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GRCh38/hg38 5p15.33(chr5:49978-4014647)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:
RCV000051100.6

Allele description [Variation Report for GRCh38/hg38 5p15.33(chr5:49978-4014647)x1]

GRCh38/hg38 5p15.33(chr5:49978-4014647)x1

Genes:
  • LOC108251796:AHRR intron CAGE-defined high expression enhancer [Gene]
  • LOC129993528:ATAC-STARR-seq lymphoblastoid active region 22268 [Gene]
  • LOC129993529:ATAC-STARR-seq lymphoblastoid active region 22269 [Gene]
  • LOC129993530:ATAC-STARR-seq lymphoblastoid active region 22270 [Gene]
  • LOC129993531:ATAC-STARR-seq lymphoblastoid active region 22271 [Gene]
  • LOC129993533:ATAC-STARR-seq lymphoblastoid active region 22272 [Gene]
  • LOC129993536:ATAC-STARR-seq lymphoblastoid active region 22273 [Gene]
  • LOC129993539:ATAC-STARR-seq lymphoblastoid active region 22274 [Gene]
  • LOC129993540:ATAC-STARR-seq lymphoblastoid active region 22275 [Gene]
  • LOC129993541:ATAC-STARR-seq lymphoblastoid active region 22276 [Gene]
  • LOC129993542:ATAC-STARR-seq lymphoblastoid active region 22277 [Gene]
  • LOC129993543:ATAC-STARR-seq lymphoblastoid active region 22278 [Gene]
  • LOC129993544:ATAC-STARR-seq lymphoblastoid active region 22279 [Gene]
  • LOC129993545:ATAC-STARR-seq lymphoblastoid active region 22280 [Gene]
  • LOC129993549:ATAC-STARR-seq lymphoblastoid active region 22281 [Gene]
  • LOC129993550:ATAC-STARR-seq lymphoblastoid active region 22283 [Gene]
  • LOC129993552:ATAC-STARR-seq lymphoblastoid active region 22284 [Gene]
  • LOC129993553:ATAC-STARR-seq lymphoblastoid active region 22285 [Gene]
  • LOC129993554:ATAC-STARR-seq lymphoblastoid active region 22286 [Gene]
  • LOC129993555:ATAC-STARR-seq lymphoblastoid active region 22287 [Gene]
  • LOC129993556:ATAC-STARR-seq lymphoblastoid active region 22288 [Gene]
  • LOC129993557:ATAC-STARR-seq lymphoblastoid active region 22289 [Gene]
  • LOC129993558:ATAC-STARR-seq lymphoblastoid active region 22290 [Gene]
  • LOC129993559:ATAC-STARR-seq lymphoblastoid active region 22291 [Gene]
  • LOC129993561:ATAC-STARR-seq lymphoblastoid active region 22292 [Gene]
  • LOC129993562:ATAC-STARR-seq lymphoblastoid active region 22293 [Gene]
  • LOC129993563:ATAC-STARR-seq lymphoblastoid active region 22294 [Gene]
  • LOC129993565:ATAC-STARR-seq lymphoblastoid active region 22299 [Gene]
  • LOC129993566:ATAC-STARR-seq lymphoblastoid active region 22300 [Gene]
  • LOC129993567:ATAC-STARR-seq lymphoblastoid active region 22301 [Gene]
  • LOC129993568:ATAC-STARR-seq lymphoblastoid active region 22302 [Gene]
  • LOC129993570:ATAC-STARR-seq lymphoblastoid active region 22303 [Gene]
  • LOC129993571:ATAC-STARR-seq lymphoblastoid active region 22304 [Gene]
  • LOC129993572:ATAC-STARR-seq lymphoblastoid active region 22305 [Gene]
  • LOC129993573:ATAC-STARR-seq lymphoblastoid active region 22306 [Gene]
  • LOC129993574:ATAC-STARR-seq lymphoblastoid active region 22307 [Gene]
  • LOC129993580:ATAC-STARR-seq lymphoblastoid active region 22308 [Gene]
  • LOC129993581:ATAC-STARR-seq lymphoblastoid active region 22309 [Gene]
