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GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1 AND 3p- syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 27, 2023
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:
RCV003330127.1

Allele description [Variation Report for GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1]

GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1

Genes:
  • 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]
  • EDEM1:ER degradation enhancing alpha-mannosidase like protein 1 [Gene - OMIM - HGNC]
  • LHFPL4:LHFPL tetraspan subfamily member 4 [Gene - OMIM - HGNC]
  • LMCD1:LIM and cysteine rich domains 1 [Gene - OMIM - HGNC]
  • RAD18:RAD18 E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
  • RPUSD3:RNA pseudouridine synthase D3 [Gene - OMIM - HGNC]
  • SETMAR:SET domain and mariner transposase fusion gene [Gene - OMIM - HGNC]
  • SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
  • SRGAP3:SLIT-ROBO Rho GTPase activating protein 3 [Gene - OMIM - HGNC]
  • THUMPD3:THUMP domain containing 3 [Gene - HGNC]
  • ARPC4:actin related protein 2/3 complex subunit 4 [Gene - OMIM - HGNC]
  • BHLHE40:basic helix-loop-helix family member e40 [Gene - OMIM - HGNC]
  • BRPF1:bromodomain and PHD finger containing 1 [Gene - OMIM - HGNC]
  • CAMK1:calcium/calmodulin dependent protein kinase I [Gene - OMIM - HGNC]
  • CAV3:caveolin 3 [Gene - OMIM - HGNC]
  • CIDEC:cell death inducing DFFA like effector c [Gene - OMIM - HGNC]
  • CPNE9:copine family member 9 [Gene - HGNC]
  • EGOT:eosinophil granule ontogeny transcript [Gene - OMIM - HGNC]
  • GRM7:glutamate metabotropic receptor 7 [Gene - OMIM - HGNC]
  • ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]
  • JAGN1:jagunal homolog 1 [Gene - OMIM - HGNC]
  • LRRN1:leucine rich repeat neuronal 1 [Gene - OMIM - HGNC]
  • LINC00312:long intergenic non-protein coding RNA 312 [Gene - OMIM - HGNC]
  • MTMR14:myotubularin related protein 14 [Gene - OMIM - HGNC]
  • OXTR:oxytocin receptor [Gene - OMIM - HGNC]
  • SSUH2:ssu-2 homolog [Gene - OMIM - HGNC]
  • SUMF1:sulfatase modifying factor 1 [Gene - OMIM - HGNC]
  • TADA3:transcriptional adaptor 3 [Gene - OMIM - HGNC]
  • TTLL3:tubulin tyrosine ligase like 3 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
3p26.2-25.3
Genomic location:
Chr3: 3669542 - 9937745 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1
HGVS:
    Observations:
    1

    Condition(s)

    Name:
    3p- syndrome
    Synonyms:
    Chromosome 3, monosomy 3p; Monosomy 3p; Chromosome 3, deletion 3p; See all synonyms [MedGen]
    Identifiers:
    MONDO: MONDO:0013424; MedGen: C4706503; OMIM: 613792

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV004036167Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ
    no assertion criteria provided
    		Pathogenic
    (Sep 27, 2023)     		de novoclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedde novoyes1not providednot providednot providednot providedclinical testing

    Citations

    PubMed

    Case Report: A Case Report and Literature Review of 3p Deletion Syndrome.

    Fu J, Wang T, Fu Z, Li T, Zhang X, Zhao J, Yang G.

    Front Pediatr. 2021;9:618059. doi: 10.3389/fped.2021.618059.

    PubMed [citation]
    PMID:
    33643973
    PMCID:
    PMC7902511

    Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome.

    Cargile CB, Goh DL, Goodman BK, Chen XN, Korenberg JR, Semenza GL, Thomas GH.

    Am J Med Genet. 2002 Apr 22;109(2):133-8.

    PubMed [citation]
    PMID:
    11977162
    See all PubMed Citations (3)

    Details of each submission

    From Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ, SCV004036167.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    11not providednot providedclinical testing PubMed (3)
    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1de novoyesnot providednot providednot provided1not providednot providednot provided

    Last Updated: Dec 2, 2023