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GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)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:
RCV000052192.4

Allele description [Variation Report for GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)x1]

GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)x1

Genes:
  • NT5E:5'-nucleotidase ecto [Gene - OMIM - HGNC]
  • HTR1E:5-hydroxytryptamine receptor 1E [Gene - OMIM - HGNC]
  • LOC129996759:ATAC-STARR-seq lymphoblastoid active region 24780 [Gene]
  • LOC129996760:ATAC-STARR-seq lymphoblastoid active region 24781 [Gene]
  • LOC129996762:ATAC-STARR-seq lymphoblastoid active region 24782 [Gene]
  • LOC129996763:ATAC-STARR-seq lymphoblastoid active region 24783 [Gene]
  • LOC129996765:ATAC-STARR-seq lymphoblastoid active region 24784 [Gene]
  • LOC129996775:ATAC-STARR-seq lymphoblastoid active region 24787 [Gene]
  • LOC129996779:ATAC-STARR-seq lymphoblastoid active region 24790 [Gene]
  • LOC129996780:ATAC-STARR-seq lymphoblastoid active region 24791 [Gene]
  • LOC129996781:ATAC-STARR-seq lymphoblastoid active region 24792 [Gene]
  • LOC129996782:ATAC-STARR-seq lymphoblastoid active region 24793 [Gene]
  • LOC129996783:ATAC-STARR-seq lymphoblastoid active region 24794 [Gene]
  • LOC129996786:ATAC-STARR-seq lymphoblastoid active region 24795 [Gene]
  • LOC129996787:ATAC-STARR-seq lymphoblastoid active region 24796 [Gene]
  • LOC129996788:ATAC-STARR-seq lymphoblastoid active region 24797 [Gene]
  • LOC129996791:ATAC-STARR-seq lymphoblastoid active region 24799 [Gene]
  • LOC129996792:ATAC-STARR-seq lymphoblastoid active region 24800 [Gene]
  • LOC129996793:ATAC-STARR-seq lymphoblastoid active region 24801 [Gene]
  • LOC129996794:ATAC-STARR-seq lymphoblastoid active region 24802 [Gene]
  • LOC129996795:ATAC-STARR-seq lymphoblastoid active region 24803 [Gene]
  • LOC129996796:ATAC-STARR-seq lymphoblastoid active region 24804 [Gene]
  • LOC129996797:ATAC-STARR-seq lymphoblastoid active region 24805 [Gene]
  • LOC129996798:ATAC-STARR-seq lymphoblastoid active region 24806 [Gene]
  • LOC129996799:ATAC-STARR-seq lymphoblastoid active region 24807 [Gene]
  • LOC129996800:ATAC-STARR-seq lymphoblastoid active region 24808 [Gene]
  • LOC129996801:ATAC-STARR-seq lymphoblastoid active region 24810 [Gene]
  • LOC129996802:ATAC-STARR-seq lymphoblastoid active region 24811 [Gene]
  • LOC129996803:ATAC-STARR-seq lymphoblastoid active region 24812 [Gene]
  • LOC129996808:ATAC-STARR-seq lymphoblastoid active region 24814 [Gene]
  • LOC129996809:ATAC-STARR-seq lymphoblastoid active region 24815 [Gene]
  • LOC129996811:ATAC-STARR-seq lymphoblastoid active region 24816 [Gene]
  • LOC129996812:ATAC-STARR-seq lymphoblastoid active region 24817 [Gene]
  • LOC129996813:ATAC-STARR-seq lymphoblastoid active region 24818 [Gene]
  • LOC129996817:ATAC-STARR-seq lymphoblastoid active region 24819 [Gene]
  • LOC129996820:ATAC-STARR-seq lymphoblastoid active region 24820 [Gene]
  • LOC129996822:ATAC-STARR-seq lymphoblastoid active region 24822 [Gene]
  • LOC129996824:ATAC-STARR-seq lymphoblastoid active region 24823 [Gene]
  • LOC129996825:ATAC-STARR-seq lymphoblastoid active region 24824 [Gene]
  • LOC129996826:ATAC-STARR-seq lymphoblastoid active region 24826 [Gene]
  • LOC129996827:ATAC-STARR-seq lymphoblastoid active region 24827 [Gene]
