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GRCh37/hg19 10q25.3-26.3(chr10:118247181-135435319)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 20, 2019
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:
RCV001537903.4

Allele description [Variation Report for GRCh37/hg19 10q25.3-26.3(chr10:118247181-135435319)x3]

GRCh37/hg19 10q25.3-26.3(chr10:118247181-135435319)x3

Genes:
  • ADAM12:ADAM metallopeptidase domain 12 [Gene - OMIM - HGNC]
  • ADAM8:ADAM metallopeptidase domain 8 [Gene - OMIM - HGNC]
  • BAG3:BAG cochaperone 3 [Gene - OMIM - HGNC]
  • BNIP3:BCL2 interacting protein 3 [Gene - OMIM - HGNC]
  • BCCIP:BRCA2 and CDKN1A interacting protein [Gene - OMIM - HGNC]
  • BTBD16:BTB domain containing 16 [Gene - HGNC]
  • BUB3:BUB3 mitotic checkpoint protein [Gene - OMIM - HGNC]
  • CTBP2:C-terminal binding protein 2 [Gene - OMIM - HGNC]
  • CACUL1:CDK2 associated cullin domain 1 [Gene - OMIM - HGNC]
  • CUZD1:CUB and zona pellucida like domains 1 [Gene - OMIM - HGNC]
  • DHX32:DEAH-box helicase 32 (putative) [Gene - OMIM - HGNC]
  • DENND10:DENN domain containing 10 [Gene - HGNC]
  • EBF3:EBF transcription factor 3 [Gene - OMIM - HGNC]
  • EEF1AKMT2:EEF1A lysine methyltransferase 2 [Gene - OMIM - HGNC]
  • EMX2OS:EMX2 opposite strand/antisense RNA [Gene - OMIM - HGNC]
  • GPR26:G protein-coupled receptor 26 [Gene - OMIM - HGNC]
  • GRK5:G protein-coupled receptor kinase 5 [Gene - OMIM - HGNC]
  • HMX2:H6 family homeobox 2 [Gene - OMIM - HGNC]
  • HMX3:H6 family homeobox 3 [Gene - OMIM - HGNC]
  • HTRA1:HtrA serine peptidase 1 [Gene - OMIM - HGNC]
  • IKZF5:IKAROS family zinc finger 5 [Gene - OMIM - HGNC]
  • JAKMIP3:Janus kinase and microtubule interacting protein 3 [Gene - OMIM - HGNC]
  • NKX1-2:NK1 homeobox 2 [Gene - HGNC]
  • NKX6-2:NK6 homeobox 2 [Gene - OMIM - HGNC]
  • NSMCE4A:NSE4 homolog A, SMC5-SMC6 complex component [Gene - OMIM - HGNC]
  • MGMT:O-6-methylguanine-DNA methyltransferase [Gene - OMIM - HGNC]
  • PDZD8:PDZ domain containing 8 [Gene - OMIM - HGNC]
  • PWWP2B:PWWP domain containing 2B [Gene - HGNC]
  • RAB11FIP2:RAB11 family interacting protein 2 [Gene - OMIM - HGNC]
  • SEC23IP:SEC23 interacting protein [Gene - OMIM - HGNC]
  • TCERG1L-AS1:TCERG1L antisense RNA 1 [Gene - HGNC]
  • TIAL1:TIA1 cytotoxic granule associated RNA binding protein like 1 [Gene - OMIM - HGNC]
  • VENTX:VENT homeobox [Gene - OMIM - HGNC]
  • WDR11:WD repeat domain 11 [Gene - OMIM - HGNC]
  • ABRAXAS2:abraxas 2, BRISC complex subunit [Gene - OMIM - HGNC]
  • ACADSB:acyl-CoA dehydrogenase short/branched chain [Gene - OMIM - HGNC]
  • ADGRA1:adhesion G protein-coupled receptor A1 [Gene - OMIM - HGNC]
  • ARMS2:age-related maculopathy susceptibility 2 [Gene - OMIM - HGNC]
  • ATE1:arginyltransferase 1 [Gene - OMIM - HGNC]
  • CALY:calcyon neuron specific vesicular protein [Gene - OMIM - HGNC]
  • CASC2:cancer susceptibility 2 [Gene - OMIM - HGNC]
  • CHST15:carbohydrate sulfotransferase 15 [Gene - OMIM - HGNC]
  • CPXM2:carboxypeptidase X, M14 family member 2 [Gene - OMIM - HGNC]
  • C10orf120:chromosome 10 open reading frame 120 [Gene - HGNC]
  • C10orf82:chromosome 10 open reading frame 82 [Gene - HGNC]
  • C10orf88:chromosome 10 open reading frame 88 [Gene - HGNC]
  • C10orf90:chromosome 10 open reading frame 90 [Gene - OMIM - HGNC]
  • CFAP46:cilia and flagella associated protein 46 [Gene - OMIM - HGNC]
  • CLRN3:clarin 3 [Gene - OMIM - HGNC]
  • CYP2E1:cytochrome P450 family 2 subfamily E member 1 [Gene - OMIM - HGNC]
  • DOCK1:dedicator of cytokinesis 1 [Gene - OMIM - HGNC]
  • DMBT1:deleted in malignant brain tumors 1 [Gene - OMIM - HGNC]
  • DPYSL4:dihydropyrimidinase like 4 [Gene - OMIM - HGNC]
  • EMX2:empty spiracles homeobox 2 [Gene - OMIM - HGNC]
  • ENO4:enolase 4 [Gene - OMIM - HGNC]
  • ECHS1:enoyl-CoA hydratase, short chain 1 [Gene - OMIM - HGNC]
  • EDRF1:erythroid differentiation regulatory factor 1 [Gene - HGNC]
