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GRCh38/hg38 6p25.1-24.3(chr6:4427090-8391140)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:
RCV000052177.6

Allele description [Variation Report for GRCh38/hg38 6p25.1-24.3(chr6:4427090-8391140)x1]

GRCh38/hg38 6p25.1-24.3(chr6:4427090-8391140)x1

Genes:
  • LOC129995659:ATAC-STARR-seq lymphoblastoid active region 23897 [Gene]
  • LOC129995660:ATAC-STARR-seq lymphoblastoid active region 23898 [Gene]
  • LOC129995664:ATAC-STARR-seq lymphoblastoid active region 23899 [Gene]
  • LOC129995665:ATAC-STARR-seq lymphoblastoid active region 23900 [Gene]
  • LOC129995670:ATAC-STARR-seq lymphoblastoid active region 23901 [Gene]
  • LOC129995671:ATAC-STARR-seq lymphoblastoid active region 23902 [Gene]
  • LOC129995675:ATAC-STARR-seq lymphoblastoid active region 23903 [Gene]
  • LOC129995677:ATAC-STARR-seq lymphoblastoid active region 23904 [Gene]
  • LOC129995678:ATAC-STARR-seq lymphoblastoid active region 23906 [Gene]
  • LOC129995679:ATAC-STARR-seq lymphoblastoid active region 23907 [Gene]
  • LOC129995680:ATAC-STARR-seq lymphoblastoid active region 23908 [Gene]
  • LOC129995681:ATAC-STARR-seq lymphoblastoid active region 23910 [Gene]
  • LOC129995682:ATAC-STARR-seq lymphoblastoid active region 23911 [Gene]
  • LOC129995683:ATAC-STARR-seq lymphoblastoid active region 23912 [Gene]
  • LOC129995684:ATAC-STARR-seq lymphoblastoid active region 23913 [Gene]
  • LOC129995685:ATAC-STARR-seq lymphoblastoid active region 23914 [Gene]
  • LOC129995688:ATAC-STARR-seq lymphoblastoid active region 23915 [Gene]
  • LOC129995689:ATAC-STARR-seq lymphoblastoid active region 23916 [Gene]
  • LOC129995690:ATAC-STARR-seq lymphoblastoid active region 23917 [Gene]
  • LOC129995691:ATAC-STARR-seq lymphoblastoid active region 23918 [Gene]
  • LOC129995692:ATAC-STARR-seq lymphoblastoid active region 23919 [Gene]
  • LOC129995693:ATAC-STARR-seq lymphoblastoid active region 23920 [Gene]
  • LOC129995694:ATAC-STARR-seq lymphoblastoid active region 23921 [Gene]
  • LOC129995695:ATAC-STARR-seq lymphoblastoid active region 23922 [Gene]
  • LOC129995696:ATAC-STARR-seq lymphoblastoid active region 23923 [Gene]
  • LOC129995697:ATAC-STARR-seq lymphoblastoid active region 23924 [Gene]
  • LOC129995698:ATAC-STARR-seq lymphoblastoid active region 23925 [Gene]
  • LOC129995699:ATAC-STARR-seq lymphoblastoid active region 23927 [Gene]
  • LOC129995700:ATAC-STARR-seq lymphoblastoid active region 23932 [Gene]
  • LOC129995702:ATAC-STARR-seq lymphoblastoid active region 23933 [Gene]
  • LOC129995703:ATAC-STARR-seq lymphoblastoid active region 23934 [Gene]
  • LOC129995705:ATAC-STARR-seq lymphoblastoid active region 23935 [Gene]
  • LOC129995710:ATAC-STARR-seq lymphoblastoid active region 23936 [Gene]
  • LOC129995712:ATAC-STARR-seq lymphoblastoid active region 23937 [Gene]
  • LOC129995713:ATAC-STARR-seq lymphoblastoid active region 23938 [Gene]
  • LOC129995714:ATAC-STARR-seq lymphoblastoid active region 23939 [Gene]
  • LOC129995715:ATAC-STARR-seq lymphoblastoid active region 23940 [Gene]