  • LOC129996828:ATAC-STARR-seq lymphoblastoid active region 24828 [Gene]
  • LOC129996834:ATAC-STARR-seq lymphoblastoid active region 24832 [Gene]
  • LOC129996835:ATAC-STARR-seq lymphoblastoid active region 24833 [Gene]
  • LOC129996836:ATAC-STARR-seq lymphoblastoid active region 24834 [Gene]
  • LOC129996839:ATAC-STARR-seq lymphoblastoid active region 24835 [Gene]
  • LOC129996840:ATAC-STARR-seq lymphoblastoid active region 24836 [Gene]
  • LOC129996844:ATAC-STARR-seq lymphoblastoid active region 24837 [Gene]
  • LOC129996761:ATAC-STARR-seq lymphoblastoid silent region 17355 [Gene]
  • LOC129996764:ATAC-STARR-seq lymphoblastoid silent region 17356 [Gene]
  • LOC129996766:ATAC-STARR-seq lymphoblastoid silent region 17358 [Gene]
  • LOC129996767:ATAC-STARR-seq lymphoblastoid silent region 17359 [Gene]
  • LOC129996768:ATAC-STARR-seq lymphoblastoid silent region 17360 [Gene]
  • LOC129996769:ATAC-STARR-seq lymphoblastoid silent region 17361 [Gene]
  • LOC129996770:ATAC-STARR-seq lymphoblastoid silent region 17362 [Gene]
  • LOC129996771:ATAC-STARR-seq lymphoblastoid silent region 17363 [Gene]
  • LOC129996772:ATAC-STARR-seq lymphoblastoid silent region 17364 [Gene]
  • LOC129996773:ATAC-STARR-seq lymphoblastoid silent region 17365 [Gene]
  • LOC129996774:ATAC-STARR-seq lymphoblastoid silent region 17366 [Gene]
  • LOC129996776:ATAC-STARR-seq lymphoblastoid silent region 17368 [Gene]
  • LOC129996777:ATAC-STARR-seq lymphoblastoid silent region 17369 [Gene]
  • LOC129996778:ATAC-STARR-seq lymphoblastoid silent region 17370 [Gene]
  • LOC129996784:ATAC-STARR-seq lymphoblastoid silent region 17372 [Gene]
  • LOC129996785:ATAC-STARR-seq lymphoblastoid silent region 17373 [Gene]
  • LOC129996789:ATAC-STARR-seq lymphoblastoid silent region 17375 [Gene]
  • LOC129996790:ATAC-STARR-seq lymphoblastoid silent region 17376 [Gene]
  • LOC129996804:ATAC-STARR-seq lymphoblastoid silent region 17377 [Gene]
  • LOC129996805:ATAC-STARR-seq lymphoblastoid silent region 17378 [Gene]
  • LOC129996806:ATAC-STARR-seq lymphoblastoid silent region 17379 [Gene]
  • LOC129996807:ATAC-STARR-seq lymphoblastoid silent region 17380 [Gene]
  • LOC129996810:ATAC-STARR-seq lymphoblastoid silent region 17381 [Gene]
  • LOC129996814:ATAC-STARR-seq lymphoblastoid silent region 17382 [Gene]
  • LOC129996815:ATAC-STARR-seq lymphoblastoid silent region 17383 [Gene]
  • LOC129996816:ATAC-STARR-seq lymphoblastoid silent region 17385 [Gene]
  • LOC129996818:ATAC-STARR-seq lymphoblastoid silent region 17386 [Gene]
  • LOC129996819:ATAC-STARR-seq lymphoblastoid silent region 17387 [Gene]
  • LOC129996821:ATAC-STARR-seq lymphoblastoid silent region 17388 [Gene]
  • LOC129996823:ATAC-STARR-seq lymphoblastoid silent region 17391 [Gene]
  • LOC129996829:ATAC-STARR-seq lymphoblastoid silent region 17392 [Gene]
  • LOC129996830:ATAC-STARR-seq lymphoblastoid silent region 17393 [Gene]
  • LOC129996831:ATAC-STARR-seq lymphoblastoid silent region 17394 [Gene]
  • LOC129996832:ATAC-STARR-seq lymphoblastoid silent region 17395 [Gene]
  • LOC129996833:ATAC-STARR-seq lymphoblastoid silent region 17396 [Gene]
  • LOC129996837:ATAC-STARR-seq lymphoblastoid silent region 17397 [Gene]
  • LOC129996838:ATAC-STARR-seq lymphoblastoid silent region 17398 [Gene]
