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GRCh38/hg38 16q11.2-12.1(chr16:46471520-52405956)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:
RCV000053328.6

Allele description [Variation Report for GRCh38/hg38 16q11.2-12.1(chr16:46471520-52405956)x1]

GRCh38/hg38 16q11.2-12.1(chr16:46471520-52405956)x1

Genes:
  • LOC130058916:ATAC-STARR-seq lymphoblastoid active region 10770 [Gene]
  • LOC130058918:ATAC-STARR-seq lymphoblastoid active region 10771 [Gene]
  • LOC130058919:ATAC-STARR-seq lymphoblastoid active region 10772 [Gene]
  • LOC130058920:ATAC-STARR-seq lymphoblastoid active region 10773 [Gene]
  • LOC130058921:ATAC-STARR-seq lymphoblastoid active region 10774 [Gene]
  • LOC130058923:ATAC-STARR-seq lymphoblastoid active region 10775 [Gene]
  • LOC130058924:ATAC-STARR-seq lymphoblastoid active region 10776 [Gene]
  • LOC130058925:ATAC-STARR-seq lymphoblastoid active region 10777 [Gene]
  • LOC130058927:ATAC-STARR-seq lymphoblastoid active region 10778 [Gene]
  • LOC130058928:ATAC-STARR-seq lymphoblastoid active region 10779 [Gene]
  • LOC130058930:ATAC-STARR-seq lymphoblastoid active region 10781 [Gene]
  • LOC130058936:ATAC-STARR-seq lymphoblastoid active region 10782 [Gene]
  • LOC130058937:ATAC-STARR-seq lymphoblastoid active region 10783 [Gene]
  • LOC130058940:ATAC-STARR-seq lymphoblastoid active region 10784 [Gene]
  • LOC130058941:ATAC-STARR-seq lymphoblastoid active region 10785 [Gene]
  • LOC130058948:ATAC-STARR-seq lymphoblastoid active region 10786 [Gene]
  • LOC130058949:ATAC-STARR-seq lymphoblastoid active region 10787 [Gene]
  • LOC130058950:ATAC-STARR-seq lymphoblastoid active region 10788 [Gene]
  • LOC130058951:ATAC-STARR-seq lymphoblastoid active region 10789 [Gene]
  • LOC130058953:ATAC-STARR-seq lymphoblastoid active region 10791 [Gene]
  • LOC130058957:ATAC-STARR-seq lymphoblastoid active region 10792 [Gene]
  • LOC130058958:ATAC-STARR-seq lymphoblastoid active region 10793 [Gene]
  • LOC130058959:ATAC-STARR-seq lymphoblastoid active region 10795 [Gene]
  • LOC130058960:ATAC-STARR-seq lymphoblastoid active region 10796 [Gene]
  • LOC130058961:ATAC-STARR-seq lymphoblastoid active region 10797 [Gene]
  • LOC130058962:ATAC-STARR-seq lymphoblastoid active region 10798 [Gene]
  • LOC130058964:ATAC-STARR-seq lymphoblastoid active region 10799 [Gene]
  • LOC130058965:ATAC-STARR-seq lymphoblastoid active region 10800 [Gene]
  • LOC130058966:ATAC-STARR-seq lymphoblastoid active region 10801 [Gene]
  • LOC130058968:ATAC-STARR-seq lymphoblastoid active region 10802 [Gene]
  • LOC130058972:ATAC-STARR-seq lymphoblastoid active region 10804 [Gene]
  • LOC130058973:ATAC-STARR-seq lymphoblastoid active region 10805 [Gene]
  • LOC130058974:ATAC-STARR-seq lymphoblastoid active region 10807 [Gene]
  • LOC130058986:ATAC-STARR-seq lymphoblastoid active region 10808 [Gene]
  • LOC130058987:ATAC-STARR-seq lymphoblastoid active region 10809 [Gene]
  • LOC130058988:ATAC-STARR-seq lymphoblastoid active region 10810 [Gene]
  • LOC130058990:ATAC-STARR-seq lymphoblastoid active region 10811 [Gene]
