GRCh38/hg38 16p13.3(chr16:46766-3214623)x3 AND See cases

Clinical significance:Pathogenic (Last evaluated: Aug 12, 2011)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000052370.5

Allele description [Variation Report for GRCh38/hg38 16p13.3(chr16:46766-3214623)x3]

GRCh38/hg38 16p13.3(chr16:46766-3214623)x3

Genes:
  • LOC110596865:16p subtelomeric meiotic recombination hotspot [Gene]
  • DECR2:2,4-dienoyl-CoA reductase 2 [Gene - OMIM - HGNC]
  • PDPK1:3-phosphoinositide dependent protein kinase 1 [Gene - OMIM - HGNC]
  • ABCA3:ATP binding cassette subfamily A member 3 [Gene - OMIM - HGNC]
  • ATP6V0C:ATPase H+ transporting V0 subunit c [Gene - OMIM - HGNC]
  • BAIAP3:BAI1 associated protein 3 [Gene - OMIM - HGNC]
  • BICDL2:BICD family like cargo adaptor 2 [Gene - OMIM - HGNC]
  • BRICD5:BRICHOS domain containing 5 [Gene - HGNC]
  • C1QTNF8:C1q and TNF related 8 [Gene - OMIM - HGNC]
  • CASKIN1:CASK interacting protein 1 [Gene - OMIM - HGNC]
  • E4F1:E4F transcription factor 1 [Gene - OMIM - HGNC]
  • FBXL16:F-box and leucine rich repeat protein 16 [Gene - OMIM - HGNC]
  • FLYWCH2:FLYWCH family member 2 [Gene - HGNC]
  • FLYWCH1:FLYWCH-type zinc finger 1 [Gene - HGNC]
  • GNG13:G protein subunit gamma 13 [Gene - OMIM - HGNC]
  • JPT2:Jupiter microtubule associated homolog 2 [Gene - HGNC]
  • LMF1-AS1:LMF1 antisense RNA 1 [Gene - HGNC]
  • LUC7L:LUC7 like [Gene - OMIM - HGNC]
  • MCRIP2:MAPK regulated corepressor interacting protein 2 [Gene - HGNC]
  • MMP25-AS1:MMP25 antisense RNA 1 [Gene - HGNC]
  • LOC110596863:MS205 minisatellite repeat instability region [Gene]
  • LOC111188163:MSLN promoter region [Gene]
  • MLST8:MTOR associated protein, LST8 homolog [Gene - OMIM - HGNC]
  • GNPTG:N-acetylglucosamine-1-phosphate transferase gamma subunit [Gene - OMIM - HGNC]
  • MPG:N-methylpurine DNA glycosylase [Gene - OMIM - HGNC]
  • NDUFB10:NADH:ubiquinone oxidoreductase subunit B10 [Gene - OMIM - HGNC]
  • NOXO1:NADPH oxidase organizer 1 [Gene - OMIM - HGNC]
  • NHLRC4:NHL repeat containing 4 [Gene - HGNC]
  • NME3:NME/NM23 nucleoside diphosphate kinase 3 [Gene - OMIM - HGNC]
  • NME4:NME/NM23 nucleoside diphosphate kinase 4 [Gene - OMIM - HGNC]
  • NPRL3:NPR3 like, GATOR1 complex subunit [Gene - OMIM - HGNC]
  • RAB11FIP3:RAB11 family interacting protein 3 [Gene - OMIM - HGNC]
  • RAB26:RAB26, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAB40C:RAB40C, member RAS oncogene family [Gene - HGNC]
  • RNPS1:RNA binding protein with serine rich domain 1 [Gene - OMIM - HGNC]
  • POLR3K:RNA polymerase III subunit K [Gene - OMIM - HGNC]
  • RPUSD1:RNA pseudouridylate synthase domain containing 1 [Gene - HGNC]
  • ARHGDIG:Rho GDP dissociation inhibitor gamma [Gene - OMIM - HGNC]
  • SLC9A3R2:SLC9A3 regulator 2 [Gene - OMIM - HGNC]
  • SRRM2-AS1:SRRM2 antisense RNA 1 [Gene - HGNC]
  • SOX8:SRY-box 8 [Gene - OMIM - HGNC]
  • SSTR5-AS1:SSTR5 antisense RNA 1 [Gene - HGNC]
  • STUB1:STIP1 homology and U-box containing protein 1 [Gene - OMIM - HGNC]
  • TBC1D24:TBC1 domain family member 24 [Gene - OMIM - HGNC]
  • THOC6:THO complex 6 [Gene - OMIM - HGNC]
  • TRAF7:TNF receptor associated factor 7 [Gene - OMIM - HGNC]
  • TNFRSF12A:TNF receptor superfamily member 12A [Gene - OMIM - HGNC]
  • TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