  • LOC129993582:ATAC-STARR-seq lymphoblastoid active region 22310 [Gene]
  • LOC129993583:ATAC-STARR-seq lymphoblastoid active region 22311 [Gene]
  • LOC129993584:ATAC-STARR-seq lymphoblastoid active region 22312 [Gene]
  • LOC129993586:ATAC-STARR-seq lymphoblastoid active region 22313 [Gene]
  • LOC129993587:ATAC-STARR-seq lymphoblastoid active region 22314 [Gene]
  • LOC129993532:ATAC-STARR-seq lymphoblastoid silent region 15861 [Gene]
  • LOC129993534:ATAC-STARR-seq lymphoblastoid silent region 15862 [Gene]
  • LOC129993535:ATAC-STARR-seq lymphoblastoid silent region 15863 [Gene]
  • LOC129993537:ATAC-STARR-seq lymphoblastoid silent region 15866 [Gene]
  • LOC129993538:ATAC-STARR-seq lymphoblastoid silent region 15867 [Gene]
  • LOC129993546:ATAC-STARR-seq lymphoblastoid silent region 15868 [Gene]
  • LOC129993547:ATAC-STARR-seq lymphoblastoid silent region 15869 [Gene]
  • LOC129993548:ATAC-STARR-seq lymphoblastoid silent region 15870 [Gene]
  • LOC129993551:ATAC-STARR-seq lymphoblastoid silent region 15871 [Gene]
  • LOC129993560:ATAC-STARR-seq lymphoblastoid silent region 15872 [Gene]
  • LOC129993564:ATAC-STARR-seq lymphoblastoid silent region 15876 [Gene]
  • LOC129993569:ATAC-STARR-seq lymphoblastoid silent region 15879 [Gene]
  • LOC129993575:ATAC-STARR-seq lymphoblastoid silent region 15882 [Gene]
  • LOC129993576:ATAC-STARR-seq lymphoblastoid silent region 15883 [Gene]
  • LOC129993577:ATAC-STARR-seq lymphoblastoid silent region 15884 [Gene]
  • LOC129993578:ATAC-STARR-seq lymphoblastoid silent region 15886 [Gene]
  • LOC129993579:ATAC-STARR-seq lymphoblastoid silent region 15887 [Gene]
  • LOC129993585:ATAC-STARR-seq lymphoblastoid silent region 15888 [Gene]
  • LOC129993588:ATAC-STARR-seq lymphoblastoid silent region 15890 [Gene]
  • LOC126807285:BRD4-independent group 4 enhancer GRCh37_chr5:1455983-1457182 [Gene]
  • LOC126807286:BRD4-independent group 4 enhancer GRCh37_chr5:1494052-1495251 [Gene]
  • LOC126807287:BRD4-independent group 4 enhancer GRCh37_chr5:1950332-1951531 [Gene]
  • LOC126807288:BRD4-independent group 4 enhancer GRCh37_chr5:2136525-2137724 [Gene]
  • LOC126807289:BRD4-independent group 4 enhancer GRCh37_chr5:2393157-2394356 [Gene]
  • LOC126807292:BRD4-independent group 4 enhancer GRCh37_chr5:2697069-2698268 [Gene]
  • LOC126807293:BRD4-independent group 4 enhancer GRCh37_chr5:2850224-2851423 [Gene]
  • LOC126807294:BRD4-independent group 4 enhancer GRCh37_chr5:3176917-3178116 [Gene]
  • LOC126807281:BRD4-independent group 4 enhancer GRCh37_chr5:399561-400760 [Gene]
  • LOC126807282:BRD4-independent group 4 enhancer GRCh37_chr5:458642-459841 [Gene]
  • LOC126807284:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:1404958-1406157 [Gene]
  • LOC126807283:CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:618691-619890 [Gene]
  • CEP72-DT:CEP72 divergent transcript [Gene - HGNC]
  • CLPTM1L:CLPTM1 like [Gene - OMIM - HGNC]
  • LOC116158511:CRISPRi-validated cis-regulatory element chr5.422 [Gene]
  • EXOC3-AS1:EXOC3 antisense RNA 1 [Gene - HGNC]
