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NC_000016.9:g.(?_624055)_(2153916_?)dup AND Epilepsy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 27, 2020
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:
RCV001344085.1

Allele description [Variation Report for NC_000016.9:g.(?_624055)_(2153916_?)dup]

NC_000016.9:g.(?_624055)_(2153916_?)dup

Genes:
  • BAIAP3:BAI1 associated protein 3 [Gene - OMIM - HGNC]
  • C1QTNF8:C1q and TNF related 8 [Gene - OMIM - HGNC]
  • FBXL16:F-box and leucine rich repeat protein 16 [Gene - OMIM - HGNC]
  • GNG13:G protein subunit gamma 13 [Gene - OMIM - HGNC]
  • JPT2:Jupiter microtubule associated homolog 2 [Gene - OMIM - HGNC]
  • MCRIP2:MAPK regulated corepressor interacting protein 2 [Gene - HGNC]
  • GNPTG:N-acetylglucosamine-1-phosphate transferase subunit gamma [Gene - OMIM - HGNC]
  • NDUFB10:NADH:ubiquinone oxidoreductase subunit B10 [Gene - OMIM - HGNC]
  • NOXO1:NADPH oxidase organizer 1 [Gene - OMIM - HGNC]
  • NHERF2:NHERF family PDZ scaffold protein 2 [Gene - OMIM - HGNC]
  • NME3:NME/NM23 nucleoside diphosphate kinase 3 [Gene - OMIM - HGNC]
  • NUBP2:NUBP iron-sulfur cluster assembly factor 2, cytosolic [Gene - OMIM - HGNC]
  • RAB40C:RAB40C, member RAS oncogene family [Gene - OMIM - HGNC]
  • RPUSD1:RNA pseudouridine synthase domain containing 1 [Gene - HGNC]
  • SOX8:SRY-box transcription factor 8 [Gene - OMIM - HGNC]
  • STUB1:STIP1 homology and U-box containing protein 1 [Gene - OMIM - HGNC]
  • TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
  • TSR3:TSR3 ribosome maturation factor [Gene - OMIM - HGNC]
  • WFIKKN1:WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 [Gene - OMIM - HGNC]
  • WDR24:WD repeat domain 24 [Gene - OMIM - HGNC]
  • WDR90:WD repeat domain 90 [Gene - OMIM - HGNC]
  • ANTKMT:adenine nucleotide translocase lysine methyltransferase [Gene - OMIM - HGNC]
  • CACNA1H:calcium voltage-gated channel subunit alpha1 H [Gene - OMIM - HGNC]
  • CLCN7:chloride voltage-gated channel 7 [Gene - OMIM - HGNC]
  • CHTF18:chromosome transmission fidelity factor 18 [Gene - OMIM - HGNC]
  • CCDC154:coiled-coil domain containing 154 [Gene - OMIM - HGNC]
  • CCDC78:coiled-coil domain containing 78 [Gene - OMIM - HGNC]
  • CRAMP1:cramped chromatin regulator homolog 1 [Gene - HGNC]
  • CIAO3:cytosolic iron-sulfur assembly component 3 [Gene - OMIM - HGNC]
  • EME2:essential meiotic structure-specific endonuclease subunit 2 [Gene - OMIM - HGNC]
  • FAHD1:fumarylacetoacetate hydrolase domain containing 1 [Gene - OMIM - HGNC]
  • GFER:growth factor, augmenter of liver regeneration [Gene - OMIM - HGNC]
  • HS3ST6:heparan sulfate-glucosamine 3-sulfotransferase 6 [Gene - OMIM - HGNC]
  • HAGHL:hydroxyacylglutathione hydrolase like [Gene - HGNC]
  • HAGH:hydroxyacylglutathione hydrolase [Gene - OMIM - HGNC]
  • IGFALS:insulin like growth factor binding protein acid labile subunit [Gene - OMIM - HGNC]
  • IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]
  • JMJD8:jumonji domain containing 8 [Gene - HGNC]
  • LMF1:lipase maturation factor 1 [Gene - OMIM - HGNC]
  • MEIOB:meiosis specific with OB-fold [Gene - OMIM - HGNC]
  • MSLN:mesothelin [Gene - OMIM - HGNC]
  • METRN:meteorin, glial cell differentiation regulator [Gene - OMIM - HGNC]
  • MSRB1:methionine sulfoxide reductase B1 [Gene - OMIM - HGNC]
  • METTL26:methyltransferase like 26 [Gene - HGNC]
  • MIR1225:microRNA 1225 [Gene - OMIM - HGNC]
  • MRPS34:mitochondrial ribosomal protein S34 [Gene - OMIM - HGNC]
  • MAPK8IP3:mitogen-activated protein kinase 8 interacting protein 3 [Gene - OMIM - HGNC]
  • NPW:neuropeptide W [Gene - OMIM - HGNC]
  • NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
  • PTX4:pentraxin 4 [Gene - OMIM - HGNC]
  • PIGQ:phosphatidylinositol glycan anchor biosynthesis class Q [Gene - OMIM - HGNC]
  • PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]
  • PRR25:proline rich 25 [Gene - HGNC]
  • RHOT2:ras homolog family member T2 [Gene - OMIM - HGNC]
  • RHBDL1:rhomboid like 1 [Gene - OMIM - HGNC]
  • RPL3L:ribosomal protein L3 like [Gene - OMIM - HGNC]
  • RPS2:ribosomal protein S2 [Gene - OMIM - HGNC]
  • RNF151:ring finger protein 151 [Gene - HGNC]
  • SNHG9:small nucleolar RNA host gene 9 [Gene - HGNC]
  • SSTR5:somatostatin receptor 5 [Gene - OMIM - HGNC]
  • SPSB3:splA/ryanodine receptor domain and SOCS box containing 3 [Gene - OMIM - HGNC]
  • SYNGR3:synaptogyrin 3 [Gene - OMIM - HGNC]
  • TELO2:telomere maintenance 2 [Gene - OMIM - HGNC]
  • TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
  • TMEM204:transmembrane protein 204 [Gene - OMIM - HGNC]
  • TPSAB1:tryptase alpha/beta 1 [Gene - OMIM - HGNC]
  • TPSB2:tryptase beta 2 [Gene - OMIM - HGNC]
  • TPSD1:tryptase delta 1 [Gene - OMIM - HGNC]
  • TPSG1:tryptase gamma 1 [Gene - OMIM - HGNC]
  • UQCC4:ubiquinol-cytochrome c reductase complex assembly factor 4 [Gene - OMIM - HGNC]
  • UBE2I:ubiquitin conjugating enzyme E2 I [Gene - OMIM - HGNC]
  • UNKL:unk like zinc finger [Gene - OMIM - HGNC]
  • ZNF598:zinc finger protein 598, E3 ubiquitin ligase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16p13.3
Genomic location:
Chr16: 624055 - 2153916 (on Assembly GRCh37)
Preferred name:
NC_000016.9:g.(?_624055)_(2153916_?)dup
HGVS:
NC_000016.9:g.(?_624055)_(2153916_?)dup

Condition(s)

Name:
Epilepsy
Synonyms:
Seizure Disorders; Seizure disorder
Identifiers:
MONDO: MONDO:0005027; MeSH: D004827; MedGen: C0014544

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001538121Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 27, 2020) 		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 Invitae, SCV001538121.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the PIGQ gene. 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 with PIGQ-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: Jul 15, 2024