  • TSR3:TSR3, acp transferase ribosome maturation factor [Gene - OMIM - HGNC]
  • WFIKKN1:WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 [Gene - OMIM - HGNC]
  • WDR24:WD repeat domain 24 [Gene - HGNC]
  • WDR90:WD repeat domain 90 [Gene - HGNC]
  • ZNF205-AS1:ZNF205 antisense RNA 1 [Gene - HGNC]
  • ZNF213-AS1:ZNF213 antisense RNA 1 (head to head) [Gene - HGNC]
  • HBA-LCR:alpha-globin locus control region [Gene]
  • AMDHD2:amidohydrolase domain containing 2 [Gene - HGNC]
  • AXIN1:axin 1 [Gene - OMIM - HGNC]
  • CACNA1H:calcium voltage-gated channel subunit alpha1 H [Gene - OMIM - HGNC]
  • CAPN15:calpain 15 [Gene - OMIM - HGNC]
  • CEMP1:cementum protein 1 [Gene - OMIM - HGNC]
  • CLCN7:chloride voltage-gated channel 7 [Gene - OMIM - HGNC]
  • C16orf91:chromosome 16 open reading frame 91 [Gene - HGNC]
  • CHTF18:chromosome transmission fidelity factor 18 [Gene - OMIM - HGNC]
  • CLDN6:claudin 6 [Gene - OMIM - HGNC]
  • CLDN9:claudin 9 [Gene - OMIM - HGNC]
  • CCDC154:coiled-coil domain containing 154 [Gene - HGNC]
  • CCDC78:coiled-coil domain containing 78 [Gene - OMIM - HGNC]
  • LOC106783500:conserved acetylation island sequence C01 enhancer [Gene]
  • CRAMP1:cramped chromatin regulator homolog 1 [Gene - HGNC]
  • CCNF:cyclin F [Gene - OMIM - HGNC]
  • DNASE1L2:deoxyribonuclease 1 like 2 [Gene - OMIM - HGNC]
  • ELOB:elongin B [Gene - OMIM - HGNC]
  • ERVK13-1:endogenous retrovirus group K13 member 1 [Gene - HGNC]
  • ECI1:enoyl-CoA delta isomerase 1 [Gene - OMIM - HGNC]
  • EME2:essential meiotic structure-specific endonuclease subunit 2 [Gene - OMIM - HGNC]
  • FAM173A:family with sequence similarity 173 member A [Gene - HGNC]
  • FAM234A:family with sequence similarity 234 member A [Gene - HGNC]
  • FAHD1:fumarylacetoacetate hydrolase domain containing 1 [Gene - OMIM - HGNC]
  • GFER:growth factor, augmenter of liver regeneration [Gene - OMIM - HGNC]
  • LOC106804613:hemoglobin subunit alpha 1 recombination region [Gene]
  • HBA1:hemoglobin subunit alpha 1 [Gene - OMIM - HGNC]
  • LOC106804612:hemoglobin subunit alpha 2 recombination region [Gene]
  • HBA2:hemoglobin subunit alpha 2 [Gene - OMIM - HGNC]
  • HBM:hemoglobin subunit mu [Gene - OMIM - HGNC]
  • HBQ1:hemoglobin subunit theta 1 [Gene - OMIM - HGNC]
  • HBZ:hemoglobin subunit zeta [Gene - OMIM - HGNC]
  • HS3ST6:heparan sulfate-glucosamine 3-sulfotransferase 6 [Gene - HGNC]
  • HCFC1R1:host cell factor C1 regulator 1 [Gene - HGNC]
  • HAGHL:hydroxyacylglutathione hydrolase like [Gene - HGNC]
  • HAGH:hydroxyacylglutathione hydrolase [Gene - OMIM - HGNC]
  • IGFALS:insulin like growth factor binding protein acid labile subunit [Gene - OMIM - HGNC]
  • IL32:interleukin 32 [Gene - OMIM - HGNC]
  • IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]
  • JMJD8:jumonji domain containing 8 [Gene - HGNC]
  • KREMEN2:kringle containing transmembrane protein 2 [Gene - OMIM - HGNC]
  • LMF1:lipase maturation factor 1 [Gene - OMIM - HGNC]
  • LINC02124:long intergenic non-protein coding RNA 2124 [Gene - HGNC]
  • LINC00235:long intergenic non-protein coding RNA 235 [Gene - HGNC]
  • LINC00254:long intergenic non-protein coding RNA 254 [Gene - HGNC]
  • LINC00514:long intergenic non-protein coding RNA 514 [Gene - HGNC]
