U.S. flag

An official website of the United States government

GRCh37/hg19 16p13.3(chr16:513767-5555136)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 2, 2024
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:
RCV004819313.1

Allele description [Variation Report for GRCh37/hg19 16p13.3(chr16:513767-5555136)x3]

GRCh37/hg19 16p13.3(chr16:513767-5555136)x3

Genes:
  • PDPK1:3-phosphoinositide dependent protein kinase 1 [Gene - OMIM - HGNC]
  • ALG1:ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase [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]
  • CORO7-PAM16:CORO7-PAM16 readthrough [Gene - HGNC]
  • CREBBP:CREB binding protein [Gene - OMIM - HGNC]
  • DNAJA3:DnaJ heat shock protein family (Hsp40) member A3 [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 - OMIM - HGNC]
  • GNG13:G protein subunit gamma 13 [Gene - OMIM - HGNC]
  • GLIS2:GLIS family zinc finger 2 [Gene - OMIM - HGNC]
  • JPT2:Jupiter microtubule associated homolog 2 [Gene - OMIM - HGNC]
  • MCRIP2:MAPK regulated corepressor interacting protein 2 [Gene - HGNC]
  • MEFV:MEFV innate immunity regulator, pyrin [Gene - OMIM - HGNC]
  • MTRNR2L4:MT-RNR2 like 4 [Gene - HGNC]
  • MLST8:MTOR associated protein, LST8 homolog [Gene - OMIM - HGNC]
  • GNPTG:N-acetylglucosamine-1-phosphate transferase subunit gamma [Gene - OMIM - HGNC]
  • NAGPA:N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [Gene - OMIM - HGNC]
  • NAA60:N-alpha-acetyltransferase 60, NatF catalytic subunit [Gene - OMIM - HGNC]
  • NDUFB10:NADH:ubiquinone oxidoreductase subunit B10 [Gene - OMIM - HGNC]
  • NOXO1:NADPH oxidase organizer 1 [Gene - OMIM - HGNC]
  • NHERF2:NHERF family PDZ scaffold protein 2 [Gene - OMIM - HGNC]
  • NHLRC4:NHL repeat containing 4 [Gene - HGNC]
  • NLRC3:NLR family CARD domain containing 3 [Gene - OMIM - HGNC]
  • NME3:NME/NM23 nucleoside diphosphate kinase 3 [Gene - OMIM - HGNC]
  • NUBP2:NUBP iron-sulfur cluster assembly factor 2, cytosolic [Gene - OMIM - HGNC]
  • NMRAL1:NmrA like redox sensor 1 [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 - OMIM - HGNC]
  • RNPS1:RNA binding protein with serine rich domain 1 [Gene - OMIM - HGNC]
  • RPUSD1:RNA pseudouridine synthase domain containing 1 [Gene - HGNC]
  • SEC14L5:SEC14 like lipid binding 5 [Gene - OMIM - HGNC]
  • SLX4:SLX4 structure-specific endonuclease subunit [Gene - OMIM - HGNC]
  • SOX8:SRY-box transcription factor 8 [Gene - OMIM - 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 subunit 6 [Gene - OMIM - HGNC]
  • TRAF7:TNF receptor associated factor 7 [Gene - OMIM - HGNC]
  • TRAP1:TNF receptor associated protein 1 [Gene - OMIM - HGNC]
  • TNFRSF12A:TNF receptor superfamily member 12A [Gene - OMIM - HGNC]
  • TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
  • TSR3:TSR3 ribosome maturation factor [Gene - OMIM - HGNC]
  • UBALD1:UBA like domain containing 1 [Gene - HGNC]
  • WFIKKN1:WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 [Gene - OMIM - HGNC]
  • WDR24:WD repeat domain 24 [Gene - OMIM - HGNC]
  • WDR90:WD repeat domain 90 [Gene - OMIM - HGNC]
  • ANTKMT:adenine nucleotide translocase lysine methyltransferase [Gene - OMIM - HGNC]
  • ADCY9:adenylate cyclase 9 [Gene - OMIM - HGNC]
  • AMDHD2:amidohydrolase domain containing 2 [Gene - OMIM - HGNC]
  • ANKS3:ankyrin repeat and sterile alpha motif domain containing 3 [Gene - OMIM - HGNC]
  • CACNA1H:calcium voltage-gated channel subunit alpha1 H [Gene - OMIM - HGNC]
  • CAPN15:calpain 15 [Gene - OMIM - HGNC]
  • CDIP1:cell death inducing p53 target 1 [Gene - OMIM - HGNC]
  • CEMP1:cementum protein 1 [Gene - OMIM - HGNC]
  • CLCN7:chloride voltage-gated channel 7 [Gene - OMIM - HGNC]
  • C16orf89:chromosome 16 open reading frame 89 [Gene - HGNC]
  • C16orf90:chromosome 16 open reading frame 90 [Gene - HGNC]
  • C16orf96:chromosome 16 open reading frame 96 [Gene - HGNC]
  • CHTF18:chromosome transmission fidelity factor 18 [Gene - OMIM - HGNC]
  • CLDN6:claudin 6 [Gene - OMIM - HGNC]
  • CLDN9:claudin 9 [Gene - OMIM - HGNC]
  • CLUAP1:clusterin associated protein 1 [Gene - OMIM - HGNC]
  • CCDC154:coiled-coil domain containing 154 [Gene - OMIM - HGNC]