  • LOC129995716:ATAC-STARR-seq lymphoblastoid active region 23941 [Gene]
  • LOC129995717:ATAC-STARR-seq lymphoblastoid active region 23942 [Gene]
  • LOC129995719:ATAC-STARR-seq lymphoblastoid active region 23947 [Gene]
  • LOC129995720:ATAC-STARR-seq lymphoblastoid active region 23948 [Gene]
  • LOC129995721:ATAC-STARR-seq lymphoblastoid active region 23951 [Gene]
  • LOC129995725:ATAC-STARR-seq lymphoblastoid active region 23952 [Gene]
  • LOC129995726:ATAC-STARR-seq lymphoblastoid active region 23953 [Gene]
  • LOC129995727:ATAC-STARR-seq lymphoblastoid active region 23954 [Gene]
  • LOC129995729:ATAC-STARR-seq lymphoblastoid active region 23956 [Gene]
  • LOC129995730:ATAC-STARR-seq lymphoblastoid active region 23957 [Gene]
  • LOC129995733:ATAC-STARR-seq lymphoblastoid active region 23958 [Gene]
  • LOC129995658:ATAC-STARR-seq lymphoblastoid silent region 16862 [Gene]
  • LOC129995661:ATAC-STARR-seq lymphoblastoid silent region 16863 [Gene]
  • LOC129995662:ATAC-STARR-seq lymphoblastoid silent region 16864 [Gene]
  • LOC129995663:ATAC-STARR-seq lymphoblastoid silent region 16865 [Gene]
  • LOC129995666:ATAC-STARR-seq lymphoblastoid silent region 16866 [Gene]
  • LOC129995667:ATAC-STARR-seq lymphoblastoid silent region 16867 [Gene]
  • LOC129995668:ATAC-STARR-seq lymphoblastoid silent region 16868 [Gene]
  • LOC129995669:ATAC-STARR-seq lymphoblastoid silent region 16869 [Gene]
  • LOC129995672:ATAC-STARR-seq lymphoblastoid silent region 16873 [Gene]
  • LOC129995673:ATAC-STARR-seq lymphoblastoid silent region 16874 [Gene]
  • LOC129995674:ATAC-STARR-seq lymphoblastoid silent region 16875 [Gene]
  • LOC129995676:ATAC-STARR-seq lymphoblastoid silent region 16876 [Gene]
  • LOC129995686:ATAC-STARR-seq lymphoblastoid silent region 16877 [Gene]
  • LOC129995687:ATAC-STARR-seq lymphoblastoid silent region 16878 [Gene]
  • LOC129995701:ATAC-STARR-seq lymphoblastoid silent region 16880 [Gene]
  • LOC129995704:ATAC-STARR-seq lymphoblastoid silent region 16881 [Gene]
  • LOC129995706:ATAC-STARR-seq lymphoblastoid silent region 16882 [Gene]
  • LOC129995707:ATAC-STARR-seq lymphoblastoid silent region 16883 [Gene]
  • LOC129995708:ATAC-STARR-seq lymphoblastoid silent region 16884 [Gene]
  • LOC129995709:ATAC-STARR-seq lymphoblastoid silent region 16885 [Gene]
  • LOC129995711:ATAC-STARR-seq lymphoblastoid silent region 16886 [Gene]
  • LOC129995718:ATAC-STARR-seq lymphoblastoid silent region 16890 [Gene]
  • LOC129995722:ATAC-STARR-seq lymphoblastoid silent region 16891 [Gene]
  • LOC129995723:ATAC-STARR-seq lymphoblastoid silent region 16892 [Gene]
  • LOC129995724:ATAC-STARR-seq lymphoblastoid silent region 16893 [Gene]
  • LOC129995728:ATAC-STARR-seq lymphoblastoid silent region 16894 [Gene]
  • LOC129995731:ATAC-STARR-seq lymphoblastoid silent region 16895 [Gene]
  • LOC129995732:ATAC-STARR-seq lymphoblastoid silent region 16896 [Gene]
  • BLOC1S5-TXNDC5:BLOC1S5-TXNDC5 readthrough (NMD candidate) [Gene - HGNC]
  • LOC126859560:BRD4-independent group 4 enhancer GRCh37_chr6:4466860-4468059 [Gene]
  • LOC126859563:BRD4-independent group 4 enhancer GRCh37_chr6:5044856-5046055 [Gene]