  • IRX2-DT:IRX2 divergent transcript [Gene - OMIM - HGNC]
  • IRX4-AS1:IRX4 antisense RNA 1 [Gene - HGNC]
  • LOC126807280:MED14-independent group 3 enhancer GRCh37_chr5:169157-170356 [Gene]
  • LOC126807290:MED14-independent group 3 enhancer GRCh37_chr5:2655710-2656909 [Gene]
  • LOC126807291:MED14-independent group 3 enhancer GRCh37_chr5:2658151-2659350 [Gene]
  • LOC126807295:MED14-independent group 3 enhancer GRCh37_chr5:3310881-3312080 [Gene]
  • MNS16A:MNS16A minisatellite promoter [Gene]
  • NDUFS6:NADH:ubiquinone oxidoreductase subunit S6 [Gene - OMIM - HGNC]
  • NKD2:NKD inhibitor of WNT signaling pathway 2 [Gene - OMIM - HGNC]
  • LOC132090724:Neanderthal introgressed variant-containing enhancer experimental_80773 [Gene]
  • LOC132090725:Neanderthal introgressed variant-containing enhancer experimental_83860 [Gene]
  • LOC132089231:Neanderthal introgressed variant-containing enhancer experimental_83872 [Gene]
  • LOC132090726:Neanderthal introgressed variant-containing enhancer experimental_83887 [Gene]
  • LOC132089232:Neanderthal introgressed variant-containing enhancer experimental_83908 [Gene]
  • LOC132089233:Neanderthal introgressed variant-containing enhancer experimental_83940 [Gene]
  • LOC132089234:Neanderthal introgressed variant-containing enhancer experimental_83970 [Gene]
  • LOC132089235:Neanderthal introgressed variant-containing enhancer experimental_83975 [Gene]
  • LOC132089236:Neanderthal introgressed variant-containing enhancer experimental_84195 [Gene]
  • LOC132089237:Neanderthal introgressed variant-containing enhancer experimental_84199 [Gene]
  • LOC132089249:Neanderthal introgressed variant-containing enhancer experimental_85003 [Gene]
  • LOC132090719:Neanderthal introgressed variant-containing enhancer experimental_85008 [Gene]
  • LOC132089250:Neanderthal introgressed variant-containing enhancer experimental_85009 [Gene]
  • LOC132089251:Neanderthal introgressed variant-containing enhancer experimental_85011 [Gene]
  • LOC132089252:Neanderthal introgressed variant-containing enhancer experimental_85012 [Gene]
  • LOC132090720:Neanderthal introgressed variant-containing enhancer experimental_85017 [Gene]
  • LOC132089253:Neanderthal introgressed variant-containing enhancer experimental_85030 [Gene]
  • LOC132089272:Neanderthal introgressed variant-containing enhancer experimental_85954 [Gene]
  • LOC132089273:Neanderthal introgressed variant-containing enhancer experimental_85959 [Gene]
  • LOC132089275:Neanderthal introgressed variant-containing enhancer experimental_86175 [Gene]
  • LOC132089289:Neanderthal introgressed variant-containing enhancer experimental_86692/86693 [Gene]
  • LOC132090721:Neanderthal introgressed variant-containing enhancer experimental_86701 [Gene]
  • LOC132089290:Neanderthal introgressed variant-containing enhancer experimental_86736 [Gene]
  • LOC132089291:Neanderthal introgressed variant-containing enhancer experimental_86741 [Gene]
  • LOC132089292:Neanderthal introgressed variant-containing enhancer experimental_86745 [Gene]
