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GRCh37/hg19 1p13.3-13.2(chr1:109483388-112293512)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 20, 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:
RCV003483272.1

Allele description [Variation Report for GRCh37/hg19 1p13.3-13.2(chr1:109483388-112293512)x1]

GRCh37/hg19 1p13.3-13.2(chr1:109483388-112293512)x1

Genes:
  • ALX3:ALX homeobox 3 [Gene - OMIM - HGNC]
  • ATP5PB:ATP synthase peripheral stalk-membrane subunit b [Gene - OMIM - HGNC]
  • CD53:CD53 molecule [Gene - OMIM - HGNC]
  • DENND2D:DENN domain containing 2D [Gene - OMIM - HGNC]
  • DRAM2:DNA damage regulated autophagy modulator 2 [Gene - OMIM - HGNC]
  • EPS8L3:EPS8 signaling adaptor L3 [Gene - OMIM - HGNC]
  • GNAI3:G protein subunit alpha i3 [Gene - OMIM - HGNC]
  • GNAT2:G protein subunit alpha transducin 2 [Gene - OMIM - HGNC]
  • GPR61:G protein-coupled receptor 61 [Gene - OMIM - HGNC]
  • RAP1A:RAP1A, member of RAS oncogene family [Gene - OMIM - HGNC]
  • RBM15:RNA binding motif protein 15 [Gene - OMIM - HGNC]
  • TAF13:TATA-box binding protein associated factor 13 [Gene - OMIM - HGNC]
  • WDR47:WD repeat domain 47 [Gene - OMIM - HGNC]
  • WDR77:WD repeat domain 77 [Gene - OMIM - HGNC]
  • ADORA3:adenosine A3 receptor [Gene - OMIM - HGNC]
  • AMPD2:adenosine monophosphate deaminase 2 [Gene - OMIM - HGNC]
  • AHCYL1:adenosylhomocysteinase like 1 [Gene - OMIM - HGNC]
  • AMIGO1:adhesion molecule with Ig like domain 1 [Gene - OMIM - HGNC]
  • ATXN7L2:ataxin 7 like 2 [Gene - HGNC]
  • CELSR2:cadherin EGF LAG seven-pass G-type receptor 2 [Gene - OMIM - HGNC]
  • CHI3L2:chitinase 3 like 2 [Gene - OMIM - HGNC]
  • CHIA:chitinase acidic [Gene - OMIM - HGNC]
  • CLCC1:chloride channel CLIC like 1 [Gene - OMIM - HGNC]
  • CEPT1:choline/ethanolamine phosphotransferase 1 [Gene - OMIM - HGNC]
  • C1orf162:chromosome 1 open reading frame 162 [Gene - HGNC]
  • CFAP276:cilia and flagella associated protein 276 [Gene - OMIM - HGNC]
  • CIMAP3:ciliary microtubule associated protein 3 [Gene - OMIM - HGNC]
  • CSF1:colony stimulating factor 1 [Gene - OMIM - HGNC]
  • CYB561D1:cytochrome b561 family member D1 [Gene - HGNC]
  • ELAPOR1:endosome-lysosome associated apoptosis and autophagy regulator 1 [Gene - OMIM - HGNC]
  • GSTM1:glutathione S-transferase mu 1 [Gene - OMIM - HGNC]
  • GSTM2:glutathione S-transferase mu 2 [Gene - OMIM - HGNC]
  • GSTM3:glutathione S-transferase mu 3 [Gene - OMIM - HGNC]
  • GSTM4:glutathione S-transferase mu 4 [Gene - OMIM - HGNC]
  • GSTM5:glutathione S-transferase mu 5 [Gene - OMIM - HGNC]
  • INKA2:inka box actin regulator 2 [Gene - OMIM - HGNC]
  • LAMTOR5:late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 [Gene - OMIM - HGNC]
  • LRIF1:ligand dependent nuclear receptor interacting factor 1 [Gene - OMIM - HGNC]
  • MIR197:microRNA 197 [Gene - OMIM - HGNC]
  • MYBPHL:myosin binding protein H like [Gene - OMIM - HGNC]
  • OVGP1:oviductal glycoprotein 1 [Gene - OMIM - HGNC]
  • KCNA10:potassium voltage-gated channel subfamily A member 10 [Gene - OMIM - HGNC]
  • KCNA2:potassium voltage-gated channel subfamily A member 2 [Gene - OMIM - HGNC]
  • KCNA3:potassium voltage-gated channel subfamily A member 3 [Gene - OMIM - HGNC]
  • KCNC4:potassium voltage-gated channel subfamily C member 4 [Gene - OMIM - HGNC]
  • PROK1:prokineticin 1 [Gene - OMIM - HGNC]
  • PSRC1:proline and serine rich coiled-coil 1 [Gene - OMIM - HGNC]
  • PSMA5:proteasome 20S subunit alpha 5 [Gene - OMIM - HGNC]
  • SARS1:seryl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • SLC16A4:solute carrier family 16 member 4 [Gene - OMIM - HGNC]
  • SLC6A17:solute carrier family 6 member 17 [Gene - OMIM - HGNC]
  • SORT1:sortilin 1 [Gene - OMIM - HGNC]
  • STRIP1:striatin interacting protein 1 [Gene - OMIM - HGNC]
  • SYPL2:synaptophysin like 2 [Gene - HGNC]
  • TMEM167B:transmembrane protein 167B [Gene - HGNC]
  • UBL4B:ubiquitin like 4B [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
1p13.3-13.2
Genomic location:
Chr1: 109483388 - 112293512 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 1p13.3-13.2(chr1:109483388-112293512)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
    SCV004230187Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Dec 20, 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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004230187.1

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

    Description

    This deletion involves numerous protein-coding genes, including WDR47 (OMIM 615734), ELAPOR1 (OMIM 611298), GSTM5 (OMIM 138385), and LRIF1 (OMIM 615354), which have recently been proposed as candidate genes for neurodevelopmental phenotypes (Ben-Mahmoud 2022). A heterozygous deletion that lies within the current interval has been reported in a patient, which was inherited from their mother who had the same neurodevelopmental phenotype (Ben-Mahmoud 2022). One individual with complete gene deletion has been reported with generalized epilepsy and intellectual disability (Lai 2015, Doring 2021). Thus, based on current medical literature and gene content, this copy number variant is classified as pathogenic. References Ben-Mahmoud et al., Front Mol Neurosci. 2022 Oct 6;15:979061. PMID: 36277487 Doring et al., Int J Mol Sci 2021 Mar 10;22(6):2824 PMID: 33802230 Lal et al., PLoS Genet. 2015 May 7;11(5):e1005226. PMID: 25950944 Syrbe et al., Nat Genet. 2015 Apr;47(4):393-399. PMID: 25751627

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

    Last Updated: Feb 4, 2024