  • LOC130058991:ATAC-STARR-seq lymphoblastoid active region 10812 [Gene]
  • LOC130058992:ATAC-STARR-seq lymphoblastoid active region 10814 [Gene]
  • LOC130058993:ATAC-STARR-seq lymphoblastoid active region 10815 [Gene]
  • LOC130058994:ATAC-STARR-seq lymphoblastoid active region 10816 [Gene]
  • LOC130058997:ATAC-STARR-seq lymphoblastoid active region 10817 [Gene]
  • LOC130059001:ATAC-STARR-seq lymphoblastoid active region 10818 [Gene]
  • LOC130059004:ATAC-STARR-seq lymphoblastoid active region 10819 [Gene]
  • LOC130059005:ATAC-STARR-seq lymphoblastoid active region 10820 [Gene]
  • LOC130059006:ATAC-STARR-seq lymphoblastoid active region 10821 [Gene]
  • LOC130059008:ATAC-STARR-seq lymphoblastoid active region 10822 [Gene]
  • LOC130059009:ATAC-STARR-seq lymphoblastoid active region 10823 [Gene]
  • LOC130059010:ATAC-STARR-seq lymphoblastoid active region 10824 [Gene]
  • LOC130059011:ATAC-STARR-seq lymphoblastoid active region 10825 [Gene]
  • LOC130059013:ATAC-STARR-seq lymphoblastoid active region 10826 [Gene]
  • LOC130059014:ATAC-STARR-seq lymphoblastoid active region 10827 [Gene]
  • LOC130059016:ATAC-STARR-seq lymphoblastoid active region 10828 [Gene]
  • LOC130058917:ATAC-STARR-seq lymphoblastoid silent region 7430 [Gene]
  • LOC130058922:ATAC-STARR-seq lymphoblastoid silent region 7434 [Gene]
  • LOC130058926:ATAC-STARR-seq lymphoblastoid silent region 7435 [Gene]
  • LOC130058929:ATAC-STARR-seq lymphoblastoid silent region 7437 [Gene]
  • LOC130058931:ATAC-STARR-seq lymphoblastoid silent region 7439 [Gene]
  • LOC130058932:ATAC-STARR-seq lymphoblastoid silent region 7440 [Gene]
  • LOC130058933:ATAC-STARR-seq lymphoblastoid silent region 7441 [Gene]
  • LOC130058934:ATAC-STARR-seq lymphoblastoid silent region 7442 [Gene]
  • LOC130058935:ATAC-STARR-seq lymphoblastoid silent region 7443 [Gene]
  • LOC130058938:ATAC-STARR-seq lymphoblastoid silent region 7444 [Gene]
  • LOC130058939:ATAC-STARR-seq lymphoblastoid silent region 7445 [Gene]
  • LOC130058942:ATAC-STARR-seq lymphoblastoid silent region 7446 [Gene]
  • LOC130058943:ATAC-STARR-seq lymphoblastoid silent region 7447 [Gene]
  • LOC130058944:ATAC-STARR-seq lymphoblastoid silent region 7448 [Gene]
  • LOC130058945:ATAC-STARR-seq lymphoblastoid silent region 7449 [Gene]
  • LOC130058946:ATAC-STARR-seq lymphoblastoid silent region 7450 [Gene]
  • LOC130058947:ATAC-STARR-seq lymphoblastoid silent region 7451 [Gene]
  • LOC130058952:ATAC-STARR-seq lymphoblastoid silent region 7452 [Gene]
  • LOC130058954:ATAC-STARR-seq lymphoblastoid silent region 7454 [Gene]
  • LOC130058955:ATAC-STARR-seq lymphoblastoid silent region 7455 [Gene]
  • LOC130058956:ATAC-STARR-seq lymphoblastoid silent region 7456 [Gene]
  • LOC130058963:ATAC-STARR-seq lymphoblastoid silent region 7457 [Gene]
  • LOC130058967:ATAC-STARR-seq lymphoblastoid silent region 7458 [Gene]
  • LOC130058969:ATAC-STARR-seq lymphoblastoid silent region 7459 [Gene]
  • LOC130058970:ATAC-STARR-seq lymphoblastoid silent region 7460 [Gene]
  • LOC130058971:ATAC-STARR-seq lymphoblastoid silent region 7461 [Gene]
