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GRCh37/hg19 7q33-36.3(chr7:135639005-159119707)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 28, 2022
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:
RCV003482988.1

Allele description [Variation Report for GRCh37/hg19 7q33-36.3(chr7:135639005-159119707)x1]

GRCh37/hg19 7q33-36.3(chr7:135639005-159119707)x1

Genes:
  • HTR5A:5-hydroxytryptamine receptor 5A [Gene - OMIM - HGNC]
  • ABCB8:ATP binding cassette subfamily B member 8 [Gene - OMIM - HGNC]
  • ABCF2:ATP binding cassette subfamily F member 2 [Gene - OMIM - HGNC]
  • ATP6V0A4:ATPase H+ transporting V0 subunit a4 [Gene - OMIM - HGNC]
  • ATP6V0E2:ATPase H+ transporting V0 subunit e2 [Gene - OMIM - HGNC]
  • AGAP3:ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 [Gene - OMIM - HGNC]
  • BRAF:B-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
  • CLEC5A:C-type lectin domain containing 5A [Gene - OMIM - HGNC]
  • CLEC2L:C-type lectin domain family 2 member L [Gene - HGNC]
  • CTAGE15:CTAGE family member 15 [Gene - HGNC]
  • CTAGE4:CTAGE family member 4 [Gene - OMIM - HGNC]
  • CTAGE6:CTAGE family member 6 [Gene - HGNC]
  • CTAGE8:CTAGE family member 8 [Gene - HGNC]
  • DENND11:DENN domain containing 11 [Gene - OMIM - HGNC]
  • DENND2A:DENN domain containing 2A [Gene - OMIM - HGNC]
  • DNAJB6:DnaJ heat shock protein family (Hsp40) member B6 [Gene - OMIM - HGNC]
  • EPHA1:EPH receptor A1 [Gene - OMIM - HGNC]
  • EPHB6:EPH receptor B6 [Gene - OMIM - HGNC]
  • FMC1-LUC7L2:FMC1-LUC7L2 readthrough [Gene - HGNC]
  • FASTK:Fas activated serine/threonine kinase [Gene - OMIM - HGNC]
  • GIMAP1:GTPase, IMAP family member 1 [Gene - OMIM - HGNC]
  • GIMAP2:GTPase, IMAP family member 2 [Gene - OMIM - HGNC]
  • GIMAP4:GTPase, IMAP family member 4 [Gene - OMIM - HGNC]
  • GIMAP5:GTPase, IMAP family member 5 [Gene - OMIM - HGNC]
  • GIMAP6:GTPase, IMAP family member 6 [Gene - OMIM - HGNC]
  • GIMAP7:GTPase, IMAP family member 7 [Gene - OMIM - HGNC]
  • GIMAP8:GTPase, IMAP family member 8 [Gene - OMIM - HGNC]
  • KIAA1549:KIAA1549 [Gene - OMIM - HGNC]
  • KRBA1:KRAB-A domain containing 1 [Gene - HGNC]
  • KEL:Kell metallo-endopeptidase (Kell blood group) [Gene - OMIM - HGNC]
  • LLCFC1:LLLL and CFNLAS motif containing 1 [Gene - OMIM - HGNC]
  • LUC7L2:LUC7 like 2, pre-mRNA splicing factor [Gene - OMIM - HGNC]
  • MTRNR2L6:MT-RNR2 like 6 [Gene - HGNC]
  • NDUFB2:NADH:ubiquinone oxidoreductase subunit B2 [Gene - OMIM - HGNC]
  • NOBOX:NOBOX oogenesis homeobox [Gene - OMIM - HGNC]
  • PAXIP1:PAX interacting protein 1 [Gene - OMIM - HGNC]
  • RAB19:RAB19, member RAS oncogene family [Gene - HGNC]
  • RBM33:RNA binding motif protein 33 [Gene - HGNC]
  • RNY1:RNA, Ro60-associated Y1 [Gene - OMIM - HGNC]
  • RNY3:RNA, Ro60-associated Y3 [Gene - OMIM - HGNC]
  • RNY4:RNA, Ro60-associated Y4 [Gene - OMIM - HGNC]
  • RNY5:RNA, Ro60-associated Y5 [Gene - OMIM - HGNC]
  • RHEB:Ras homolog, mTORC1 binding [Gene - OMIM - HGNC]
  • ARHGEF35:Rho guanine nucleotide exchange factor 35 [Gene - HGNC]
