LOC130057044:ATAC-STARR-seq lymphoblastoid active region 9395 [Gene]
  • LOC130057046:ATAC-STARR-seq lymphoblastoid active region 9397 [Gene]
  • LOC130057048:ATAC-STARR-seq lymphoblastoid active region 9398 [Gene]
  • LOC130057049:ATAC-STARR-seq lymphoblastoid active region 9399 [Gene]
  • LOC130057050:ATAC-STARR-seq lymphoblastoid active region 9400 [Gene]
  • LOC130057051:ATAC-STARR-seq lymphoblastoid active region 9403 [Gene]
  • LOC130057052:ATAC-STARR-seq lymphoblastoid active region 9404 [Gene]
  • LOC130057055:ATAC-STARR-seq lymphoblastoid active region 9405 [Gene]
  • LOC130057056:ATAC-STARR-seq lymphoblastoid active region 9406 [Gene]
  • LOC130057061:ATAC-STARR-seq lymphoblastoid active region 9407 [Gene]
  • LOC130057066:ATAC-STARR-seq lymphoblastoid active region 9408 [Gene]
  • LOC130057067:ATAC-STARR-seq lymphoblastoid active region 9409 [Gene]
  • LOC130057068:ATAC-STARR-seq lymphoblastoid active region 9411 [Gene]
  • LOC130057069:ATAC-STARR-seq lymphoblastoid active region 9412 [Gene]
  • LOC130057070:ATAC-STARR-seq lymphoblastoid active region 9413 [Gene]
  • LOC130057071:ATAC-STARR-seq lymphoblastoid active region 9414 [Gene]
  • LOC130057074:ATAC-STARR-seq lymphoblastoid active region 9415 [Gene]
  • LOC130057075:ATAC-STARR-seq lymphoblastoid active region 9416 [Gene]
  • LOC130057076:ATAC-STARR-seq lymphoblastoid active region 9417 [Gene]
  • LOC130057077:ATAC-STARR-seq lymphoblastoid active region 9419 [Gene]
  • LOC130057078:ATAC-STARR-seq lymphoblastoid active region 9420 [Gene]
  • LOC130057079:ATAC-STARR-seq lymphoblastoid active region 9421 [Gene]
  • LOC130057080:ATAC-STARR-seq lymphoblastoid active region 9422 [Gene]
  • LOC130057082:ATAC-STARR-seq lymphoblastoid active region 9423 [Gene]
  • LOC130057084:ATAC-STARR-seq lymphoblastoid active region 9425 [Gene]
  • LOC130057086:ATAC-STARR-seq lymphoblastoid active region 9426 [Gene]
  • LOC130057087:ATAC-STARR-seq lymphoblastoid active region 9427 [Gene]
  • LOC130057088:ATAC-STARR-seq lymphoblastoid active region 9428 [Gene]
  • LOC130057089:ATAC-STARR-seq lymphoblastoid active region 9429 [Gene]
  • LOC130057015:ATAC-STARR-seq lymphoblastoid silent region 6412 [Gene]
  • LOC130057016:ATAC-STARR-seq lymphoblastoid silent region 6413 [Gene]
  • LOC130057017:ATAC-STARR-seq lymphoblastoid silent region 6416 [Gene]
  • LOC130057019:ATAC-STARR-seq lymphoblastoid silent region 6417 [Gene]
  • LOC130057020:ATAC-STARR-seq lymphoblastoid silent region 6418 [Gene]
  • LOC130057021:ATAC-STARR-seq lymphoblastoid silent region 6419 [Gene]
  • LOC130057022:ATAC-STARR-seq lymphoblastoid silent region 6420 [Gene]
  • LOC130057031:ATAC-STARR-seq lymphoblastoid silent region 6422 [Gene]
  • LOC130057036:ATAC-STARR-seq lymphoblastoid silent region 6423 [Gene]
  • LOC130057037:ATAC-STARR-seq lymphoblastoid silent region 6424 [Gene]
  • LOC130057039:ATAC-STARR-seq lymphoblastoid silent region 6425 [Gene]
  • LOC130057040:ATAC-STARR-seq lymphoblastoid silent region 6426 [Gene]