  • CCDC78:coiled-coil domain containing 78 [Gene - OMIM - HGNC]
  • CORO7:coronin 7 [Gene - OMIM - HGNC]
  • CRAMP1:cramped chromatin regulator homolog 1 [Gene - HGNC]
  • CCNF:cyclin F [Gene - OMIM - HGNC]
  • CIAO3:cytosolic iron-sulfur assembly component 3 [Gene - OMIM - HGNC]
  • DNASE1L2:deoxyribonuclease 1 like 2 [Gene - OMIM - HGNC]
  • DNASE1:deoxyribonuclease 1 [Gene - OMIM - HGNC]
  • DNAAF8:dynein axonemal assembly factor 8 [Gene - HGNC]
  • ELOB:elongin B [Gene - OMIM - HGNC]
  • ECI1:enoyl-CoA delta isomerase 1 [Gene - OMIM - HGNC]
  • EME2:essential meiotic structure-specific endonuclease subunit 2 [Gene - OMIM - HGNC]
  • EEF2KMT:eukaryotic elongation factor 2 lysine methyltransferase [Gene - OMIM - HGNC]
  • FAHD1:fumarylacetoacetate hydrolase domain containing 1 [Gene - OMIM - HGNC]
  • GLYR1:glyoxylate reductase 1 homolog [Gene - OMIM - HGNC]
  • GFER:growth factor, augmenter of liver regeneration [Gene - OMIM - HGNC]
  • HMOX2:heme oxygenase 2 [Gene - OMIM - HGNC]
  • HS3ST6:heparan sulfate-glucosamine 3-sulfotransferase 6 [Gene - OMIM - HGNC]
  • HCFC1R1:host cell factor C1 regulator 1 [Gene - OMIM - 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]
  • MGRN1:mahogunin ring finger 1 [Gene - OMIM - HGNC]
  • MMP25:matrix metallopeptidase 25 [Gene - OMIM - HGNC]
  • MEIOB:meiosis specific with OB-fold [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]
  • 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]
  • NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
  • NUDT16L1:nudix hydrolase 16 like 1 [Gene - OMIM - HGNC]
  • OR1F1:olfactory receptor family 1 subfamily F member 1 [Gene - OMIM - HGNC]
  • OR2C1:olfactory receptor family 2 subfamily C member 1 [Gene - HGNC]
  • PTX4:pentraxin 4 [Gene - OMIM - HGNC]
  • PPL:periplakin [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]
  • PAM16:presequence translocase associated motor 16 [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]
  • PKMYT1:protein kinase, membrane associated tyrosine/threonine 1 [Gene - OMIM - HGNC]
  • RHOT2:ras homolog family member T2 [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]
  • ROGDI:rogdi atypical leucine zipper [Gene - OMIM - HGNC]
  • SRL:sarcalumenin [Gene - OMIM - HGNC]
  • SEPTIN12:septin 12 [Gene - OMIM - 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]
  • SMIM22:small integral membrane protein 22 [Gene - HGNC]
  • SNHG9:small nucleolar RNA host gene 9 [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]
  • TIGD7:tigger transposable element derived 7 [Gene - OMIM - HGNC]
  • TFAP4:transcription factor AP-4 [Gene - OMIM - HGNC]
  • TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
  • TMEM204:transmembrane protein 204 [Gene - OMIM - HGNC]
  • TPSAB1:tryptase alpha/beta 1 [Gene - OMIM - HGNC]
  • TPSB2:tryptase beta 2 [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]
  • UBN1:ubinuclein 1 [Gene - OMIM - HGNC]
  • UQCC4:ubiquinol-cytochrome c reductase complex assembly factor 4 [Gene - OMIM - HGNC]
  • UBE2I:ubiquitin conjugating enzyme E2 I [Gene - OMIM - HGNC]
  • UNKL:unk like zinc finger [Gene - OMIM - HGNC]
  • VASN:vasorin [Gene - OMIM - HGNC]
  • ZSCAN10:zinc finger and SCAN domain containing 10 [Gene - OMIM - HGNC]
  • ZSCAN32:zinc finger and SCAN domain containing 32 [Gene - HGNC]
  • ZNF174:zinc finger protein 174 [Gene - OMIM - HGNC]
  • ZNF200:zinc finger protein 200 [Gene - OMIM - HGNC]
  • ZNF205:zinc finger protein 205 [Gene - OMIM - HGNC]
  • ZNF213:zinc finger protein 213 [Gene - OMIM - HGNC]
  • ZNF263:zinc finger protein 263 [Gene - OMIM - HGNC]
  • ZNF500:zinc finger protein 500 [Gene - HGNC]
  • ZNF597:zinc finger protein 597 [Gene - OMIM - HGNC]
  • ZNF598:zinc finger protein 598, E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • ZNF75A:zinc finger protein 75A [Gene - OMIM - HGNC]
  • ZG16B:zymogen granule protein 16B [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
16p13.3
Genomic location:
Chr16: 513767 - 5555136 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 16p13.3(chr16:513767-5555136)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
    Identifiers:
    MedGen: C3661900