  • LOC129996841:ATAC-STARR-seq lymphoblastoid silent region 17399 [Gene]
  • LOC129996842:ATAC-STARR-seq lymphoblastoid silent region 17400 [Gene]
  • LOC129996843:ATAC-STARR-seq lymphoblastoid silent region 17401 [Gene]
  • LOC129996845:ATAC-STARR-seq lymphoblastoid silent region 17402 [Gene]
  • LOC129996846:ATAC-STARR-seq lymphoblastoid silent region 17403 [Gene]
  • LOC126859730:BRD4-independent group 4 enhancer GRCh37_chr6:87497596-87498795 [Gene]
  • LOC126859737:BRD4-independent group 4 enhancer GRCh37_chr6:90007048-90008247 [Gene]
  • LOC126859738:BRD4-independent group 4 enhancer GRCh37_chr6:90347214-90348413 [Gene]
  • LOC126859739:BRD4-independent group 4 enhancer GRCh37_chr6:90367565-90368764 [Gene]
  • LOC126859743:BRD4-independent group 4 enhancer GRCh37_chr6:91078586-91079785 [Gene]
  • LOC126859745:BRD4-independent group 4 enhancer GRCh37_chr6:93097885-93099084 [Gene]
  • LOC126859746:BRD4-independent group 4 enhancer GRCh37_chr6:93327456-93328655 [Gene]
  • BACH2:BTB domain and CNC homolog 2 [Gene - OMIM - HGNC]
  • LOC108348029:CAGE-defined B cell enhancer in LOC101928911-SPACA1 intergenic region [Gene]
  • LOC126859726:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:83747652-83748851 [Gene]
  • LOC113175019:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:84686166-84687365 [Gene]
  • LOC126859734:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:88834755-88835954 [Gene]
  • LOC126859736:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:89239515-89240714 [Gene]
  • LOC126859740:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:90866333-90867532 [Gene]
  • LOC116183065:CRISPRi-validated cis-regulatory element chr6.3721 [Gene]
  • LOC116183066:CRISPRi-validated cis-regulatory element chr6.3824 [Gene]
  • DOP1A:DOP1 leucine zipper like protein A [Gene - OMIM - HGNC]
  • EPHA7:EPH receptor A7 [Gene - OMIM - HGNC]
  • LOC111413030:FOXA motif-containing MPRA enhancer 167 [Gene]
  • LOC111429613:FOXA motif-containing MPRA enhancer 210/211 [Gene]
  • LYRM2:LYR motif containing 2 [Gene - HGNC]
  • MDN1-AS1:MDN1 antisense RNA 1 [Gene - HGNC]
  • LOC126859727:MED14-independent group 3 enhancer GRCh37_chr6:84140986-84142185 [Gene]
  • LOC126859728:MED14-independent group 3 enhancer GRCh37_chr6:87291002-87292201 [Gene]
  • LOC126859729:MED14-independent group 3 enhancer GRCh37_chr6:87433363-87434562 [Gene]
  • LOC126859735:MED14-independent group 3 enhancer GRCh37_chr6:89060126-89061325 [Gene]
  • LOC126859741:MED14-independent group 3 enhancer GRCh37_chr6:90894000-90895199 [Gene]
  • LOC126859744:MED14-independent group 3 enhancer GRCh37_chr6:91617235-91618434 [Gene]
  • LOC129389564:MPRA-validated peak5925 silencer [Gene]
  • LOC129389565:MPRA-validated peak5926 silencer [Gene]
  • LOC129389566:MPRA-validated peak5928 silencer [Gene]
  • LOC129389567:MPRA-validated peak5930 silencer [Gene]
  • LOC129389568:MPRA-validated peak5932 silencer [Gene]
  • LOC129389569:MPRA-validated peak5934 silencer [Gene]
  • LOC129389570:MPRA-validated peak5939 silencer [Gene]
  • LOC129389571:MPRA-validated peak5941 silencer [Gene]
  • LOC129389572:MPRA-validated peak5943 silencer [Gene]
  • LOC129389573:MPRA-validated peak5945 silencer [Gene]
  • LOC129389574:MPRA-validated peak5946 silencer [Gene]
  • LOC129389575:MPRA-validated peak5947 silencer [Gene]