  • LOC132090722:Neanderthal introgressed variant-containing enhancer experimental_86749/86750 [Gene]
  • LOC132089293:Neanderthal introgressed variant-containing enhancer experimental_86753 [Gene]
  • LOC132089294:Neanderthal introgressed variant-containing enhancer experimental_86779 [Gene]
  • LOC132089295:Neanderthal introgressed variant-containing enhancer experimental_86783 [Gene]
  • LOC132089296:Neanderthal introgressed variant-containing enhancer experimental_86799 [Gene]
  • LOC132089297:Neanderthal introgressed variant-containing enhancer experimental_86803 [Gene]
  • LOC132089298:Neanderthal introgressed variant-containing enhancer experimental_86807 [Gene]
  • LOC132089299:Neanderthal introgressed variant-containing enhancer experimental_86811 [Gene]
  • LOC132089300:Neanderthal introgressed variant-containing enhancer experimental_86819 [Gene]
  • LOC132089301:Neanderthal introgressed variant-containing enhancer experimental_86831 [Gene]
  • LOC132089302:Neanderthal introgressed variant-containing enhancer experimental_86835 [Gene]
  • LOC132090723:Neanderthal introgressed variant-containing enhancer experimental_86841/86842 [Gene]
  • LOC132089303:Neanderthal introgressed variant-containing enhancer experimental_86882 [Gene]
  • LOC132205959:Neanderthal introgressed variant-containing enhancers experimental_86823 and experimental_86827 [Gene]
  • PDCD6-DT:PDCD6 divergent transcript [Gene - HGNC]
  • PDCD6-AHRR:PDCD6-AHRR readthrough (NMD candidate) [Gene - HGNC]
  • SLC9A3-OT1:SLC9A3 3' UTR overlapping transcript 1 [Gene - HGNC]
  • SLC9A3-AS1:SLC9A3 antisense RNA 1 [Gene - HGNC]
  • LOC121725197:Sharpr-MPRA regulatory region 11960 [Gene]
  • LOC123493259:Sharpr-MPRA regulatory region 13256 [Gene]
  • LOC123493257:Sharpr-MPRA regulatory region 15179 [Gene]
  • LOC123493258:Sharpr-MPRA regulatory region 1606 [Gene]
  • LOC112997586:Sharpr-MPRA regulatory region 1936 [Gene]
  • LOC123493256:Sharpr-MPRA regulatory region 259 [Gene]
  • LOC123493262:Sharpr-MPRA regulatory region 3294 [Gene]
  • LOC112997549:Sharpr-MPRA regulatory region 3968 [Gene]
  • LOC121056758:Sharpr-MPRA regulatory region 4144 [Gene]
  • LOC123493261:Sharpr-MPRA regulatory region 501 [Gene]
  • LOC112997548:Sharpr-MPRA regulatory region 8068 [Gene]
  • LOC123493260:Sharpr-MPRA regulatory region 9592 [Gene]
  • LOC110806263:TERT 5' regulatory region [Gene]
  • LOC110806264:TERT enhancer in intron 2 [Gene]
  • TERLR1:TERT regulating lncRNA 1 [Gene - HGNC]
  • LOC110121060:VISTA enhancer hs1327 [Gene]
  • LOC114827841:VISTA enhancer hs2567 [Gene]
  • LOC110120635:VISTA enhancer hs261 [Gene]
  • LOC110120695:VISTA enhancer hs533 [Gene]
  • LOC110120713:VISTA enhancer hs603 [Gene]
  • LOC110120722:VISTA enhancer hs633 [Gene]
  • LOC110120760:VISTA enhancer hs754 [Gene]
  • AHRR:aryl hydrocarbon receptor repressor [Gene - OMIM - HGNC]
  • BRD9:bromodomain containing 9 [Gene - OMIM - HGNC]
  • CEP72:centrosomal protein 72 [Gene - OMIM - HGNC]
  • CCDC127:coiled-coil domain containing 127 [Gene - HGNC]
  • LOC124901163:eukaryotic translation initiation factor 3 subunit A [Gene]