  • LOC130058975:ATAC-STARR-seq lymphoblastoid silent region 7462 [Gene]
  • LOC130058976:ATAC-STARR-seq lymphoblastoid silent region 7463 [Gene]
  • LOC130058977:ATAC-STARR-seq lymphoblastoid silent region 7464 [Gene]
  • LOC130058978:ATAC-STARR-seq lymphoblastoid silent region 7465 [Gene]
  • LOC130058979:ATAC-STARR-seq lymphoblastoid silent region 7468 [Gene]
  • LOC130058980:ATAC-STARR-seq lymphoblastoid silent region 7469 [Gene]
  • LOC130058981:ATAC-STARR-seq lymphoblastoid silent region 7470 [Gene]
  • LOC130058982:ATAC-STARR-seq lymphoblastoid silent region 7471 [Gene]
  • LOC130058983:ATAC-STARR-seq lymphoblastoid silent region 7475 [Gene]
  • LOC130058984:ATAC-STARR-seq lymphoblastoid silent region 7476 [Gene]
  • LOC130058985:ATAC-STARR-seq lymphoblastoid silent region 7477 [Gene]
  • LOC130058989:ATAC-STARR-seq lymphoblastoid silent region 7478 [Gene]
  • LOC130058995:ATAC-STARR-seq lymphoblastoid silent region 7481 [Gene]
  • LOC130058996:ATAC-STARR-seq lymphoblastoid silent region 7482 [Gene]
  • LOC130058998:ATAC-STARR-seq lymphoblastoid silent region 7483 [Gene]
  • LOC130058999:ATAC-STARR-seq lymphoblastoid silent region 7484 [Gene]
  • LOC130059000:ATAC-STARR-seq lymphoblastoid silent region 7485 [Gene]
  • LOC130059002:ATAC-STARR-seq lymphoblastoid silent region 7486 [Gene]
  • LOC130059003:ATAC-STARR-seq lymphoblastoid silent region 7487 [Gene]
  • LOC130059007:ATAC-STARR-seq lymphoblastoid silent region 7489 [Gene]
  • LOC130059012:ATAC-STARR-seq lymphoblastoid silent region 7490 [Gene]
  • LOC130059015:ATAC-STARR-seq lymphoblastoid silent region 7491 [Gene]
  • LOC130059017:ATAC-STARR-seq lymphoblastoid silent region 7492 [Gene]
  • ABCC11:ATP binding cassette subfamily C member 11 [Gene - OMIM - HGNC]
  • ABCC12:ATP binding cassette subfamily C member 12 [Gene - OMIM - HGNC]
  • LOC126862337:BRD4-independent group 4 enhancer GRCh37_chr16:47920785-47921984 [Gene]
  • LOC126862336:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:47767625-47768824 [Gene]
  • LOC126862340:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:48997204-48998403 [Gene]
  • LOC126862341:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:49681934-49683133 [Gene]
  • LOC126862343:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:50353005-50354204 [Gene]
  • LOC126862344:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:50430839-50432038 [Gene]
  • LOC126862345:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:51426797-51427996 [Gene]
  • CNEP1R1:CTD nuclear envelope phosphatase 1 regulatory subunit 1 [Gene - OMIM - HGNC]
  • CYLD-AS1:CYLD antisense RNA 1 [Gene - HGNC]
  • CYLD-AS2:CYLD antisense RNA 2 [Gene - HGNC]
  • CYLD:CYLD lysine 63 deubiquitinase [Gene - OMIM - HGNC]
  • DNAJA2-DT:DNAJA2 divergent transcript [Gene - HGNC]
  • DNAJA2:DnaJ heat shock protein family (Hsp40) member A2 [Gene - OMIM - HGNC]
  • HEATR3:HEAT repeat containing 3 [Gene - OMIM - HGNC]
  • HEATR3-AS1:HEATR3 antisense RNA 1 [Gene - HGNC]
  • ITFG1-AS1:ITFG1 antisense RNA 1 [Gene - HGNC]