  • LOC126859567:BRD4-independent group 4 enhancer GRCh37_chr6:5581546-5582745 [Gene]
  • LOC126859568:BRD4-independent group 4 enhancer GRCh37_chr6:5665450-5666649 [Gene]
  • LOC126859575:BRD4-independent group 4 enhancer GRCh37_chr6:6856889-6858088 [Gene]
  • LOC126859577:BRD4-independent group 4 enhancer GRCh37_chr6:7763783-7764982 [Gene]
  • LOC126859565:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:5368745-5369944 [Gene]
  • LOC126859570:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:5998084-5999283 [Gene]
  • LOC126859571:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:6218631-6219830 [Gene]
  • LOC126859572:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:6361855-6363054 [Gene]
  • LOC126859580:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:8387849-8389048 [Gene]
  • CDYL-AS1:CDYL antisense RNA 1 [Gene - HGNC]
  • DSP-AS1:DSP antisense RNA 1 [Gene - HGNC]
  • EEF1E1-BLOC1S5:EEF1E1-BLOC1S5 readthrough (NMD candidate) [Gene - HGNC]
  • FARS2-AS1:FARS2 antisense RNA 1 [Gene - HGNC]
  • LY86-AS1:LY86 antisense RNA 1 [Gene - HGNC]
  • LYRM4:LYR motif containing 4 [Gene - OMIM - HGNC]
  • LYRM4-AS1:LYRM4 antisense RNA 1 [Gene - HGNC]
  • LOC126859569:MED14-independent group 3 enhancer GRCh37_chr6:5905761-5906960 [Gene]
  • LOC126859573:MED14-independent group 3 enhancer GRCh37_chr6:6803278-6804477 [Gene]
  • LOC126859576:MED14-independent group 3 enhancer GRCh37_chr6:7505263-7506462 [Gene]
  • LOC126859578:MED14-independent group 3 enhancer GRCh37_chr6:7882299-7883498 [Gene]
  • LOC129389430:MPRA-validated peak5629 silencer [Gene]
  • LOC129389431:MPRA-validated peak5630 silencer [Gene]
  • LOC129389432:MPRA-validated peak5632 silencer [Gene]
  • LOC129389433:MPRA-validated peak5636 silencer [Gene]
  • LOC129389434:MPRA-validated peak5639 silencer [Gene]
  • LOC129389435:MPRA-validated peak5642 silencer [Gene]
  • LOC129389436:MPRA-validated peak5644 silencer [Gene]
  • LOC129389437:MPRA-validated peak5647 silencer [Gene]
  • LOC129389438:MPRA-validated peak5648 silencer [Gene]
  • LOC132089447:Neanderthal introgressed variant-containing enhancer experimental_94357 [Gene]
  • LOC132089483:Neanderthal introgressed variant-containing enhancer experimental_96039 [Gene]
  • LOC126859561:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:4487436-4488635 [Gene]
  • LOC126859562:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:4864691-4865890 [Gene]
  • LOC126859564:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5230418-5231617 [Gene]
  • LOC126859566:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5541695-5542894 [Gene]
  • LOC126859574:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:6811111-6812310 [Gene]
  • LOC126859579:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:7919793-7920992 [Gene]
  • RIOK1:RIO kinase 1 [Gene - OMIM - HGNC]
  • LOC123575662:Sharpr-MPRA regulatory region 12169 [Gene]
  • LOC113175008:Sharpr-MPRA regulatory region 12260 [Gene]
  • LOC113175013:Sharpr-MPRA regulatory region 13455 [Gene]