  • LOC129389576:MPRA-validated peak5948 silencer [Gene]
  • LOC129389577:MPRA-validated peak5950 silencer [Gene]
  • LOC129389578:MPRA-validated peak5952 silencer [Gene]
  • LOC129389579:MPRA-validated peak5956 silencer [Gene]
  • LOC129389580:MPRA-validated peak5961 silencer [Gene]
  • LOC129389581:MPRA-validated peak5962 silencer [Gene]
  • LOC129389582:MPRA-validated peak5963 silencer [Gene]
  • LOC132089501:Neanderthal introgressed variant-containing enhancer experimental_96858 [Gene]
  • LOC132089502:Neanderthal introgressed variant-containing enhancer experimental_96913 [Gene]
  • LOC132089503:Neanderthal introgressed variant-containing enhancer experimental_97174 [Gene]
  • LOC126859731:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:87679014-87680213 [Gene]
  • LOC126859732:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:87922894-87924093 [Gene]
  • LOC126859733:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:88193750-88194949 [Gene]
  • LOC126859742:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:90931785-90932984 [Gene]
  • PNRC1-DT:PNRC1 divergent transcript [Gene - HGNC]
  • RIPPLY2-CYB5R4:RIPPLY2-CYB5R4 readthrough [Gene]
  • RNGTT:RNA guanylyltransferase and 5'-phosphatase [Gene - OMIM - HGNC]
  • RWDD2A:RWD domain containing 2A [Gene - HGNC]
  • RRAGD:Ras related GTP binding D [Gene - OMIM - HGNC]
  • LOC121740658:Sharpr-MPRA regulatory region 13381 [Gene]
  • LOC121132697:Sharpr-MPRA regulatory region 13581 [Gene]
  • LOC123775379:Sharpr-MPRA regulatory region 13924 [Gene]
  • LOC123775381:Sharpr-MPRA regulatory region 143 [Gene]
  • LOC123775383:Sharpr-MPRA regulatory region 14578 [Gene]
  • LOC123775385:Sharpr-MPRA regulatory region 15648 [Gene]
  • LOC121132699:Sharpr-MPRA regulatory region 1684 [Gene]
  • LOC121132696:Sharpr-MPRA regulatory region 2176 [Gene]
  • LOC123775380:Sharpr-MPRA regulatory region 3398 [Gene]
  • LOC121132698:Sharpr-MPRA regulatory region 4618 [Gene]
  • LOC113175020:Sharpr-MPRA regulatory region 5254 [Gene]
  • LOC123775384:Sharpr-MPRA regulatory region 6453 [Gene]
  • LOC121132700:Sharpr-MPRA regulatory region 8521 [Gene]
  • LOC123775382:Sharpr-MPRA regulatory region 852 [Gene]
  • TBX18:T-box transcription factor 18 [Gene - OMIM - HGNC]
  • TBX18-AS1:TBX18 antisense RNA 1 [Gene - HGNC]
  • LOC110121249:VISTA enhancer hs2063 [Gene]
  • AKIRIN2:akirin 2 [Gene - OMIM - HGNC]
  • ANKRD6:ankyrin repeat domain 6 [Gene - OMIM - HGNC]
  • RARS2:arginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
  • CASC6:cancer susceptibility 6 [Gene - HGNC]
  • CNR1:cannabinoid receptor 1 [Gene - OMIM - HGNC]
  • CASP8AP2:caspase 8 associated protein 2 [Gene - OMIM - HGNC]
  • CEP162:centrosomal protein 162 [Gene - OMIM - HGNC]
  • C6orf163:chromosome 6 open reading frame 163 [Gene - HGNC]
  • CFAP206:cilia and flagella associated protein 206 [Gene - HGNC]
  • CYB5R4:cytochrome b5 reductase 4 [Gene - OMIM - HGNC]
  • GABRR1:gamma-aminobutyric acid type A receptor subunit rho1 [Gene - OMIM - HGNC]
  • GABRR2:gamma-aminobutyric acid type A receptor subunit rho2 [Gene - OMIM - HGNC]
  • GJA10:gap junction protein alpha 10 [Gene - OMIM - HGNC]
  • GJB7:gap junction protein beta 7 [Gene - OMIM - HGNC]
  • CGA:glycoprotein hormones, alpha polypeptide [Gene - OMIM - HGNC]
  • LINC01590:long intergenic non-protein coding RNA 1590 [Gene - HGNC]