  • EXOC3:exocyst complex component 3 [Gene - OMIM - HGNC]
  • IRX1:iroquois homeobox 1 [Gene - OMIM - HGNC]
  • IRX2:iroquois homeobox 2 [Gene - OMIM - HGNC]
  • IRX4:iroquois homeobox 4 [Gene - OMIM - HGNC]
  • LRRC14B:leucine rich repeat containing 14B [Gene - HGNC]
  • LINC01017:long intergenic non-protein coding RNA 1017 [Gene - HGNC]
  • LINC01019:long intergenic non-protein coding RNA 1019 [Gene - HGNC]
  • LINC01377:long intergenic non-protein coding RNA 1377 [Gene - HGNC]
  • LINC01511:long intergenic non-protein coding RNA 1511 [Gene - HGNC]
  • LINC02116:long intergenic non-protein coding RNA 2116 [Gene - HGNC]
  • LINC02162:long intergenic non-protein coding RNA 2162 [Gene - HGNC]
  • LINC02982:long intergenic non-protein coding RNA 2982 [Gene - HGNC]
  • LSINCT5:long stress-induced non-coding transcript 5 [Gene - OMIM - HGNC]
  • LPCAT1:lysophosphatidylcholine acyltransferase 1 [Gene - OMIM - HGNC]
  • LOC107758904:meiotic recombination hotspot 5A [Gene]
  • LOC128772262:melanoma risk locus-associated MPRA allelic enhancer 5:1320136 [Gene]
  • LOC128772263:melanoma risk locus-associated MPRA allelic enhancer 5:1330840 [Gene]
  • LOC128772264:melanoma risk locus-associated MPRA allelic enhancer 5:1341101 [Gene]
  • MIR4277:microRNA 4277 [Gene - HGNC]
  • MIR4456:microRNA 4456 [Gene - HGNC]
  • MIR4457:microRNA 4457 [Gene - HGNC]
  • MIR4635:microRNA 4635 [Gene - HGNC]
  • MIR6075:microRNA 6075 [Gene - HGNC]
  • MRPL36:mitochondrial ribosomal protein L36 [Gene - OMIM - HGNC]
  • PLEKHG4B:pleckstrin homology and RhoGEF domain containing G4B [Gene - OMIM - HGNC]
  • PDCD6:programmed cell death 6 [Gene - OMIM - HGNC]
  • SLC12A7:solute carrier family 12 member 7 [Gene - OMIM - HGNC]
  • SLC6A18:solute carrier family 6 member 18 [Gene - OMIM - HGNC]
  • SLC6A19:solute carrier family 6 member 19 [Gene - OMIM - HGNC]
  • SLC6A3:solute carrier family 6 member 3 [Gene - OMIM - HGNC]
  • SLC9A3:solute carrier family 9 member A3 [Gene - OMIM - HGNC]
  • SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]
  • TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
  • TRIP13:thyroid hormone receptor interactor 13 [Gene - OMIM - HGNC]
  • TPPP:tubulin polymerization promoting protein [Gene - OMIM - HGNC]
  • LOC100506858:uncharacterized LOC100506858 [Gene]
  • CTD-2194D22.4:uncharacterized LOC101929081 [Gene]
  • LOC105374618:uncharacterized LOC105374618 [Gene]
  • LOC105374620:uncharacterized LOC105374620 [Gene]
  • ZDHHC11:zinc finger DHHC-type containing 11 [Gene - HGNC]
  • ZDHHC11B:zinc finger DHHC-type containing 11B [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
5p15.33
Genomic location:
Preferred name:
GRCh38/hg38 5p15.33(chr5:49978-4014647)x1
HGVS:
  • NC_000005.10:g.(?_49978)_(4014647_?)del
  • NC_000005.8:g.(?_103093)_(4067761_?)del
  • NC_000005.9:g.(?_50093)_(4014761_?)del
Links:
dbVar: nssv578042; dbVar: nsv529648
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
SCV000078440ISCA 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, SCV000078440.5

#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