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GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 24, 2015
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000510429.3

Allele description [Variation Report for GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3]

GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3

Genes:
  • HACL1:2-hydroxyacyl-CoA lyase 1 [Gene - OMIM - HGNC]
  • OXSM:3-oxoacyl-ACP synthase, mitochondrial [Gene - OMIM - HGNC]
  • AZI2:5-azacytidine induced 2 [Gene - OMIM - HGNC]
  • OGG1:8-oxoguanine DNA glycosylase [Gene - OMIM - HGNC]
  • ARL8B:ADP ribosylation factor like GTPase 8B [Gene - OMIM - HGNC]
  • ARPC4-TTLL3:ARPC4-TTLL3 readthrough [Gene - HGNC]
  • ATP2B2:ATPase plasma membrane Ca2+ transporting 2 [Gene - OMIM - HGNC]
  • BRK1:BRICK1 subunit of SCAR/WAVE actin nucleating complex [Gene - OMIM - HGNC]
  • CCR4:C-C motif chemokine receptor 4 [Gene - OMIM - HGNC]
  • CMC1:C-X9-C motif containing 1 [Gene - OMIM - HGNC]
  • CNOT10:CCR4-NOT transcription complex subunit 10 [Gene - OMIM - HGNC]
  • CMTM6:CKLF like MARVEL transmembrane domain containing 6 [Gene - OMIM - HGNC]
  • CMTM7:CKLF like MARVEL transmembrane domain containing 7 [Gene - OMIM - HGNC]
  • CMTM8:CKLF like MARVEL transmembrane domain containing 8 [Gene - OMIM - HGNC]
  • TOP2B:DNA topoisomerase II beta [Gene - OMIM - HGNC]
  • EFHB:EF-hand domain family member B [Gene - HGNC]
  • EAF1:ELL associated factor 1 [Gene - OMIM - HGNC]
  • EDEM1:ER degradation enhancing alpha-mannosidase like protein 1 [Gene - OMIM - HGNC]
  • EMC3:ER membrane protein complex subunit 3 [Gene - OMIM - HGNC]
  • FBXL2:F-box and leucine rich repeat protein 2 [Gene - OMIM - HGNC]
  • FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]
  • FANCD2OS:FANCD2 opposite strand [Gene - HGNC]
  • FGD5-AS1:FGD5 antisense RNA 1 [Gene - HGNC]
  • FGD5:FYVE, RhoGEF and PH domain containing 5 [Gene - OMIM - HGNC]
  • IQSEC1:IQ motif and Sec7 domain ArfGEF 1 [Gene - OMIM - HGNC]
  • LHFPL4:LHFPL tetraspan subfamily member 4 [Gene - OMIM - HGNC]
  • LMCD1:LIM and cysteine rich domains 1 [Gene - OMIM - HGNC]
  • LSM3:LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated [Gene - OMIM - HGNC]
  • NGLY1:N-glycanase 1 [Gene - OMIM - HGNC]
  • NKIRAS1:NFKB inhibitor interacting Ras like 1 [Gene - OMIM - HGNC]
  • NEK10:NIMA related kinase 10 [Gene - OMIM - HGNC]
  • RAB5A:RAB5A, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAD18:RAD18 E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
  • RBMS3:RNA binding motif single stranded interacting protein 3 [Gene - OMIM - HGNC]
  • RPUSD3:RNA pseudouridine synthase D3 [Gene - OMIM - HGNC]
  • RAF1:Raf-1 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
  • SATB1:SATB homeobox 1 [Gene - OMIM - HGNC]
  • SEC13:SEC13 homolog, nuclear pore and COPII coat complex component [Gene - OMIM - HGNC]
  • SETMAR:SET domain and mariner transposase fusion gene [Gene - OMIM - HGNC]
  • SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
  • SH3BP5:SH3 domain binding protein 5 [Gene - OMIM - HGNC]
  • SRGAP3:SLIT-ROBO Rho GTPase activating protein 3 [Gene - OMIM - HGNC]
  • STT3B:STT3 oligosaccharyltransferase complex catalytic subunit B [Gene - OMIM - HGNC]
  • TAMM41:TAM41 mitochondrial translocator assembly and maintenance homolog [Gene - OMIM - HGNC]
  • TBC1D5:TBC1 domain family member 5 [Gene - OMIM - HGNC]
  • THUMPD3:THUMP domain containing 3 [Gene - HGNC]
  • TIMP4:TIMP metallopeptidase inhibitor 4 [Gene - OMIM - HGNC]
  • TATDN2:TatD DNase domain containing 2 [Gene - OMIM - HGNC]