  • LOC130057045:ATAC-STARR-seq lymphoblastoid silent region 6429 [Gene]
  • LOC130057047:ATAC-STARR-seq lymphoblastoid silent region 6430 [Gene]
  • LOC130057053:ATAC-STARR-seq lymphoblastoid silent region 6432 [Gene]
  • LOC130057054:ATAC-STARR-seq lymphoblastoid silent region 6433 [Gene]
  • LOC130057057:ATAC-STARR-seq lymphoblastoid silent region 6434 [Gene]
  • LOC130057058:ATAC-STARR-seq lymphoblastoid silent region 6435 [Gene]
  • LOC130057059:ATAC-STARR-seq lymphoblastoid silent region 6436 [Gene]
  • LOC130057060:ATAC-STARR-seq lymphoblastoid silent region 6437 [Gene]
  • LOC130057062:ATAC-STARR-seq lymphoblastoid silent region 6438 [Gene]
  • LOC130057063:ATAC-STARR-seq lymphoblastoid silent region 6439 [Gene]
  • LOC130057064:ATAC-STARR-seq lymphoblastoid silent region 6440 [Gene]
  • LOC130057065:ATAC-STARR-seq lymphoblastoid silent region 6441 [Gene]
  • LOC130057072:ATAC-STARR-seq lymphoblastoid silent region 6442 [Gene]
  • LOC130057073:ATAC-STARR-seq lymphoblastoid silent region 6443 [Gene]
  • LOC130057081:ATAC-STARR-seq lymphoblastoid silent region 6444 [Gene]
  • LOC130057083:ATAC-STARR-seq lymphoblastoid silent region 6445 [Gene]
  • LOC130057085:ATAC-STARR-seq lymphoblastoid silent region 6446 [Gene]
  • LOC108251795:ATP8B4 intron CAGE-defined high expression enhancer [Gene]
  • ATP8B4:ATPase phospholipid transporting 8B4 (putative) [Gene - OMIM - HGNC]
  • BCL2L10:BCL2 like 10 [Gene - OMIM - HGNC]
  • LOC126862120:BRD4-independent group 4 enhancer GRCh37_chr15:48056535-48057734 [Gene]
  • LOC126862122:BRD4-independent group 4 enhancer GRCh37_chr15:48324991-48326190 [Gene]
  • LOC126862130:BRD4-independent group 4 enhancer GRCh37_chr15:50884350-50885549 [Gene]
  • LOC126862121:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48143210-48144409 [Gene]
  • LOC126862123:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48543423-48544622 [Gene]
  • LOC126862124:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48764566-48765765 [Gene]
  • LOC126862125:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48821930-48823129 [Gene]
  • LOC126862127:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:49237854-49239053 [Gene]
  • COPS2:COP9 signalosome subunit 2 [Gene - OMIM - HGNC]
  • LOC116268465:CRISPRi-validated cis-regulatory element chr15.1149 [Gene]
  • LOC116268466:CRISPRi-validated cis-regulatory element chr15.1151 [Gene]
  • CTXN2-AS1:CTXN2 antisense RNA 1 [Gene - HGNC]
  • LOC110386947:CYP19A1 promoter I.1 [Gene]
  • LOC110386948:CYP19A1 promoter I.4 [Gene]
  • LOC110386949:CYP19A1 promoter I.7 [Gene]
  • LOC110386951:CYP19A1 promoter II/1.3 [Gene]
  • DTWD1:DTW domain containing 1 [Gene - HGNC]
  • DUT-AS1:DUT antisense RNA 1 [Gene - HGNC]
  • DMXL2:Dmx like 2 [Gene - OMIM - HGNC]
  • EID1:EP300 interacting inhibitor of differentiation 1 [Gene - OMIM - HGNC]
  • FBN1-DT:FBN1 divergent transcript [Gene - HGNC]
  • GNB5:G protein subunit beta 5 [Gene - OMIM - HGNC]
  • GABPB1:GA binding protein transcription factor subunit beta 1 [Gene - OMIM - HGNC]