  • MMP25:matrix metallopeptidase 25 [Gene - OMIM - HGNC]
  • MEIOB:meiosis specific with OB domains [Gene - OMIM - HGNC]
  • MSLN:mesothelin [Gene - OMIM - HGNC]
  • METRN:meteorin, glial cell differentiation regulator [Gene - OMIM - HGNC]
  • MSRB1:methionine sulfoxide reductase B1 [Gene - OMIM - HGNC]
  • METTL26:methyltransferase like 26 [Gene - HGNC]
  • MIR1225:microRNA 1225 [Gene - OMIM - HGNC]
  • MIR3176:microRNA 3176 [Gene - HGNC]
  • MIR3177:microRNA 3177 [Gene - HGNC]
  • MIR3178:microRNA 3178 [Gene - HGNC]
  • MIR3180-5:microRNA 3180-5 [Gene - HGNC]
  • MIR3677:microRNA 3677 [Gene - HGNC]
  • MIR4516:microRNA 4516 [Gene - HGNC]
  • MIR4717:microRNA 4717 [Gene - HGNC]
  • MIR5587:microRNA 5587 [Gene - HGNC]
  • MIR6511B1:microRNA 6511b-1 [Gene - HGNC]
  • MIR662:microRNA 662 [Gene - HGNC]
  • MIR6767:microRNA 6767 [Gene - HGNC]
  • MIR6768:microRNA 6768 [Gene - HGNC]
  • MIR940:microRNA 940 [Gene - HGNC]
  • MRPL28:mitochondrial ribosomal protein L28 [Gene - OMIM - HGNC]
  • MRPS34:mitochondrial ribosomal protein S34 [Gene - OMIM - HGNC]
  • MAPK8IP3:mitogen-activated protein kinase 8 interacting protein 3 [Gene - OMIM - HGNC]
  • NTN3:netrin 3 [Gene - OMIM - HGNC]
  • NPW:neuropeptide W [Gene - OMIM - HGNC]
  • LOC106799915:nonconserved acetylation island sequence 122 enhancer [Gene]
  • NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
  • NARFL:nuclear prelamin A recognition factor like [Gene - OMIM - HGNC]
  • NUBP2:nucleotide binding protein 2 [Gene - OMIM - HGNC]
  • OR1F1:olfactory receptor family 1 subfamily F member 1 [Gene - OMIM - HGNC]
  • PTX4:pentraxin 4 [Gene - OMIM - HGNC]
  • PIGQ:phosphatidylinositol glycan anchor biosynthesis class Q [Gene - OMIM - HGNC]
  • PGP:phosphoglycolate phosphatase [Gene - OMIM - HGNC]
  • PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]
  • KCTD5:potassium channel tetramerization domain containing 5 [Gene - OMIM - HGNC]
  • PAQR4:progestin and adipoQ receptor family member 4 [Gene - OMIM - HGNC]
  • PRR25:proline rich 25 [Gene - HGNC]
  • PRR35:proline rich 35 [Gene - HGNC]
  • PDIA2:protein disulfide isomerase family A member 2 [Gene - OMIM - HGNC]
  • PKMYT1:protein kinase, membrane associated tyrosine/threonine 1 [Gene - OMIM - HGNC]
  • RHOT2:ras homolog family member T2 [Gene - OMIM - HGNC]
  • RGS11:regulator of G protein signaling 11 [Gene - OMIM - HGNC]
  • RHBDF1:rhomboid 5 homolog 1 [Gene - OMIM - HGNC]
  • RHBDL1:rhomboid like 1 [Gene - OMIM - HGNC]
  • RPL3L:ribosomal protein L3 like [Gene - OMIM - HGNC]
  • RPS2:ribosomal protein S2 [Gene - OMIM - HGNC]
  • RNF151:ring finger protein 151 [Gene - HGNC]
  • PRSS21:serine protease 21 [Gene - OMIM - HGNC]
  • PRSS22:serine protease 22 [Gene - OMIM - HGNC]
  • PRSS27:serine protease 27 [Gene - OMIM - HGNC]
  • PRSS33:serine protease 33 [Gene - OMIM - HGNC]
  • PRSS41:serine protease 41 [Gene - HGNC]
  • SRRM2:serine/arginine repetitive matrix 2 [Gene - OMIM - HGNC]
  • SNRNP25:small nuclear ribonucleoprotein U11/U12 subunit 25 [Gene - HGNC]
  • SNHG19:small nucleolar RNA host gene 19 [Gene - HGNC]
  • SNHG9:small nucleolar RNA host gene 9 [Gene - HGNC]
  • SNORD60:small nucleolar RNA, C/D box 60 [Gene - HGNC]
  • SNORA10:small nucleolar RNA, H/ACA box 10 [Gene - HGNC]
  • SNORA3C:small nucleolar RNA, H/ACA box 3C [Gene - HGNC]
