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GRCh38/hg38 16p12.1-11.2(chr16:28456967-30295107)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:
RCV000052520.7

Allele description [Variation Report for GRCh38/hg38 16p12.1-11.2(chr16:28456967-30295107)x1]

GRCh38/hg38 16p12.1-11.2(chr16:28456967-30295107)x1

Genes:
  • LOC130058728:ATAC-STARR-seq lymphoblastoid active region 10641 [Gene]
  • LOC130058729:ATAC-STARR-seq lymphoblastoid active region 10642 [Gene]
  • LOC130058731:ATAC-STARR-seq lymphoblastoid active region 10643 [Gene]
  • LOC130058735:ATAC-STARR-seq lymphoblastoid active region 10645 [Gene]
  • LOC130058736:ATAC-STARR-seq lymphoblastoid active region 10646 [Gene]
  • LOC130058738:ATAC-STARR-seq lymphoblastoid active region 10648 [Gene]
  • LOC130058739:ATAC-STARR-seq lymphoblastoid active region 10649 [Gene]
  • LOC130058742:ATAC-STARR-seq lymphoblastoid active region 10650 [Gene]
  • LOC130058743:ATAC-STARR-seq lymphoblastoid active region 10651 [Gene]
  • LOC130058746:ATAC-STARR-seq lymphoblastoid active region 10652 [Gene]
  • LOC130058747:ATAC-STARR-seq lymphoblastoid active region 10653 [Gene]
  • LOC130058748:ATAC-STARR-seq lymphoblastoid active region 10654 [Gene]
  • LOC130058754:ATAC-STARR-seq lymphoblastoid active region 10655 [Gene]
  • LOC130058755:ATAC-STARR-seq lymphoblastoid active region 10656 [Gene]
  • LOC130058757:ATAC-STARR-seq lymphoblastoid active region 10657 [Gene]
  • LOC130058760:ATAC-STARR-seq lymphoblastoid active region 10658 [Gene]
  • LOC130058761:ATAC-STARR-seq lymphoblastoid active region 10659 [Gene]
  • LOC130058762:ATAC-STARR-seq lymphoblastoid active region 10660 [Gene]
  • LOC130058763:ATAC-STARR-seq lymphoblastoid active region 10661 [Gene]
  • LOC130058764:ATAC-STARR-seq lymphoblastoid active region 10662 [Gene]
  • LOC130058765:ATAC-STARR-seq lymphoblastoid active region 10663 [Gene]
  • LOC130058766:ATAC-STARR-seq lymphoblastoid active region 10664 [Gene]
  • LOC130058769:ATAC-STARR-seq lymphoblastoid active region 10665 [Gene]
  • LOC130058770:ATAC-STARR-seq lymphoblastoid active region 10667 [Gene]
  • LOC130058772:ATAC-STARR-seq lymphoblastoid active region 10668 [Gene]
  • LOC130058773:ATAC-STARR-seq lymphoblastoid active region 10669 [Gene]
  • LOC130058774:ATAC-STARR-seq lymphoblastoid active region 10670 [Gene]
  • LOC130058775:ATAC-STARR-seq lymphoblastoid active region 10671 [Gene]
  • LOC130058777:ATAC-STARR-seq lymphoblastoid active region 10672 [Gene]
  • LOC130058778:ATAC-STARR-seq lymphoblastoid active region 10673 [Gene]
  • LOC130058780:ATAC-STARR-seq lymphoblastoid active region 10674 [Gene]
  • LOC130058781:ATAC-STARR-seq lymphoblastoid active region 10675 [Gene]
  • LOC130058783:ATAC-STARR-seq lymphoblastoid active region 10676 [Gene]
  • LOC130058787:ATAC-STARR-seq lymphoblastoid active region 10677 [Gene]
  • LOC130058790:ATAC-STARR-seq lymphoblastoid active region 10679 [Gene]
  • LOC130058792:ATAC-STARR-seq lymphoblastoid active region 10680 [Gene]
  • LOC130058793:ATAC-STARR-seq lymphoblastoid active region 10682 [Gene]
  • LOC130058794:ATAC-STARR-seq lymphoblastoid active region 10683 [Gene]
  • LOC130058799:ATAC-STARR-seq lymphoblastoid active region 10684 [Gene]
  • LOC130058802:ATAC-STARR-seq lymphoblastoid active region 10686 [Gene]
  • LOC130058803:ATAC-STARR-seq lymphoblastoid active region 10687 [Gene]
  • LOC130058808:ATAC-STARR-seq lymphoblastoid active region 10688 [Gene]