  • ARHGEF5:Rho guanine nucleotide exchange factor 5 [Gene - OMIM - HGNC]
  • SVOPL:SVOP like [Gene - OMIM - HGNC]
  • SMARCD3:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Gene - OMIM - HGNC]
  • TRB:T cell receptor beta locus [Gene - HGNC]
  • TCAF1:TRPM8 channel associated factor 1 [Gene - OMIM - HGNC]
  • TCAF2:TRPM8 channel associated factor 2 [Gene - OMIM - HGNC]
  • WDR86:WD repeat domain 86 [Gene - HGNC]
  • WEE2:WEE2 oocyte meiosis inhibiting kinase [Gene - OMIM - HGNC]
  • XRCC2:X-ray repair cross complementing 2 [Gene - OMIM - HGNC]
  • ZBED6CL:ZBED6 C-terminal like [Gene - OMIM - HGNC]
  • ADCK2:aarF domain containing kinase 2 [Gene - HGNC]
  • ASIC3:acid sensing ion channel subunit 3 [Gene - OMIM - HGNC]
  • ACTR3B:actin related protein 3B [Gene - HGNC]
  • ACTR3C:actin related protein 3C [Gene - HGNC]
  • AGK:acylglycerol kinase [Gene - OMIM - HGNC]
  • AKR1D1:aldo-keto reductase family 1 member D1 [Gene - OMIM - HGNC]
  • AOC1:amine oxidase copper containing 1 [Gene - OMIM - HGNC]
  • ASB10:ankyrin repeat and SOCS box containing 10 [Gene - OMIM - HGNC]
  • ATG9B:autophagy related 9B [Gene - OMIM - HGNC]
  • CREB3L2:cAMP responsive element binding protein 3 like 2 [Gene - OMIM - HGNC]
  • CNPY1:canopy FGF signaling regulator 1 [Gene - OMIM - HGNC]
  • CASP2:caspase 2 [Gene - OMIM - HGNC]
  • CLCN1:chloride voltage-gated channel 1 [Gene - OMIM - HGNC]
  • CHRM2:cholinergic receptor muscarinic 2 [Gene - OMIM - HGNC]
  • CHPF2:chondroitin polymerizing factor 2 [Gene - OMIM - HGNC]
  • C7orf33:chromosome 7 open reading frame 33 [Gene - HGNC]
  • CNTNAP2:contactin associated protein 2 [Gene - OMIM - HGNC]
  • CRYGN:crystallin gamma N [Gene - OMIM - HGNC]
  • CUL1:cullin 1 [Gene - OMIM - HGNC]
  • CDK5:cyclin dependent kinase 5 [Gene - OMIM - HGNC]
  • DGKI:diacylglycerol kinase iota [Gene - OMIM - HGNC]
  • DYNC2I1:dynein 2 intermediate chain 1 [Gene - OMIM - HGNC]
  • EN2:engrailed homeobox 2 [Gene - OMIM - HGNC]
  • EZH2:enhancer of zeste 2 polycomb repressive complex 2 subunit [Gene - OMIM - HGNC]
  • ESYT2:extended synaptotagmin 2 [Gene - OMIM - HGNC]
  • FAM131B:family with sequence similarity 131 member B [Gene - OMIM - HGNC]
  • FMC1:formation of mitochondrial complex V assembly factor 1 homolog [Gene - HGNC]
  • GBX1:gastrulation brain homeobox 1 [Gene - OMIM - HGNC]
  • GSTK1:glutathione S-transferase kappa 1 [Gene - OMIM - HGNC]
  • INSIG1:insulin induced gene 1 [Gene - OMIM - HGNC]
  • IFT56:intraflagellar transport 56 [Gene - OMIM - HGNC]
  • KLRG2:killer cell lectin like receptor G2 [Gene - HGNC]
  • LRRC61:leucine rich repeat containing 61 [Gene - HGNC]
  • LUZP6:leucine zipper protein 6 [Gene - OMIM - HGNC]
  • LMBR1:limb development membrane protein 1 [Gene - OMIM - HGNC]
  • KDM7A:lysine demethylase 7A [Gene - OMIM - HGNC]
  • KMT2C:lysine methyltransferase 2C [Gene - OMIM - HGNC]
  • MKRN1:makorin ring finger protein 1 [Gene - OMIM - HGNC]
  • MGAM:maltase-glucoamylase [Gene - OMIM - HGNC]
  • MIR671:microRNA 671 [Gene - OMIM - HGNC]
  • MRPS33:mitochondrial ribosomal protein S33 [Gene - OMIM - HGNC]