  • WNT7A:Wnt family member 7A [Gene - OMIM - HGNC]
  • XPC:XPC complex subunit, DNA damage recognition and repair factor [Gene - OMIM - HGNC]
  • ARPC4:actin related protein 2/3 complex subunit 4 [Gene - OMIM - HGNC]
  • ANKRD28:ankyrin repeat domain 28 [Gene - OMIM - HGNC]
  • ATG7:autophagy related 7 [Gene - OMIM - HGNC]
  • BHLHE40:basic helix-loop-helix family member e40 [Gene - OMIM - HGNC]
  • BTD:biotinidase [Gene - OMIM - HGNC]
  • BRPF1:bromodomain and PHD finger containing 1 [Gene - OMIM - HGNC]
  • CAMK1:calcium/calmodulin dependent protein kinase I [Gene - OMIM - HGNC]
  • CAPN7:calpain 7 [Gene - OMIM - HGNC]
  • CRTAP:cartilage associated protein [Gene - OMIM - HGNC]
  • CAV3:caveolin 3 [Gene - OMIM - HGNC]
  • CHL1:cell adhesion molecule L1 like [Gene - OMIM - HGNC]
  • CIDEC:cell death inducing DFFA like effector c [Gene - OMIM - HGNC]
  • CRBN:cereblon [Gene - OMIM - HGNC]
  • C3orf20:chromosome 3 open reading frame 20 [Gene - OMIM - HGNC]
  • CCDC174:coiled-coil domain containing 174 [Gene - OMIM - HGNC]
  • CHCHD4:coiled-coil-helix-coiled-coil-helix domain containing 4 [Gene - OMIM - HGNC]
  • COLQ:collagen like tail subunit of asymmetric acetylcholinesterase [Gene - OMIM - HGNC]
  • CNTN4:contactin 4 [Gene - OMIM - HGNC]
  • CNTN6:contactin 6 [Gene - OMIM - HGNC]
  • CPNE9:copine family member 9 [Gene - HGNC]
  • CAND2:cullin associated and neddylation dissociated 2 (putative) [Gene - OMIM - HGNC]
  • CRELD1:cysteine rich with EGF like domains 1 [Gene - OMIM - HGNC]
  • CLASP2:cytoplasmic linker associated protein 2 [Gene - OMIM - HGNC]
  • DAZL:deleted in azoospermia like [Gene - OMIM - HGNC]
  • DPH3:diphthamide biosynthesis 3 [Gene - OMIM - HGNC]
  • DYNC1LI1:dynein cytoplasmic 1 light intermediate chain 1 [Gene - OMIM - HGNC]
  • EOMES:eomesodermin [Gene - OMIM - HGNC]
  • EGOT:eosinophil granule ontogeny transcript [Gene - OMIM - HGNC]
  • FBLN2:fibulin 2 [Gene - OMIM - HGNC]
  • GLB1:galactosidase beta 1 [Gene - OMIM - HGNC]
  • GHRL:ghrelin and obestatin prepropeptide [Gene - OMIM - HGNC]
  • GHRLOS:ghrelin opposite strand/antisense RNA [Gene - OMIM - HGNC]
  • GADL1:glutamate decarboxylase like 1 [Gene - OMIM - HGNC]
  • GRM7:glutamate metabotropic receptor 7 [Gene - OMIM - HGNC]
  • GRIP2:glutamate receptor interacting protein 2 [Gene - HGNC]
  • GPD1L:glycerol-3-phosphate dehydrogenase 1 like [Gene - OMIM - HGNC]
  • HRH1:histamine receptor H1 [Gene - OMIM - HGNC]
  • HDAC11:histone deacetylase 11 [Gene - OMIM - HGNC]
  • ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]
  • IRAK2:interleukin 1 receptor associated kinase 2 [Gene - OMIM - HGNC]
  • IL17RC:interleukin 17 receptor C [Gene - OMIM - HGNC]
  • IL17RE:interleukin 17 receptor E [Gene - OMIM - HGNC]
  • IL5RA:interleukin 5 receptor subunit alpha [Gene - OMIM - HGNC]
  • JAGN1:jagunal homolog 1 [Gene - OMIM - HGNC]
  • LRRC3B:leucine rich repeat containing 3B [Gene - OMIM - HGNC]
  • LRRN1:leucine rich repeat neuronal 1 [Gene - OMIM - HGNC]
  • LINC00312:long intergenic non-protein coding RNA 312 [Gene - OMIM - HGNC]
  • KAT2B:lysine acetyltransferase 2B [Gene - OMIM - HGNC]
  • MKRN2:makorin ring finger protein 2 [Gene - OMIM - HGNC]
  • METTL6:methyltransferase 6, tRNA N3-cytidine [Gene - OMIM - HGNC]
  • MRPS25:mitochondrial ribosomal protein S25 [Gene - OMIM - HGNC]
  • MTMR14:myotubularin related protein 14 [Gene - OMIM - HGNC]
  • NR1D2:nuclear receptor subfamily 1 group D member 2 [Gene - OMIM - HGNC]
  • NR2C2:nuclear receptor subfamily 2 group C member 2 [Gene - OMIM - HGNC]
  • NUP210:nucleoporin 210 [Gene - OMIM - HGNC]
