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NC_000019.9:g.(?_1456055)_(2456931_?)dup AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 7, 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:
RCV003122897.3

Allele description [Variation Report for NC_000019.9:g.(?_1456055)_(2456931_?)dup]

NC_000019.9:g.(?_1456055)_(2456931_?)dup

Genes:
  • ADAMTSL5:ADAMTS like 5 [Gene - HGNC]
  • APC2:APC regulator of WNT signaling pathway 2 [Gene - OMIM - HGNC]
  • ATP8B3:ATPase phospholipid transporting 8B3 [Gene - OMIM - HGNC]
  • BTBD2:BTB domain containing 2 [Gene - OMIM - HGNC]
  • DOT1L:DOT1 like histone lysine methyltransferase [Gene - OMIM - HGNC]
  • IZUMO4:IZUMO family member 4 [Gene - OMIM - HGNC]
  • KLF16:KLF transcription factor 16 [Gene - OMIM - HGNC]
  • LSM7:LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated [Gene - OMIM - HGNC]
  • MKNK2:MAPK interacting serine/threonine kinase 2 [Gene - OMIM - HGNC]
  • MOB3A:MOB kinase activator 3A [Gene - OMIM - HGNC]
  • PEAK3:PEAK family member 3 [Gene - OMIM - HGNC]
  • REXO1:RNA exonuclease 1 homolog [Gene - OMIM - HGNC]
  • ABHD17A:abhydrolase domain containing 17A, depalmitoylase [Gene - OMIM - HGNC]
  • AP3D1:adaptor related protein complex 3 subunit delta 1 [Gene - OMIM - HGNC]
  • ADAT3:adenosine deaminase tRNA specific 3 [Gene - OMIM - HGNC]
  • AMH:anti-Mullerian hormone [Gene - OMIM - HGNC]
  • CSNK1G2:casein kinase 1 gamma 2 [Gene - OMIM - HGNC]
  • C19orf25:chromosome 19 open reading frame 25 [Gene - HGNC]
  • JSRP1:junctional sarcoplasmic reticulum protein 1 [Gene - OMIM - HGNC]
  • LMNB2:lamin B2 [Gene - OMIM - HGNC]
  • LINGO3:leucine rich repeat and Ig domain containing 3 [Gene - OMIM - HGNC]
  • MBD3:methyl-CpG binding domain protein 3 [Gene - OMIM - HGNC]
  • MEX3D:mex-3 RNA binding family member D [Gene - OMIM - HGNC]
  • MIR1909:microRNA 1909 [Gene - OMIM - HGNC]
  • ONECUT3:one cut homeobox 3 [Gene - OMIM - HGNC]
  • OAZ1:ornithine decarboxylase antizyme 1 [Gene - OMIM - HGNC]
  • PLEKHJ1:pleckstrin homology domain containing J1 [Gene - OMIM - HGNC]
  • PLK5:polo like kinase 5 (inactive) [Gene - HGNC]
  • PCSK4:proprotein convertase subtilisin/kexin type 4 [Gene - OMIM - HGNC]
  • REEP6:receptor accessory protein 6 [Gene - OMIM - HGNC]
  • SCAMP4:secretory carrier membrane protein 4 [Gene - OMIM - HGNC]
  • SPPL2B:signal peptide peptidase like 2B [Gene - OMIM - HGNC]
  • SF3A2:splicing factor 3a subunit 2 [Gene - OMIM - HGNC]
  • TCF3:transcription factor 3 [Gene - OMIM - HGNC]
  • TIMM13:translocase of inner mitochondrial membrane 13 [Gene - OMIM - HGNC]
  • TMPRSS9:transmembrane serine protease 9 [Gene - OMIM - HGNC]
  • UQCR11:ubiquinol-cytochrome c reductase, complex III subunit XI [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
19p13.3
Genomic location:
Chr19: 1456055 - 2456931 (on Assembly GRCh37)
Preferred name:
NC_000019.9:g.(?_1456055)_(2456931_?)dup
HGVS:
NC_000019.9:g.(?_1456055)_(2456931_?)dup

Condition(s)

Name:
Progressive myoclonic epilepsy type 9
Identifiers:
MONDO: MONDO:0014685; MedGen: C4225289; Orphanet: 457265; OMIM: 616540
Name:
Lipodystrophy, partial, acquired, susceptibility to (APLD)
Synonyms:
APLD, SUSCEPTIBILITY TO
Identifiers:
MONDO: MONDO:0100476; MedGen: C3887501; OMIM: 608709

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795763Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 7, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003795763.1

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the LMNB2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with LMNB2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024