  • LOC130058810:ATAC-STARR-seq lymphoblastoid active region 10689 [Gene]
  • LOC130058812:ATAC-STARR-seq lymphoblastoid active region 10690 [Gene]
  • LOC130058814:ATAC-STARR-seq lymphoblastoid active region 10691 [Gene]
  • LOC130058815:ATAC-STARR-seq lymphoblastoid active region 10692 [Gene]
  • LOC130058816:ATAC-STARR-seq lymphoblastoid active region 10693 [Gene]
  • LOC130058819:ATAC-STARR-seq lymphoblastoid active region 10695 [Gene]
  • LOC130058726:ATAC-STARR-seq lymphoblastoid silent region 7308 [Gene]
  • LOC130058727:ATAC-STARR-seq lymphoblastoid silent region 7309 [Gene]
  • LOC130058730:ATAC-STARR-seq lymphoblastoid silent region 7310 [Gene]
  • LOC130058732:ATAC-STARR-seq lymphoblastoid silent region 7311 [Gene]
  • LOC130058733:ATAC-STARR-seq lymphoblastoid silent region 7312 [Gene]
  • LOC130058734:ATAC-STARR-seq lymphoblastoid silent region 7313 [Gene]
  • LOC130058737:ATAC-STARR-seq lymphoblastoid silent region 7314 [Gene]
  • LOC130058740:ATAC-STARR-seq lymphoblastoid silent region 7315 [Gene]
  • LOC130058741:ATAC-STARR-seq lymphoblastoid silent region 7316 [Gene]
  • LOC130058744:ATAC-STARR-seq lymphoblastoid silent region 7317 [Gene]
  • LOC130058745:ATAC-STARR-seq lymphoblastoid silent region 7318 [Gene]
  • LOC130058749:ATAC-STARR-seq lymphoblastoid silent region 7321 [Gene]
  • LOC130058750:ATAC-STARR-seq lymphoblastoid silent region 7322 [Gene]
  • LOC130058751:ATAC-STARR-seq lymphoblastoid silent region 7323 [Gene]
  • LOC130058752:ATAC-STARR-seq lymphoblastoid silent region 7324 [Gene]
  • LOC130058753:ATAC-STARR-seq lymphoblastoid silent region 7325 [Gene]
  • LOC130058756:ATAC-STARR-seq lymphoblastoid silent region 7326 [Gene]
  • LOC130058758:ATAC-STARR-seq lymphoblastoid silent region 7327 [Gene]
  • LOC130058759:ATAC-STARR-seq lymphoblastoid silent region 7328 [Gene]
  • LOC130058767:ATAC-STARR-seq lymphoblastoid silent region 7329 [Gene]
  • LOC130058768:ATAC-STARR-seq lymphoblastoid silent region 7330 [Gene]
  • LOC130058771:ATAC-STARR-seq lymphoblastoid silent region 7331 [Gene]
  • LOC130058776:ATAC-STARR-seq lymphoblastoid silent region 7332 [Gene]
  • LOC130058779:ATAC-STARR-seq lymphoblastoid silent region 7333 [Gene]
  • LOC130058782:ATAC-STARR-seq lymphoblastoid silent region 7334 [Gene]
  • LOC130058784:ATAC-STARR-seq lymphoblastoid silent region 7335 [Gene]
  • LOC130058785:ATAC-STARR-seq lymphoblastoid silent region 7336 [Gene]
  • LOC130058786:ATAC-STARR-seq lymphoblastoid silent region 7337 [Gene]
  • LOC130058788:ATAC-STARR-seq lymphoblastoid silent region 7338 [Gene]
  • LOC130058789:ATAC-STARR-seq lymphoblastoid silent region 7339 [Gene]
  • LOC130058791:ATAC-STARR-seq lymphoblastoid silent region 7340 [Gene]
  • LOC130058795:ATAC-STARR-seq lymphoblastoid silent region 7341 [Gene]
  • LOC130058796:ATAC-STARR-seq lymphoblastoid silent region 7342 [Gene]
  • LOC130058797:ATAC-STARR-seq lymphoblastoid silent region 7343 [Gene]
  • LOC130058798:ATAC-STARR-seq lymphoblastoid silent region 7344 [Gene]
  • LOC130058800:ATAC-STARR-seq lymphoblastoid silent region 7345 [Gene]
  • LOC130058801:ATAC-STARR-seq lymphoblastoid silent region 7346 [Gene]
  • LOC130058804:ATAC-STARR-seq lymphoblastoid silent region 7347 [Gene]
  • LOC130058805:ATAC-STARR-seq lymphoblastoid silent region 7348 [Gene]
  • LOC130058806:ATAC-STARR-seq lymphoblastoid silent region 7349 [Gene]
  • LOC130058807:ATAC-STARR-seq lymphoblastoid silent region 7350 [Gene]