  • GABPB1-AS1:GABPB1 antisense RNA 1 [Gene - HGNC]
  • GABPB1-IT1:GABPB1 intronic transcript [Gene - HGNC]
  • LOC111464992:HNF4 motif-containing MPRA enhancer 243 [Gene]
  • LEO1:LEO1 homolog, Paf1/RNA polymerase II complex component [Gene - OMIM - HGNC]
  • LOC108178996:LINC01491 intron CAGE-defined high expression enhancer [Gene]
  • LYSMD2:LysM domain containing 2 [Gene - HGNC]
  • MAPK6-DT:MAPK6 divergent transcript [Gene - HGNC]
  • LOC108281154:MAPK6-RPS13P8 intergenic CAGE-defined mid-level expression enhancer [Gene]
  • LOC126862126:MED14-independent group 3 enhancer GRCh37_chr15:49204976-49206175 [Gene]
  • LOC126862128:MED14-independent group 3 enhancer GRCh37_chr15:49557847-49559046 [Gene]
  • LOC126862129:MED14-independent group 3 enhancer GRCh37_chr15:49917323-49918522 [Gene]
  • LOC126862131:MED14-independent group 3 enhancer GRCh37_chr15:51741640-51742839 [Gene]
  • MIR4713HG:MIR4713 host gene [Gene - HGNC]
  • LOC129390696:MPRA-validated peak2328 silencer [Gene]
  • LOC129390697:MPRA-validated peak2329 silencer [Gene]
  • LOC129390698:MPRA-validated peak2330 silencer [Gene]
  • LOC129390699:MPRA-validated peak2331 silencer [Gene]
  • LOC129390700:MPRA-validated peak2332 silencer [Gene]
  • LOC129390701:MPRA-validated peak2334 silencer [Gene]
  • LOC129390702:MPRA-validated peak2335 silencer [Gene]
  • LOC129390703:MPRA-validated peak2338 silencer [Gene]
  • LOC129390704:MPRA-validated peak2339 silencer [Gene]
  • LOC132090303:Neanderthal introgressed variant-containing enhancer experimental_39634 [Gene]
  • LOC132090304:Neanderthal introgressed variant-containing enhancer experimental_39679 [Gene]
  • LOC132090305:Neanderthal introgressed variant-containing enhancer experimental_39709 [Gene]
  • LOC132090306:Neanderthal introgressed variant-containing enhancer experimental_39732 [Gene]
  • LOC132090307:Neanderthal introgressed variant-containing enhancer experimental_39766 [Gene]
  • SECISBP2L:SECIS binding protein 2 like [Gene - OMIM - HGNC]
  • SHC4:SHC adaptor protein 4 [Gene - OMIM - HGNC]
  • LOC121847947:Sharpr-MPRA regulatory region 10237 [Gene]
  • LOC121847949:Sharpr-MPRA regulatory region 1269 [Gene]
  • LOC121530581:Sharpr-MPRA regulatory region 12802 [Gene]
  • LOC121530582:Sharpr-MPRA regulatory region 14256 [Gene]
  • LOC125078075:Sharpr-MPRA regulatory region 212 [Gene]
  • LOC125078080:Sharpr-MPRA regulatory region 2333 [Gene]
  • LOC112272594:Sharpr-MPRA regulatory region 3311 [Gene]
  • LOC125078079:Sharpr-MPRA regulatory region 3374 [Gene]
  • LOC125078076:Sharpr-MPRA regulatory region 3576 [Gene]
  • LOC121530580:Sharpr-MPRA regulatory region 3998 [Gene]
  • LOC125078077:Sharpr-MPRA regulatory region 4235 [Gene]
  • LOC121847948:Sharpr-MPRA regulatory region 5673 [Gene]
  • LOC125078081:Sharpr-MPRA regulatory region 7002 [Gene]
  • LOC125078078:Sharpr-MPRA regulatory region 7155 [Gene]
  • LOC112272592:Sharpr-MPRA regulatory region 771 [Gene]