    Recent activity

    Clear Turn Off Turn On

    Your browsing activity is empty.

    Activity recording is turned off.

    Turn recording back on

    See more...

    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV005439913Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Feb 2, 2024)     		unknownclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

    Citations

    PubMed

    Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

    Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

    Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV005439913.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (1)

    Description

    This gain involves at least 150 protein coding genes and overlaps the 16p13.3 duplication syndromic region (OMIM 613458); Socha 2023, Chen 2012, Demeer 2013, Lee 2016, Li 2013, Mattina 2012, Thienpont 2010, Ghasemi 2016, Westland 2015, Digilio 2009). Thus, based on gene content and current medical literature, this copy number variant (CNV) is classified as pathogenic. References: Demeer et al., Eur J Med Genet. 2013 Jan;56(1):26-31. PMID: 23063576; Digilio et al., Eur J Hum Genet. 2009 Sep;17(9):1135-40. PMID: 19293839; Ghasemi Firouzabadi et al., Int J Mol Cell Med. 2016 Fall;5(4):236-245. PMID: 28357200; Lee et al., Eur J Med Genet. 2016 Apr;59(4):210-4. PMID: 26873618; Li et al., Gene. 2013 Dec 1;531(2):502-5. PMID: 24035902; Mattina et al., Eur J Med Genet. 2012 Dec;55(12):747-52. PMID: 23032921; Socha et al., J Appl Genet. 2023 Feb;64(1):125-134. PMID: 36586055; Thienpont et al., J Med Genet. 2010 Mar;47(3):155-61. PMID: 19833603; Westland et al., Kidney Int. 2015 Dec;88(6):1402-1410. PMID: 26352300

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

    Last Updated: Jan 4, 2025