  • LOC123575664:Sharpr-MPRA regulatory region 13737 [Gene]
  • LOC123575663:Sharpr-MPRA regulatory region 14963 [Gene]
  • LOC123575661:Sharpr-MPRA regulatory region 15549 [Gene]
  • LOC113175014:Sharpr-MPRA regulatory region 2085 [Gene]
  • LOC123575660:Sharpr-MPRA regulatory region 2533 [Gene]
  • LOC113175015:Sharpr-MPRA regulatory region 2698 [Gene]
  • LOC113175016:Sharpr-MPRA regulatory region 4297 [Gene]
  • LOC113175009:Sharpr-MPRA regulatory region 4402 [Gene]
  • LOC121099722:Sharpr-MPRA regulatory region 4425 [Gene]
  • LOC121099724:Sharpr-MPRA regulatory region 4659 [Gene]
  • LOC113174999:Sharpr-MPRA regulatory region 4929 [Gene]
  • LOC121740637:Sharpr-MPRA regulatory region 6592 [Gene]
  • LOC110121247:VISTA enhancer hs2061 [Gene]
  • LOC110121274:VISTA enhancer hs2191 [Gene]
  • LOC114827828:VISTA enhancer hs2285 [Gene]
  • BLOC1S5:biogenesis of lysosomal organelles complex 1 subunit 5 [Gene - OMIM - HGNC]
  • BMP6:bone morphogenetic protein 6 [Gene - OMIM - HGNC]
  • CAGE1:cancer antigen 1 [Gene - OMIM - HGNC]
  • CDYL:chromodomain Y like [Gene - OMIM - HGNC]
  • F13A1:coagulation factor XIII A chain [Gene - OMIM - HGNC]
  • DSP:desmoplakin [Gene - OMIM - HGNC]
  • EEF1E1:eukaryotic translation elongation factor 1 epsilon 1 [Gene - OMIM - HGNC]
  • LINC02533:long intergenic non-protein coding RNA 2533 [Gene - HGNC]
  • LY86:lymphocyte antigen 86 [Gene - OMIM - HGNC]
  • MIR3691:microRNA 3691 [Gene - HGNC]
  • MIR5683:microRNA 5683 [Gene - HGNC]
  • MIR7853:microRNA 7853 [Gene - HGNC]
  • NRN1:neuritin 1 [Gene - OMIM - HGNC]
  • FARS2:phenylalanyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
  • PPP1R3G:protein phosphatase 1 regulatory subunit 3G [Gene - OMIM - HGNC]
  • RREB1:ras responsive element binding protein 1 [Gene - OMIM - HGNC]
  • RPP40:ribonuclease P/MRP subunit p40 [Gene - OMIM - HGNC]
  • SSR1:signal sequence receptor subunit 1 [Gene - OMIM - HGNC]
  • LOC111721709:skeletal muscle cis-regulatory module in RREB1 intron [Gene]
  • SCARNA27:small Cajal body-specific RNA 27 [Gene - HGNC]
  • SNRNP48:small nuclear ribonucleoprotein U11/U12 subunit 48 [Gene - HGNC]
  • TXNDC5:thioredoxin domain containing 5 [Gene - OMIM - HGNC]
  • LOC101927950:uncharacterized LOC101927950 [Gene]
  • LOC101928004:uncharacterized LOC101928004 [Gene]
  • LOC105374901:uncharacterized LOC105374901 [Gene]
  • KU-MEL-3:uncharacterized LOC497048 [Gene]
Variant type:
copy number loss
Cytogenetic location:
6p25.1-24.3
Genomic location:
Preferred name:
GRCh38/hg38 6p25.1-24.3(chr6:4427090-8391140)x1
HGVS:
  • NC_000006.12:g.(?_4427090)_(8391140_?)del
  • NC_000006.10:g.(?_4372323)_(8336372_?)del
  • NC_000006.11:g.(?_4427324)_(8391373_?)del
Links:
dbVar: nssv578110; dbVar: nsv530889
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
SCV000079526GeneDx
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]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not 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 GeneDx, SCV000079526.4

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

Last Updated: Oct 14, 2023