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GRCh37/hg19 1q25.2-31.2(chr1:179727182-192260142)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 12, 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:
RCV002473949.1

Allele description [Variation Report for GRCh37/hg19 1q25.2-31.2(chr1:179727182-192260142)x1]

GRCh37/hg19 1q25.2-31.2(chr1:179727182-192260142)x1

Genes:
  • BRINP3:BMP/retinoic acid inducible neural specific 3 [Gene - OMIM - HGNC]
  • DHX9:DExH-box helicase 9 [Gene - OMIM - HGNC]
  • EDEM3:ER degradation enhancing alpha-mannosidase like protein 3 [Gene - OMIM - HGNC]
  • KIAA1614:KIAA1614 [Gene - HGNC]
  • LHX4:LIM homeobox 4 [Gene - OMIM - HGNC]
  • NPL:N-acetylneuraminate pyruvate lyase [Gene - OMIM - HGNC]
  • SHCBP1L:SHC binding and spindle associated 1 like [Gene - OMIM - HGNC]
  • SMG7:SMG7 nonsense mediated mRNA decay factor [Gene - OMIM - HGNC]
  • SWT1:SWT1 RNA endoribonuclease homolog [Gene - OMIM - HGNC]
  • ARPC5:actin related protein 2/3 complex subunit 5 [Gene - OMIM - HGNC]
  • ACBD6:acyl-CoA binding domain containing 6 [Gene - OMIM - HGNC]
  • APOBEC4:apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4 [Gene - OMIM - HGNC]
  • CACNA1E:calcium voltage-gated channel subunit alpha1 E [Gene - OMIM - HGNC]
  • CEP350:centrosomal protein 350 [Gene - OMIM - HGNC]
  • C1orf21:chromosome 1 open reading frame 21 [Gene - HGNC]
  • COLGALT2:collagen beta(1-O)galactosyltransferase 2 [Gene - OMIM - HGNC]
  • FAM163A:family with sequence similarity 163 member A [Gene - OMIM - HGNC]
  • GLUL:glutamate-ammonia ligase [Gene - OMIM - HGNC]
  • HMCN1:hemicentin 1 [Gene - OMIM - HGNC]
  • IER5:immediate early response 5 [Gene - OMIM - HGNC]
  • IVNS1ABP:influenza virus NS1A binding protein [Gene - OMIM - HGNC]
  • LAMC1:laminin subunit gamma 1 [Gene - OMIM - HGNC]
  • LAMC2:laminin subunit gamma 2 [Gene - OMIM - HGNC]
  • MR1:major histocompatibility complex, class I-related [Gene - OMIM - HGNC]
  • NCF2:neutrophil cytosolic factor 2 [Gene - OMIM - HGNC]
  • NIBAN1:niban apoptosis regulator 1 [Gene - OMIM - HGNC]
  • NMNAT2:nicotinamide nucleotide adenylyltransferase 2 [Gene - OMIM - HGNC]
  • OCLM:oculomedin [Gene - OMIM - HGNC]
  • ODR4:odr-4 GPCR localization factor homolog [Gene - OMIM - HGNC]
  • PDC:phosducin [Gene - OMIM - HGNC]
  • PLA2G4A:phospholipase A2 group IVA [Gene - OMIM - HGNC]
  • PTGS2:prostaglandin-endoperoxide synthase 2 [Gene - OMIM - HGNC]
  • PRG4:proteoglycan 4 [Gene - OMIM - HGNC]
  • QSOX1:quiescin sulfhydryl oxidase 1 [Gene - OMIM - HGNC]
  • RGL1:ral guanine nucleotide dissociation stimulator like 1 [Gene - OMIM - HGNC]
  • RGS16:regulator of G protein signaling 16 [Gene - OMIM - HGNC]
  • RGS18:regulator of G protein signaling 18 [Gene - OMIM - HGNC]
  • RGS8:regulator of G protein signaling 8 [Gene - OMIM - HGNC]
  • RGSL1:regulator of G protein signaling like 1 [Gene - OMIM - HGNC]
  • RNASEL:ribonuclease L [Gene - OMIM - HGNC]
  • RNF2:ring finger protein 2 [Gene - OMIM - HGNC]
  • STX6:syntaxin 6 [Gene - OMIM - HGNC]
  • TRMT1L:tRNA methyltransferase 1 like [Gene - OMIM - HGNC]
  • TSEN15:tRNA splicing endonuclease subunit 15 [Gene - OMIM - HGNC]
  • TOR1AIP1:torsin 1A interacting protein 1 [Gene - OMIM - HGNC]
  • TOR1AIP2:torsin 1A interacting protein 2 [Gene - OMIM - HGNC]
  • TPR:translocated promoter region, nuclear basket protein [Gene - OMIM - HGNC]
  • TEDDM1:transmembrane epididymal protein 1 [Gene - HGNC]
  • XPR1:xenotropic and polytropic retrovirus receptor 1 [Gene - OMIM - HGNC]
  • ZNF648:zinc finger protein 648 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
1q25.2-31.2
Genomic location:
Chr1: 179727182 - 192260142 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 1q25.2-31.2(chr1:179727182-192260142)x1
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
    SCV002773815Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Apr 12, 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, SCV002773815.1

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

    Description

    The copy number loss of 1q25.2q31.2 involves multiple coding genes across multiple chromosomal bands and is expected to cause phenotypic and/or developmental abnormalities. It includes multiple genes associated with autosomal dominant disorders: LHX4 (OMIM 602146), XPR1 (OMIM 605237), CACNA1E (OMIM 601013), RNASEL (OMIM 180435), IVNS1ABP (OMIM 609209), and HMCN1 (OMIM 608548). Among these, loss-of-function of LHX4 has been associated with autosomal dominant combined pituitary hormone deficiency-4 (OMIM 262700), which causes growth deficiency due to impaired production of growth hormone and one or more anterior pituitary hormones. This deletion interval also overlaps the region of intermediate 1q25-q32 deletion syndrome, which is characterized by pre- and/or postnatal growth retardation, psychomotor retardation, lip and palate anomalies, genital abnormalities, terminal limb defects, cardiac anomalies, microcephaly, and dysmorphic features. The severity of the clinical phenotype seems to be correlated with the size of the deletion (Hu et al., Mol Cytogenet 2013;6(1):30, PMID: 23915434). LHX4 has been suggested as one of the two strongest candidates for growth retardation in the 1q25-q32 region.

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

    Last Updated: Dec 31, 2022