  • LOC130058809:ATAC-STARR-seq lymphoblastoid silent region 7351 [Gene]
  • LOC130058811:ATAC-STARR-seq lymphoblastoid silent region 7352 [Gene]
  • LOC130058813:ATAC-STARR-seq lymphoblastoid silent region 7356 [Gene]
  • LOC130058817:ATAC-STARR-seq lymphoblastoid silent region 7357 [Gene]
  • LOC130058818:ATAC-STARR-seq lymphoblastoid silent region 7358 [Gene]
  • ATP2A1-AS1:ATP2A1 antisense RNA 1 [Gene - HGNC]
  • ATP2A1:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Gene - OMIM - HGNC]
  • BOLA2-SMG1P6:BOLA2-SMG1P6 readthrough [Gene - HGNC]
  • CD19:CD19 molecule [Gene - OMIM - HGNC]
  • CDIPTOSP:CDIP transferase opposite strand, pseudogene [Gene - HGNC]
  • CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
  • CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]
  • CORO1A-AS1:CORO1A antisense RNA 1 [Gene - HGNC]
  • LOC116276452:CRISPRi-validated cis-regulatory element chr16.2261 [Gene]
  • HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
  • INO80E:INO80 complex subunit E [Gene - HGNC]
  • LOC126862326:MED14-independent group 3 enhancer GRCh37_chr16:28549089-28550288 [Gene]
  • LOC129390780:MPRA-validated peak2552 silencer [Gene]
  • LOC129390781:MPRA-validated peak2553 silencer [Gene]
  • LOC129390782:MPRA-validated peak2554 silencer [Gene]
  • LOC129390783:MPRA-validated peak2562 silencer [Gene]
  • MVP-DT:MVP divergent transcript [Gene - HGNC]
  • MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
  • NFATC2IP-AS1:NFATC2IP antisense RNA 1 [Gene - HGNC]
  • LOC126862327:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:29166386-29167585 [Gene]
  • LOC126862328:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:29196056-29197255 [Gene]
  • PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
  • LOC108281183:RRN3P2-SNX29P2 intergenic nontranscribed DNase I hypersensitive site-defined enhancer [Gene]
  • SGF29:SAGA complex associated factor 29 [Gene - OMIM - HGNC]
  • SH2B1:SH2B adaptor protein 1 [Gene - OMIM - HGNC]
  • SLX1A:SLX1 homolog A, structure-specific endonuclease subunit [Gene - OMIM - HGNC]
  • SLX1B:SLX1 homolog B, structure-specific endonuclease subunit [Gene - OMIM - HGNC]
  • SLX1A-SULT1A3:SLX1A-SULT1A3 readthrough (NMD candidate) [Gene - HGNC]
  • SLX1B-SULT1A4:SLX1B-SULT1A4 readthrough (NMD candidate) [Gene - HGNC]
  • SPNS1:SPNS lysolipid transporter 1, lysophospholipid [Gene - OMIM - HGNC]
  • LOC125146440:Sharpr-MPRA regulatory region 10200 [Gene]
  • LOC125146439:Sharpr-MPRA regulatory region 12104 [Gene]
  • LOC112352679:Sharpr-MPRA regulatory region 12377 [Gene]
  • LOC121847977:Sharpr-MPRA regulatory region 13449 [Gene]
  • LOC121847976:Sharpr-MPRA regulatory region 1439 [Gene]
  • LOC112340393:Sharpr-MPRA regulatory region 4004 [Gene]
  • LOC125146437:Sharpr-MPRA regulatory region 414 [Gene]
  • LOC112340392:Sharpr-MPRA regulatory region 4245 [Gene]
  • LOC112352680:Sharpr-MPRA regulatory region 6067 [Gene]
  • LOC121587541:Sharpr-MPRA regulatory region 7413 [Gene]
  • LOC121587540:Sharpr-MPRA regulatory region 8247 [Gene]
  • LOC125146438:Sharpr-MPRA regulatory region 8859 [Gene]
  • LOC125146441:Sharpr-MPRA regulatory region 9068 [Gene]
  • TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
  • TAOK2:TAO kinase 2 [Gene - OMIM - HGNC]
  • TLCD3B:TLC domain containing 3B [Gene - OMIM - HGNC]
  • TUFM:Tu translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