  • SNORA64:small nucleolar RNA, H/ACA box 64 [Gene - HGNC]
  • SNORA78:small nucleolar RNA, H/ACA box 78 [Gene - HGNC]
  • SSTR5:somatostatin receptor 5 [Gene - OMIM - HGNC]
  • SPSB3:splA/ryanodine receptor domain and SOCS box containing 3 [Gene - OMIM - HGNC]
  • SYNGR3:synaptogyrin 3 [Gene - OMIM - HGNC]
  • TELO2:telomere maintenance 2 [Gene - OMIM - HGNC]
  • TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
  • TRR-CCG1-3:transfer RNA-Arg (CCG) 1-3 [Gene - HGNC]
  • TRR-CCT3-1:transfer RNA-Arg (CCT) 3-1 [Gene - HGNC]
  • TRR-CCT5-1:transfer RNA-Arg (CCT) 5-1 [Gene - HGNC]
  • TRG-CCC2-2:transfer RNA-Gly (CCC) 2-2 [Gene - HGNC]
  • TRK-CTT2-5:transfer RNA-Lys (CTT) 2-5 [Gene - HGNC]
  • TRK-CTT3-1:transfer RNA-Lys (CTT) 3-1 [Gene - HGNC]
  • TRK-CTT4-1:transfer RNA-Lys (CTT) 4-1 [Gene - HGNC]
  • TRK-CTT5-1:transfer RNA-Lys (CTT) 5-1 [Gene - HGNC]
  • TRP-AGG1-1:transfer RNA-Pro (AGG) 1-1 [Gene - HGNC]
  • TRP-AGG2-7:transfer RNA-Pro (AGG) 2-7 [Gene - HGNC]
  • TRP-AGG2-8:transfer RNA-Pro (AGG) 2-8 [Gene - HGNC]
  • TRP-CGG1-2:transfer RNA-Pro (CGG) 1-2 [Gene - HGNC]
  • TRP-TGG3-3:transfer RNA-Pro (TGG) 3-3 [Gene - HGNC]
  • TRP-TGG3-4:transfer RNA-Pro (TGG) 3-4 [Gene - HGNC]
  • TRP-TGG3-5:transfer RNA-Pro (TGG) 3-5 [Gene - HGNC]
  • TMEM204:transmembrane protein 204 [Gene - OMIM - HGNC]
  • TMEM8A:transmembrane protein 8A [Gene - HGNC]
  • TPSAB1:tryptase alpha/beta 1 [Gene - OMIM - HGNC]
  • TPSB2:tryptase beta 2 (gene/pseudogene) [Gene - OMIM - HGNC]
  • TPSD1:tryptase delta 1 [Gene - OMIM - HGNC]
  • TPSG1:tryptase gamma 1 [Gene - OMIM - HGNC]
  • TEDC2:tubulin epsilon and delta complex 2 [Gene - HGNC]
  • UBE2I:ubiquitin conjugating enzyme E2 I [Gene - OMIM - HGNC]
  • LOC100128770:uncharacterized LOC100128770 [Gene]
  • LOC100134368:uncharacterized LOC100134368 [Gene]
  • LOC100287175:uncharacterized LOC100287175 [Gene]
  • LOC101929613:uncharacterized LOC101929613 [Gene]
  • LOC105371038:uncharacterized LOC105371038 [Gene]
  • LOC105371046:uncharacterized LOC105371046 [Gene]
  • LOC105371049:uncharacterized LOC105371049 [Gene]
  • LOC106660606:uncharacterized LOC106660606 [Gene]
  • FLJ42627:uncharacterized LOC645644 [Gene]
  • LOC729652:uncharacterized LOC729652 [Gene]
  • UNKL:unkempt family like zinc finger [Gene - OMIM - HGNC]
  • ZSCAN10:zinc finger and SCAN domain containing 10 [Gene - HGNC]
  • ZNF205:zinc finger protein 205 [Gene - OMIM - HGNC]
  • ZNF213:zinc finger protein 213 [Gene - OMIM - HGNC]
  • ZNF598:zinc finger protein 598 [Gene - OMIM - HGNC]
  • ZG16B:zymogen granule protein 16B [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
GRCh38/hg38 16p13.3(chr16:46766-3214623)x3
HGVS:
  • NC_000016.10:g.(?_46766)_(3214623_?)dup
  • NC_000016.8:g.(?_36766)_(3204624_?)dup
  • NC_000016.9:g.(?_96766)_(3264623_?)dup
Links:
dbVar: nssv578699; dbVar: nsv531083
Observations:
1

Condition(s)

Name:
See cases [See the Variation display for details]
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000079722GeneDxcriteria provided, single submitter
Pathogenic
(Aug 12, 2011)
de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

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, SCV000079722.5

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

Last Updated: Mar 30, 2018