  • MNX1:motor neuron and pancreas homeobox 1 [Gene - OMIM - HGNC]
  • MTPN:myotrophin [Gene - OMIM - HGNC]
  • NUB1:negative regulator of ubiquitin like proteins 1 [Gene - OMIM - HGNC]
  • NOS3:nitric oxide synthase 3 [Gene - OMIM - HGNC]
  • NCAPG2:non-SMC condensin II complex subunit G2 [Gene - OMIM - HGNC]
  • NOM1:nucleolar protein with MIF4G domain 1 [Gene - OMIM - HGNC]
  • OR2A12:olfactory receptor family 2 subfamily A member 12 [Gene - HGNC]
  • OR2A14:olfactory receptor family 2 subfamily A member 14 [Gene - HGNC]
  • OR2A1:olfactory receptor family 2 subfamily A member 1 [Gene - HGNC]
  • OR2A25:olfactory receptor family 2 subfamily A member 25 [Gene - HGNC]
  • OR2A2:olfactory receptor family 2 subfamily A member 2 [Gene - HGNC]
  • OR2A42:olfactory receptor family 2 subfamily A member 42 [Gene - HGNC]
  • OR2A5:olfactory receptor family 2 subfamily A member 5 [Gene - HGNC]
  • OR2A7:olfactory receptor family 2 subfamily A member 7 [Gene - HGNC]
  • OR2F1:olfactory receptor family 2 subfamily F member 1 [Gene - OMIM - HGNC]
  • OR2F2:olfactory receptor family 2 subfamily F member 2 [Gene - HGNC]
  • OR6B1:olfactory receptor family 6 subfamily B member 1 [Gene - HGNC]
  • OR6V1:olfactory receptor family 6 subfamily V member 1 [Gene - HGNC]
  • OR9A2:olfactory receptor family 9 subfamily A member 2 [Gene - HGNC]
  • OR9A4:olfactory receptor family 9 subfamily A member 4 [Gene - HGNC]
  • PTN:pleiotrophin [Gene - OMIM - HGNC]
  • PARP12:poly(ADP-ribose) polymerase family member 12 [Gene - OMIM - HGNC]
  • GALNT11:polypeptide N-acetylgalactosaminyltransferase 11 [Gene - OMIM - HGNC]
  • GALNTL5:polypeptide N-acetylgalactosaminyltransferase like 5 [Gene - OMIM - HGNC]
  • KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
  • PIP:prolactin induced protein [Gene - OMIM - HGNC]
  • PDIA4:protein disulfide isomerase family A member 4 [Gene - OMIM - HGNC]
  • PRKAG2:protein kinase AMP-activated non-catalytic subunit gamma 2 [Gene - OMIM - HGNC]
  • PTPRN2:protein tyrosine phosphatase receptor type N2 [Gene - OMIM - HGNC]
  • REPIN1:replication initiator 1 [Gene - OMIM - HGNC]
  • RARRES2:retinoic acid receptor responder 2 [Gene - OMIM - HGNC]
  • RNF32:ring finger protein 32 [Gene - OMIM - HGNC]
  • PRSS1:serine protease 1 [Gene - OMIM - HGNC]
  • PRSS37:serine protease 37 [Gene - HGNC]
  • PRSS58:serine protease 58 [Gene - HGNC]
  • SSBP1:single stranded DNA binding protein 1 [Gene - OMIM - HGNC]
  • SLC37A3:solute carrier family 37 member 3 [Gene - OMIM - HGNC]
  • SLC4A2:solute carrier family 4 member 2 [Gene - OMIM - HGNC]
  • SHH:sonic hedgehog signaling molecule [Gene - OMIM - HGNC]
  • TAS2R38:taste 2 receptor member 38 [Gene - OMIM - HGNC]
  • TAS2R39:taste 2 receptor member 39 [Gene - HGNC]
  • TAS2R3:taste 2 receptor member 3 [Gene - OMIM - HGNC]
  • TAS2R40:taste 2 receptor member 40 [Gene - OMIM - HGNC]
  • TAS2R41:taste 2 receptor member 41 [Gene - OMIM - HGNC]
  • TAS2R4:taste 2 receptor member 4 [Gene - OMIM - HGNC]
  • TAS2R5:taste 2 receptor member 5 [Gene - OMIM - HGNC]
  • TAS2R60:taste 2 receptor member 60 [Gene - OMIM - HGNC]