  • YPEL3-DT:YPEL3 divergent transcript [Gene - HGNC]
  • ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
  • APOBR:apolipoprotein B receptor [Gene - OMIM - HGNC]
  • ASPHD1:aspartate beta-hydroxylase domain containing 1 [Gene - HGNC]
  • ATXN2L:ataxin 2 like [Gene - OMIM - HGNC]
  • BOLA2:bolA family member 2 [Gene - OMIM - HGNC]
  • BOLA2B:bolA family member 2B [Gene - HGNC]
  • C16orf54:chromosome 16 open reading frame 54 [Gene - HGNC]
  • C16orf92:chromosome 16 open reading frame 92 [Gene - OMIM - HGNC]
  • CORO1A:coronin 1A [Gene - OMIM - HGNC]
  • DOC2A:double C2 domain alpha [Gene - OMIM - HGNC]
  • EIF3C:eukaryotic translation initiation factor 3 subunit C [Gene - OMIM - HGNC]
  • GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
  • IL27:interleukin 27 [Gene - OMIM - HGNC]
  • KIF22:kinesin family member 22 [Gene - OMIM - HGNC]
  • LAT:linker for activation of T cells [Gene - OMIM - HGNC]
  • MVP:major vault protein [Gene - OMIM - HGNC]
  • MIR3680-2:microRNA 3680-2 [Gene - HGNC]
  • MIR4517:microRNA 4517 [Gene - HGNC]
  • MIR4721:microRNA 4721 [Gene - HGNC]
  • MIR6862-2:microRNA 6862-2 [Gene - HGNC]
  • MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
  • NFATC2IP:nuclear factor of activated T cells 2 interacting protein [Gene - OMIM - HGNC]
  • NPIPB11:nuclear pore complex interacting protein family member B11 [Gene - HGNC]
  • NPIPB12:nuclear pore complex interacting protein family member B12 [Gene - HGNC]
  • NPIPB7:nuclear pore complex interacting protein family member B7 [Gene - HGNC]
  • NPIPB8:nuclear pore complex interacting protein family member B8 [Gene - HGNC]
  • NPIPB9:nuclear pore complex interacting protein family member B9 [Gene - HGNC]
  • NPIPB13:nuclear pore complex interacting protein family, member B13 [Gene - HGNC]
  • NUPR1:nuclear protein 1, transcriptional regulator [Gene - OMIM - HGNC]
  • KCTD13:potassium channel tetramerization domain containing 13 [Gene - OMIM - HGNC]
  • PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
  • PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
  • QPRT:quinolinate phosphoribosyltransferase [Gene - OMIM - HGNC]
  • RABEP2:rabaptin, RAB GTPase binding effector protein 2 [Gene - OMIM - HGNC]
  • SEZ6L2:seizure related 6 homolog like 2 [Gene - OMIM - HGNC]
  • SPN:sialophorin [Gene - OMIM - HGNC]
  • SULT1A1:sulfotransferase family 1A member 1 [Gene - OMIM - HGNC]
  • SULT1A2:sulfotransferase family 1A member 2 [Gene - OMIM - HGNC]
  • SULT1A3:sulfotransferase family 1A member 3 [Gene - OMIM - HGNC]
  • SULT1A4:sulfotransferase family 1A member 4 [Gene - OMIM - HGNC]
  • TMEM219:transmembrane protein 219 [Gene - OMIM - HGNC]
  • LOC101928188:uncharacterized LOC101928188 [Gene]
  • LOC102723708:uncharacterized LOC102723708 [Gene]
  • LOC112694756:uncharaterized LOC112694756 [Gene]
  • YPEL3:yippee like 3 [Gene - OMIM - HGNC]
  • ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
16p12.1-11.2
Genomic location:
Preferred name:
GRCh38/hg38 16p12.1-11.2(chr16:28456967-30295107)x1
HGVS:
  • NC_000016.10:g.(?_28456967)_(30295107_?)del
  • NC_000016.8:g.(?_28375789)_(30213929_?)del
  • NC_000016.9:g.(?_28468288)_(30306428_?)del
Links:
dbVar: nssv579796; dbVar: nsv531226
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
SCV000079874GeneDx
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, SCV000079874.5

#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