  • OXNAD1:oxidoreductase NAD binding domain containing 1 [Gene - OMIM - HGNC]
  • OSBPL10:oxysterol binding protein like 10 [Gene - OMIM - HGNC]
  • OXTR:oxytocin receptor [Gene - OMIM - HGNC]
  • PPARG:peroxisome proliferator activated receptor gamma [Gene - OMIM - HGNC]
  • PLCL2:phospholipase C like 2 [Gene - OMIM - HGNC]
  • GALNT15:polypeptide N-acetylgalactosaminyltransferase 15 [Gene - OMIM - HGNC]
  • KCNH8:potassium voltage-gated channel subfamily H member 8 [Gene - OMIM - HGNC]
  • PDCD6IP:programmed cell death 6 interacting protein [Gene - OMIM - HGNC]
  • PRRT3:proline rich transmembrane protein 3 [Gene - OMIM - HGNC]
  • PP2D1:protein phosphatase 2C like domain containing 1 [Gene - HGNC]
  • RBSN:rabenosyn, RAB effector [Gene - OMIM - HGNC]
  • RFTN1:raftlin, lipid raft linker 1 [Gene - OMIM - HGNC]
  • RARB:retinoic acid receptor beta [Gene - OMIM - HGNC]
  • RPL15:ribosomal protein L15 [Gene - OMIM - HGNC]
  • RPL32:ribosomal protein L32 [Gene - HGNC]
  • SGO1:shugoshin 1 [Gene - OMIM - HGNC]
  • SLC4A7:solute carrier family 4 member 7 [Gene - OMIM - HGNC]
  • SLC6A11:solute carrier family 6 member 11 [Gene - OMIM - HGNC]
  • SLC6A1:solute carrier family 6 member 1 [Gene - OMIM - HGNC]
  • SLC6A6:solute carrier family 6 member 6 [Gene - OMIM - HGNC]
  • SSUH2:ssu-2 homolog [Gene - OMIM - HGNC]
  • SUMF1:sulfatase modifying factor 1 [Gene - OMIM - HGNC]
  • SUSD5:sushi domain containing 5 [Gene - OMIM - HGNC]
  • SYN2:synapsin II [Gene - OMIM - HGNC]
  • TRNT1:tRNA nucleotidyl transferase 1 [Gene - OMIM - HGNC]
  • TSEN2:tRNA splicing endonuclease subunit 2 [Gene - OMIM - HGNC]
  • THRB:thyroid hormone receptor beta [Gene - OMIM - HGNC]
  • TADA3:transcriptional adaptor 3 [Gene - OMIM - HGNC]
  • TGFBR2:transforming growth factor beta receptor 2 [Gene - OMIM - HGNC]
  • TMEM40:transmembrane protein 40 [Gene - HGNC]
  • TMEM43:transmembrane protein 43 [Gene - OMIM - HGNC]
  • TMPPE:transmembrane protein with metallophosphoesterase domain [Gene - HGNC]
  • TRIM71:tripartite motif containing 71 [Gene - OMIM - HGNC]
  • TTLL3:tubulin tyrosine ligase like 3 [Gene - OMIM - HGNC]
  • UBE2E1:ubiquitin conjugating enzyme E2 E1 [Gene - OMIM - HGNC]
  • UBE2E2:ubiquitin conjugating enzyme E2 E2 [Gene - OMIM - HGNC]
  • UBP1:upstream binding protein 1 [Gene - OMIM - HGNC]
  • VGLL4:vestigial like family member 4 [Gene - OMIM - HGNC]
  • VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]
  • ZCWPW2:zinc finger CW-type and PWWP domain containing 2 [Gene - HGNC]
  • ZNF385D:zinc finger protein 385D [Gene - HGNC]
  • ZNF860:zinc finger protein 860 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
3p26.3-22.3
Genomic location:
Chr3: 61891 - 33958201 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3
HGVS:
    Links:
    dbVar: nssv13640045; dbVar: nsv2769263
    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
    SCV000584380ISCA site 1

    See additional submitters

    no assertion criteria provided
    		Pathogenic
    (Feb 24, 2015)     		unknownclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providednot providedyes1not providednot providednot providednot providedclinical testing

    Citations

    PubMed

    Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

    Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

    Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

    PubMed [citation]
    PMID:
    20466091
    PMCID:
    PMC2869000

    Details of each submission

    From ISCA site 1, SCV000584380.1

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

    Last Updated: May 7, 2024