  • LOC112272593:Sharpr-MPRA regulatory region 8572 [Gene]
  • LOC113939944:Sharpr-MPRA regulatory region 9539 [Gene]
  • LOC111822948:Sharpr-MPRA regulatory regions 2939 and 12041 [Gene]
  • TNFAIP8L3:TNF alpha induced protein 8 like 3 [Gene - OMIM - HGNC]
  • AP4E1:adaptor related protein complex 4 subunit epsilon 1 [Gene - OMIM - HGNC]
  • CEP152:centrosomal protein 152 [Gene - OMIM - HGNC]
  • CERNA1:competing endogenous lncRNA 1 for miR-4707-5p and miR-4767 [Gene - HGNC]
  • CTXN2:cortexin 2 [Gene - HGNC]
  • CYP19A1:cytochrome P450 family 19 subfamily A member 1 [Gene - OMIM - HGNC]
  • DUT:deoxyuridine triphosphatase [Gene - OMIM - HGNC]
  • FAM227B:family with sequence similarity 227 member B [Gene - HGNC]
  • FBN1:fibrillin 1 [Gene - OMIM - HGNC]
  • FGF7:fibroblast growth factor 7 [Gene - OMIM - HGNC]
  • GALK2:galactokinase 2 [Gene - OMIM - HGNC]
  • GLDN:gliomedin [Gene - OMIM - HGNC]
  • HDC:histidine decarboxylase [Gene - OMIM - HGNC]
  • LINC01491:long intergenic non-protein coding RNA 1491 [Gene - HGNC]
  • MIR1266:microRNA 1266 [Gene - HGNC]
  • MIR4712:microRNA 4712 [Gene - HGNC]
  • MIR4713:microRNA 4713 [Gene - HGNC]
  • MIR4716:microRNA 4716 [Gene - HGNC]
  • MIR7973-1:microRNA 7973-1 [Gene - HGNC]
  • MIR7973-2:microRNA 7973-2 [Gene - HGNC]
  • MAPK6:mitogen-activated protein kinase 6 [Gene - OMIM - HGNC]
  • MYEF2:myelin expression factor 2 [Gene - OMIM - HGNC]
  • MYO5A:myosin VA [Gene - OMIM - HGNC]
  • MYO5C:myosin VC [Gene - OMIM - HGNC]
  • LOC120807607:negCOR silencer S8 [Gene]
  • PIRC66:piwi-interacting RNA cluster 66 [Gene - HGNC]
  • SCG3:secretogranin III [Gene - OMIM - HGNC]
  • SEMA6D:semaphorin 6D [Gene - OMIM - HGNC]
  • SPPL2A:signal peptide peptidase like 2A [Gene - OMIM - HGNC]
  • SLC12A1:solute carrier family 12 member 1 [Gene - OMIM - HGNC]
  • SLC24A5:solute carrier family 24 member 5 [Gene - OMIM - HGNC]
  • SLC27A2:solute carrier family 27 member 2 [Gene - OMIM - HGNC]
  • TRPM7:transient receptor potential cation channel subfamily M member 7 [Gene - OMIM - HGNC]
  • TMOD2:tropomodulin 2 [Gene - OMIM - HGNC]
  • TMOD3:tropomodulin 3 [Gene - OMIM - HGNC]
  • USP50:ubiquitin specific peptidase 50 [Gene - OMIM - HGNC]
  • USP8:ubiquitin specific peptidase 8 [Gene - OMIM - HGNC]
  • LOC102724587:uncharacterized LOC102724587 [Gene]
  • LOC128092252:uncharacterized LOC128092252 [Gene]
Variant type:
copy number loss
Cytogenetic location:
15q21.1-21.2
Genomic location:
Preferred name:
GRCh38/hg38 15q21.1-21.2(chr15:47460844-52494222)x1
HGVS:
  • NC_000015.10:g.(?_47460844)_(52494222_?)del
  • NC_000015.8:g.(?_45540333)_(50573711_?)del
  • NC_000015.9:g.(?_47753041)_(52786419_?)del
Links:
dbVar: nssv706378; dbVar: nsv530480
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
SCV000175521ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Feb 18, 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

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 1, SCV000175521.4

#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