  • LOC126862342:MED14-independent group 3 enhancer GRCh37_chr16:50347343-50348542 [Gene]
  • LOC126862348:MED14-independent group 3 enhancer GRCh37_chr16:52331523-52332722 [Gene]
  • LOC129390785:MPRA-validated peak2574 silencer [Gene]
  • LOC129390786:MPRA-validated peak2576 silencer [Gene]
  • LOC129390787:MPRA-validated peak2577 silencer [Gene]
  • LOC129390788:MPRA-validated peak2581 silencer [Gene]
  • LOC129390789:MPRA-validated peak2585 silencer [Gene]
  • LOC129390790:MPRA-validated peak2586 silencer [Gene]
  • LOC129390791:MPRA-validated peak2587 silencer [Gene]
  • LOC129390792:MPRA-validated peak2588 silencer [Gene]
  • LOC129390793:MPRA-validated peak2589 silencer [Gene]
  • LOC129390794:MPRA-validated peak2593 silencer [Gene]
  • N4BP1:NEDD4 binding protein 1 [Gene - OMIM - HGNC]
  • NKD1:NKD inhibitor of WNT signaling pathway 1 [Gene - OMIM - HGNC]
  • LOC132090379:Neanderthal introgressed variant-containing enhancer experimental_43383 [Gene]
  • LOC132090380:Neanderthal introgressed variant-containing enhancer experimental_43384 [Gene]
  • LOC126862338:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:48156892-48158091 [Gene]
  • LOC126862339:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:48191888-48193087 [Gene]
  • LOC126862346:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:51611051-51612250 [Gene]
  • LOC126862347:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:51654939-51656138 [Gene]
  • SHCBP1:SHC binding and spindle associated 1 [Gene - OMIM - HGNC]
  • LOC121587544:Sharpr-MPRA regulatory region 10353 [Gene]
  • LOC112449713:Sharpr-MPRA regulatory region 10524 [Gene]
  • LOC125177307:Sharpr-MPRA regulatory region 11329 [Gene]
  • LOC112449712:Sharpr-MPRA regulatory region 12922 [Gene]
  • LOC125177309:Sharpr-MPRA regulatory region 1297 [Gene]
  • LOC113939954:Sharpr-MPRA regulatory region 13482 [Gene]
  • LOC112449714:Sharpr-MPRA regulatory region 13528 [Gene]
  • LOC125177308:Sharpr-MPRA regulatory region 14141 [Gene]
  • LOC125177305:Sharpr-MPRA regulatory region 14159 [Gene]
  • LOC112449709:Sharpr-MPRA regulatory region 14543 [Gene]
  • LOC113939953:Sharpr-MPRA regulatory region 1482 [Gene]
  • LOC125177304:Sharpr-MPRA regulatory region 15629 [Gene]
  • LOC113939952:Sharpr-MPRA regulatory region 1667 [Gene]
  • LOC121847987:Sharpr-MPRA regulatory region 2137 [Gene]
  • LOC125146444:Sharpr-MPRA regulatory region 3115 [Gene]
  • LOC121587545:Sharpr-MPRA regulatory region 4020 [Gene]
  • LOC112449715:Sharpr-MPRA regulatory region 4070 [Gene]
  • LOC125177306:Sharpr-MPRA regulatory region 8986 [Gene]
  • LOC125177302:Sharpr-MPRA regulatory region 9701 [Gene]
  • LOC110120823:VISTA enhancer hs101 [Gene]
  • LOC110120826:VISTA enhancer hs124 [Gene]
  • LOC110120836:VISTA enhancer hs152 [Gene]
  • LOC110120841:VISTA enhancer hs162 [Gene]
  • LOC110120912:VISTA enhancer hs625 [Gene]
  • LOC110120582:VISTA enhancer hs65 [Gene]
  • LOC110120583:VISTA enhancer hs71 [Gene]
  • LOC110120584:VISTA enhancer hs72 [Gene]
  • LOC110120585:VISTA enhancer hs73 [Gene]
  • LOC110120586:VISTA enhancer hs74 [Gene]
