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NC_000009.11:g.(?_138594085)_(140062314_?)dup AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 14, 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:
RCV001305481.1

Allele description

NC_000009.11:g.(?_138594085)_(140062314_?)dup

Genes:
  • AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 2 [Gene - OMIM - HGNC]
  • ABCA2:ATP binding cassette subfamily A member 2 [Gene - OMIM - HGNC]
  • DNLZ:DNL-type zinc finger [Gene - OMIM - HGNC]
  • EGFL7:EGF like domain multiple 7 [Gene - OMIM - HGNC]
  • FBXW5:F-box and WD repeat domain containing 5 [Gene - OMIM - HGNC]
  • GPSM1:G protein signaling modulator 1 [Gene - OMIM - HGNC]
  • LHX3:LIM homeobox 3 [Gene - OMIM - HGNC]
  • MAMDC4:MAM domain containing 4 [Gene - OMIM - HGNC]
  • NACC2:NACC family member 2 [Gene - OMIM - HGNC]
  • PAXX:PAXX non-homologous end joining factor [Gene - OMIM - HGNC]
  • RABL6:RAB, member RAS oncogene family like 6 [Gene - OMIM - HGNC]
  • SEC16A:SEC16 homolog A, endoplasmic reticulum export factor [Gene - OMIM - HGNC]
  • TRAF2:TNF receptor associated factor 2 [Gene - OMIM - HGNC]
  • UBAC1:UBA domain containing 1 [Gene - OMIM - HGNC]
  • UAP1L1:UDP-N-acetylglucosamine pyrophosphorylase 1 like 1 [Gene - HGNC]
  • AJM1:apical junction component 1 homolog [Gene - HGNC]
  • CAMSAP1:calmodulin regulated spectrin associated protein 1 [Gene - OMIM - HGNC]
  • CARD9:caspase recruitment domain family member 9 [Gene - OMIM - HGNC]
  • CLIC3:chloride intracellular channel 3 [Gene - OMIM - HGNC]
  • C9orf163:chromosome 9 putative open reading frame 163 [Gene - HGNC]
  • CCDC183:coiled-coil domain containing 183 [Gene - OMIM - HGNC]
  • C8G:complement C8 gamma chain [Gene - OMIM - HGNC]
  • DPP7:dipeptidyl peptidase 7 [Gene - OMIM - HGNC]
  • DIPK1B:divergent protein kinase domain 1B [Gene - OMIM - HGNC]
  • ENTPD2:ectonucleoside triphosphate diphosphohydrolase 2 [Gene - OMIM - HGNC]
  • ENTR1:endosome associated trafficking regulator 1 [Gene - OMIM - HGNC]
  • EDF1:endothelial differentiation related factor 1 [Gene - OMIM - HGNC]
  • FUT7:fucosyltransferase 7 [Gene - OMIM - HGNC]
  • GRIN1:glutamate ionotropic receptor NMDA type subunit 1 [Gene - OMIM - HGNC]
  • INPP5E:inositol polyphosphate-5-phosphatase E [Gene - OMIM - HGNC]
  • LCN10:lipocalin 10 [Gene - OMIM - HGNC]
  • LCN12:lipocalin 12 [Gene - OMIM - HGNC]
  • LCN15:lipocalin 15 [Gene - HGNC]
  • LCN6:lipocalin 6 [Gene - OMIM - HGNC]
  • LCN8:lipocalin 8 [Gene - OMIM - HGNC]
  • LCNL1:lipocalin like 1 [Gene - HGNC]
  • LINC02908:long intergenic non-protein coding RNA 2908 [Gene - HGNC]
  • MAN1B1:mannosidase alpha class 1B member 1 [Gene - OMIM - HGNC]
  • MIR126:microRNA 126 [Gene - OMIM - HGNC]
  • NPDC1:neural proliferation, differentiation and control 1 [Gene - OMIM - HGNC]
  • NOTCH1:notch receptor 1 [Gene - OMIM - HGNC]
  • PMPCA:peptidase, mitochondrial processing subunit alpha [Gene - OMIM - HGNC]
  • PHPT1:phosphohistidine phosphatase 1 [Gene - OMIM - HGNC]
  • KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
  • PTGDS:prostaglandin D2 synthase [Gene - OMIM - HGNC]
  • QSOX2:quiescin sulfhydryl oxidase 2 [Gene - OMIM - HGNC]
  • SNAPC4:small nuclear RNA activating complex polypeptide 4 [Gene - OMIM - HGNC]
  • SNHG7:small nucleolar RNA host gene 7 [Gene - HGNC]
  • SAPCD2:suppressor APC domain containing 2 [Gene - OMIM - HGNC]
  • TMEM141:transmembrane protein 141 [Gene - HGNC]
  • TMEM250:transmembrane protein 250 [Gene - HGNC]
Variant type:
Duplication
Cytogenetic location:
9q34.3
Genomic location:
Chr9: 138594085 - 140062314 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_138594085)_(140062314_?)dup
HGVS:
NC_000009.11:g.(?_138594085)_(140062314_?)dup

Condition(s)

Name:
Developmental and epileptic encephalopathy, 14 (DEE14)
Synonyms:
Early infantile epileptic encephalopathy 14
Identifiers:
MONDO: MONDO:0013989; MedGen: C3554195; Orphanet: 293181; OMIM: 614959
Name:
Autosomal dominant nocturnal frontal lobe epilepsy 5
Synonyms:
Epilepsy, nocturnal frontal lobe, 5; CILIARY DYSKINESIA, PRIMARY, 28, WITHOUT SITUS INVERSUS; CILIARY DYSKINESIA, PRIMARY, 28, WITH SITUS INVERSUS
Identifiers:
MONDO: MONDO:0014002; MedGen: C3554306; Orphanet: 98784; OMIM: 615005

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001494816Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 14, 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, SCV001494816.1

#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 KCNT1 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 been observed in one or more individuals who were not affected with epilepsy (Invitae). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. 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 1, 2024