  • EIF3A:eukaryotic translation initiation factor 3 subunit A [Gene - OMIM - HGNC]
  • FAM204A:family with sequence similarity 204 member A [Gene - HGNC]
  • FAM24A:family with sequence similarity 24 member A [Gene - HGNC]
  • FAM24B:family with sequence similarity 24 member B [Gene - HGNC]
  • FAM53B:family with sequence similarity 53 member B [Gene - OMIM - HGNC]
  • FGFR2:fibroblast growth factor receptor 2 [Gene - OMIM - HGNC]
  • FANK1:fibronectin type III and ankyrin repeat domains 1 [Gene - OMIM - HGNC]
  • FOXI2:forkhead box I2 [Gene - OMIM - HGNC]
  • FUOM:fucose mutarotase [Gene - OMIM - HGNC]
  • GLRX3:glutaredoxin 3 [Gene - OMIM - HGNC]
  • HSPA12A:heat shock protein family A (Hsp70) member 12A [Gene - OMIM - HGNC]
  • INSYN2A:inhibitory synaptic factor 2A [Gene - OMIM - HGNC]
  • INPP5A:inositol polyphosphate-5-phosphatase A [Gene - OMIM - HGNC]
  • INPP5F:inositol polyphosphate-5-phosphatase F [Gene - OMIM - HGNC]
  • KNDC1:kinase non-catalytic C-lobe domain containing 1 [Gene - OMIM - HGNC]
  • LRRC27:leucine rich repeat containing 27 [Gene - HGNC]
  • LINC01166:long intergenic non-protein coding RNA 1166 [Gene - HGNC]
  • LINC02870:long intergenic non-protein coding RNA 2870 [Gene - HGNC]
  • MKI67:marker of proliferation Ki-67 [Gene - OMIM - HGNC]
  • MMP21:matrix metallopeptidase 21 [Gene - OMIM - HGNC]
  • MCMBP:minichromosome maintenance complex binding protein [Gene - OMIM - HGNC]
  • MTG1:mitochondrial ribosome associated GTPase 1 [Gene - HGNC]
  • NANOS1:nanos C2HC-type zinc finger 1 [Gene - OMIM - HGNC]
  • NPS:neuropeptide S [Gene - OMIM - HGNC]
  • OAT:ornithine aminotransferase [Gene - OMIM - HGNC]
  • PNLIPRP1:pancreatic lipase related protein 1 [Gene - OMIM - HGNC]
  • PNLIPRP2:pancreatic lipase related protein 2 (gene/pseudogene) [Gene - OMIM - HGNC]
  • PNLIP:pancreatic lipase [Gene - OMIM - HGNC]
  • PRDX3:peroxiredoxin 3 [Gene - OMIM - HGNC]
  • PLPP4:phospholipid phosphatase 4 [Gene - HGNC]
  • LHPP:phospholysine phosphohistidine inorganic pyrophosphate phosphatase [Gene - OMIM - HGNC]
  • PSTK:phosphoseryl-tRNA kinase [Gene - OMIM - HGNC]
  • PLEKHA1:pleckstrin homology domain containing A1 [Gene - OMIM - HGNC]
  • PAOX:polyamine oxidase [Gene - OMIM - HGNC]
  • KCNK18:potassium two pore domain channel subfamily K member 18 [Gene - OMIM - HGNC]
  • PRLHR:prolactin releasing hormone receptor [Gene - OMIM - HGNC]
  • PRAP1:proline rich acidic protein 1 [Gene - OMIM - HGNC]
  • PPP2R2D:protein phosphatase 2 regulatory subunit Bdelta [Gene - OMIM - HGNC]
  • PTPRE:protein tyrosine phosphatase receptor type E [Gene - OMIM - HGNC]
  • RGS10:regulator of G protein signaling 10 [Gene - OMIM - HGNC]
  • STK32C:serine/threonine kinase 32C [Gene - HGNC]
  • SPRN:shadow of prion protein [Gene - OMIM - HGNC]
  • SHTN1:shootin 1 [Gene - OMIM - HGNC]
  • SFXN4:sideroflexin 4 [Gene - OMIM - HGNC]
  • SLC18A2:solute carrier family 18 member A2 [Gene - OMIM - HGNC]
  • SYCE1:synaptonemal complex central element protein 1 [Gene - OMIM - HGNC]
  • TEX36:testis expressed 36 [Gene - HGNC]
  • TCERG1L:transcription elongation regulator 1 like [Gene - HGNC]
  • TACC2:transforming acidic coiled-coil containing protein 2 [Gene - OMIM - HGNC]
  • TUBGCP2:tubulin gamma complex associated protein 2 [Gene - OMIM - HGNC]
  • UTF1:undifferentiated embryonic cell transcription factor 1 [Gene - OMIM - HGNC]
  • UROS:uroporphyrinogen III synthase [Gene - OMIM - HGNC]
  • VAX1:ventral anterior homeobox 1 [Gene - OMIM - HGNC]
  • ZRANB1:zinc finger RANBP2-type containing 1 [Gene - OMIM - HGNC]
  • ZNF511:zinc finger protein 511 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
10q25.3-26.3
Genomic location:
Chr10: 118247181 - 135435319 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 10q25.3-26.3(chr10:118247181-135435319)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: CN517202