  • LOC110120587:VISTA enhancer hs76 [Gene]
  • LOC110120588:VISTA enhancer hs79 [Gene]
  • LOC110120939:VISTA enhancer hs848 [Gene]
  • VPS35:VPS35 retromer complex component [Gene - OMIM - HGNC]
  • ADCY7:adenylate cyclase 7 [Gene - OMIM - HGNC]
  • BRD7:bromodomain containing 7 [Gene - OMIM - HGNC]
  • CASC22:cancer susceptibility 22 [Gene - HGNC]
  • CBLN1:cerebellin 1 precursor [Gene - OMIM - HGNC]
  • C16orf78:chromosome 16 open reading frame 78 [Gene - HGNC]
  • C16orf87:chromosome 16 open reading frame 87 [Gene - HGNC]
  • GPT2:glutamic--pyruvic transaminase 2 [Gene - OMIM - HGNC]
  • HNRNPA1L3:heterogeneous nuclear ribonucleoprotein A1 like 3 [Gene - HGNC]
  • ITFG1:integrin alpha FG-GAP repeat containing 1 [Gene - OMIM - HGNC]
  • LONP2:lon peptidase 2, peroxisomal [Gene - OMIM - HGNC]
  • LINC01571:long intergenic non-protein coding RNA 1571 [Gene - HGNC]
  • LINC02127:long intergenic non-protein coding RNA 2127 [Gene - HGNC]
  • LINC02128:long intergenic non-protein coding RNA 2128 [Gene - HGNC]
  • LINC02133:long intergenic non-protein coding RNA 2133 [Gene - HGNC]
  • LINC02134:long intergenic non-protein coding RNA 2134 [Gene - HGNC]
  • LINC02168:long intergenic non-protein coding RNA 2168 [Gene - HGNC]
  • LINC02178:long intergenic non-protein coding RNA 2178 [Gene - HGNC]
  • LINC02179:long intergenic non-protein coding RNA 2179 [Gene - HGNC]
  • LINC02180:long intergenic non-protein coding RNA 2180 [Gene - HGNC]
  • LINC02192:long intergenic non-protein coding RNA 2192 [Gene - HGNC]
  • LINC02911:long intergenic non-protein coding RNA 2911 [Gene - HGNC]
  • LINC00919:long intergenic non-protein coding RNA 919 [Gene - HGNC]
  • MIR3181:microRNA 3181 [Gene - HGNC]
  • MIR6771:microRNA 6771 [Gene - HGNC]
  • MYLK3:myosin light chain kinase 3 [Gene - OMIM - HGNC]
  • NETO2:neuropilin and tolloid like 2 [Gene - OMIM - HGNC]
  • NOD2:nucleotide binding oligomerization domain containing 2 [Gene - OMIM - HGNC]
  • ORC6:origin recognition complex subunit 6 [Gene - OMIM - HGNC]
  • PHKB:phosphorylase kinase regulatory subunit beta [Gene - OMIM - HGNC]
  • SIAH1:siah E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]
  • SNORD148:small nucleolar RNA, C/D box 148 [Gene - HGNC]
  • SNX20:sorting nexin 20 [Gene - OMIM - HGNC]
  • SALL1:spalt like transcription factor 1 [Gene - OMIM - HGNC]
  • TENT4B:terminal nucleotidyltransferase 4B [Gene - OMIM - HGNC]
  • LOC101927272:uncharacterized LOC101927272 [Gene]
  • LOC105371240:uncharacterized LOC105371240 [Gene]
  • ZNF423:zinc finger protein 423 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
16q11.2-12.1
Genomic location:
Preferred name:
GRCh38/hg38 16q11.2-12.1(chr16:46471520-52405956)x1
HGVS:
  • NC_000016.10:g.(?_46471520)_(52405956_?)del
  • NC_000016.8:g.(?_45062933)_(50997369_?)del
  • NC_000016.9:g.(?_46505432)_(52439868_?)del
Links:
dbVar: nssv577552; dbVar: nsv532009
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
SCV000080686GeneDx
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, SCV000080686.5

#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