  • LINC01611:long intergenic non-protein coding RNA 1611 [Gene - HGNC]
  • LINC02531:long intergenic non-protein coding RNA 2531 [Gene - HGNC]
  • LINC02535:long intergenic non-protein coding RNA 2535 [Gene - HGNC]
  • ME1:malic enzyme 1 [Gene - OMIM - HGNC]
  • MRAP2:melanocortin 2 receptor accessory protein 2 [Gene - OMIM - HGNC]
  • LOC128772296:melanoma risk locus-associated MPRA allelic enhancer 6:90866227 [Gene]
  • LOC128772297:melanoma risk locus-associated MPRA allelic enhancer 6:90883525 [Gene]
  • LOC128772298:melanoma risk locus-associated MPRA allelic enhancer 6:90941289 [Gene]
  • LOC128772299:melanoma risk locus-associated MPRA allelic enhancer 6:90981657 [Gene]
  • LOC128772300:melanoma risk locus-associated MPRA allelic enhancer 6:90982387 [Gene]
  • LOC128772301:melanoma risk locus-associated MPRA allelic enhancer 6:91012867 [Gene]
  • LOC128772302:melanoma risk locus-associated MPRA allelic enhancer 6:91036267 [Gene]
  • LOC128772303:melanoma risk locus-associated MPRA allelic enhancer 6:91037287 [Gene]
  • MIR4464:microRNA 4464 [Gene - HGNC]
  • MIR4643:microRNA 4643 [Gene - HGNC]
  • MDN1:midasin AAA ATPase 1 [Gene - OMIM - HGNC]
  • MAP3K7:mitogen-activated protein kinase kinase kinase 7 [Gene - OMIM - HGNC]
  • ORC3:origin recognition complex subunit 3 [Gene - OMIM - HGNC]
  • PM20D2:peptidase M20 domain containing 2 [Gene - OMIM - HGNC]
  • PGM3:phosphoglucomutase 3 [Gene - OMIM - HGNC]
  • PNRC1:proline rich nuclear receptor coactivator 1 [Gene - OMIM - HGNC]
  • RIPPLY2:ripply transcriptional repressor 2 [Gene - OMIM - HGNC]
  • SRSF12:serine and arginine rich splicing factor 12 [Gene - HGNC]
  • PRSS35:serine protease 35 [Gene - HGNC]
  • SMIM8:small integral membrane protein 8 [Gene - HGNC]
  • SNHG5:small nucleolar RNA host gene 5 [Gene - OMIM - HGNC]
  • SNORD50A:small nucleolar RNA, C/D box 50A [Gene - OMIM - HGNC]
  • SNORD50B:small nucleolar RNA, C/D box 50B [Gene - OMIM - HGNC]
  • SLC35A1:solute carrier family 35 member A1 [Gene - OMIM - HGNC]
  • SNX14:sorting nexin 14 [Gene - OMIM - HGNC]
  • SPACA1:sperm acrosome associated 1 [Gene - OMIM - HGNC]
  • SNAP91:synaptosome associated protein 91 [Gene - OMIM - HGNC]
  • SYNCRIP:synaptotagmin binding cytoplasmic RNA interacting protein [Gene - OMIM - HGNC]
  • TSG1:tumor suppressor TSG1 [Gene]
  • UBE2J1:ubiquitin conjugating enzyme E2 J1 [Gene - OMIM - HGNC]
  • UBE3D:ubiquitin protein ligase E3D [Gene - OMIM - HGNC]
  • LOC101928911:uncharacterized LOC101928911 [Gene]
  • LOC101928936:uncharacterized LOC101928936 [Gene]
  • LOC105377879:uncharacterized LOC105377879 [Gene]
  • ZNF292:zinc finger protein 292 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
6q14.1-16.1
Genomic location:
Preferred name:
GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)x1
HGVS:
  • NC_000006.12:g.(?_82569098)_(93753476_?)del
  • NC_000006.10:g.(?_83335534)_(94519915_?)del
  • NC_000006.11:g.(?_83278815)_(94463194_?)del
Links:
dbVar: nssv578121; dbVar: nsv530904
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
SCV000079541GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		not providedclinical 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 GeneDx, SCV000079541.4

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

Last Updated: Nov 20, 2023