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV001754831Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Jul2020Prior)    		Pathogenic
    (Feb 20, 2019)     		unknownclinical testing

    PubMed (3)
    [See all records that cite these PMIDs]

    Citation Link

    Help

    Summary from all submissions

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

    Citations

    PubMed

    Microarray delineation of familial chromosomal imbalance with deletion 5q35 and duplication 10q25 in a child showing multiple anomalies and dysmorphism.

    Masri A, Gimelli S, Hamamy H, Sloan-Béna F.

    Am J Med Genet A. 2014 May;164A(5):1254-61. doi: 10.1002/ajmg.a.36412. Epub 2014 Jan 29.

    PubMed [citation]
    PMID:
    24478242

    Distal 10q trisomy with copy number gain in chromosome region 10q23.1-10q25.1: the Wnt signaling pathway is the most pertinent to the gene content in the region of copy number gain: a case report.

    Wong SL, Chou HH, Chao CN, Leung JH, Chen YH, Hsu CD.

    BMC Res Notes. 2015 Jun 19;8:250. doi: 10.1186/s13104-015-1213-x.

    PubMed [citation]
    PMID:
    26088875
    PMCID:
    PMC4473823
    See all PubMed Citations (3)

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001754831.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (3)

    Description

    This CNV is a 17.2 Mb duplication of 10q25.3-qter, on chromosome 10, (seq[GRCh37]dup(10)(q25.3q26.3); chr10:g.118247181_135435319dup) and constitutes a gain encompassing at least 108 genes. This CNV overlaps the 10q terminal region and was observed in a de novo state. Duplication of the terminal 10q region has been reported in the literature and is estimated to be rare (Masri et al. 2014; Wong et al. 2015; Liu et al. 2016). The CNV is usually found in a de novo state and as part of an unbalanced translocation (Masri et al. 2014; Wong et al. 2015; Liu et al. 2016). Common features of the syndrome associated with 10q terminal deletions include developmental delay, hypotonia, intellectual disability, distinct craniofacial features and facial dysmorphisms. Additional features in some patients include language barrier and supernumerary nipples. This CNV has not been reported in controls. Based on the collective evidence, this CNV is classified as pathogenic.

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

    Last Updated: Apr 9, 2023