  • TPK1:thiamin pyrophosphokinase 1 [Gene - OMIM - HGNC]
  • TBXAS1:thromboxane A synthase 1 [Gene - OMIM - HGNC]
  • TRPV5:transient receptor potential cation channel subfamily V member 5 [Gene - OMIM - HGNC]
  • TRPV6:transient receptor potential cation channel subfamily V member 6 [Gene - OMIM - HGNC]
  • TMUB1:transmembrane and ubiquitin like domain containing 1 [Gene - OMIM - HGNC]
  • TMEM139:transmembrane protein 139 [Gene - OMIM - HGNC]
  • TMEM176A:transmembrane protein 176A [Gene - OMIM - HGNC]
  • TMEM176B:transmembrane protein 176B [Gene - OMIM - HGNC]
  • TMEM178B:transmembrane protein 178B [Gene - HGNC]
  • TMEM213:transmembrane protein 213 [Gene - HGNC]
  • TRIM24:tripartite motif containing 24 [Gene - OMIM - HGNC]
  • UBN2:ubinuclein 2 [Gene - OMIM - HGNC]
  • UBE3C:ubiquitin protein ligase E3C [Gene - OMIM - HGNC]
  • LOC100134040:uncharacterized LOC100134040 [Gene - OMIM]
  • VIPR2:vasoactive intestinal peptide receptor 2 [Gene - OMIM - HGNC]
  • ZC3HAV1L:zinc finger CCCH-type containing, antiviral 1 like [Gene - HGNC]
  • ZC3HAV1:zinc finger CCCH-type containing, antiviral 1 [Gene - OMIM - HGNC]
  • ZNF212:zinc finger protein 212 [Gene - OMIM - HGNC]
  • ZNF282:zinc finger protein 282 [Gene - OMIM - HGNC]
  • ZNF398:zinc finger protein 398 [Gene - OMIM - HGNC]
  • ZNF425:zinc finger protein 425 [Gene - OMIM - HGNC]
  • ZNF467:zinc finger protein 467 [Gene - OMIM - HGNC]
  • ZNF746:zinc finger protein 746 [Gene - OMIM - HGNC]
  • ZNF775:zinc finger protein 775 [Gene - HGNC]
  • ZNF777:zinc finger protein 777 [Gene - OMIM - HGNC]
  • ZNF783:zinc finger protein 783 [Gene - HGNC]
  • ZNF786:zinc finger protein 786 [Gene - HGNC]
  • ZNF862:zinc finger protein 862 [Gene - HGNC]
  • ZYX:zyxin [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
7q33-36.3
Genomic location:
Chr7: 135639005 - 159119707 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 7q33-36.3(chr7:135639005-159119707)x1
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV004231505Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Nov 28, 2022)     		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, SCV004231505.1

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

    Description

    The copy number loss of 7q33q36.3 involves numerous protein-coding genes. There are several reports of copy number losses that span the terminal region of 7q (7q35qter and 7q36qter) (Tosca 2021, Busa 2016, Rush 2013, Fan 2021). In addition, there are multiple haploinsufficient genes within this interval: SHH (OMIM 142945, 611638); MNX1 (OMIM 176450); KMT2C (OMIM 617768); and KCNH2 (OMIM 613688). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic. References: Busa et al., Eur J Med Genet. 2016 Oct;59(10):546-8. PMID: 27614115 Fan et al., Front Genet. 2021 Dec 1;12:761003. PMID: 34925452 Rush et al., Am J Med Genet A. 2013 Jul;161A(7):1726-32. PMID: 23696251 Tosca et al., Mol Genet Genomic Med. 2021 Nov;9(11):e1645. PMID: 34582124

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

    Last Updated: Feb 4, 2024