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NC_000009.11:g.(?_138645763)_(140729425_?)del AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 7, 2019
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:
RCV001362982.13

Allele description [Variation Report for NC_000009.11:g.(?_138645763)_(140729425_?)del]

NC_000009.11:g.(?_138645763)_(140729425_?)del

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]
  • NDOR1:NADPH dependent diflavin oxidoreductase 1 [Gene - OMIM - HGNC]
  • NOXA1:NADPH oxidase activator 1 [Gene - OMIM - HGNC]
  • NSMF:NMDA receptor synaptonuclear signaling and neuronal migration factor [Gene - OMIM - HGNC]
  • NRARP:NOTCH regulated ankyrin repeat protein [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]
  • SSNA1:SS nuclear autoantigen 1 [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]
  • ANAPC2:anaphase promoting complex subunit 2 [Gene - OMIM - HGNC]
  • AJM1:apical junction component 1 homolog [Gene - HGNC]
  • ARRDC1:arrestin domain containing 1 [Gene - OMIM - 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]
  • CIMIP2A:ciliary microtubule inner protein 2A [Gene - HGNC]
  • CCDC183:coiled-coil domain containing 183 [Gene - OMIM - HGNC]
  • C8G:complement C8 gamma chain [Gene - OMIM - HGNC]
  • CYSRT1:cysteine rich tail 1 [Gene - HGNC]
  • DPP7:dipeptidyl peptidase 7 [Gene - OMIM - HGNC]
  • DPH7:diphthamide biosynthesis 7 [Gene - OMIM - HGNC]
  • DIPK1B:divergent protein kinase domain 1B [Gene - OMIM - HGNC]
  • ENTPD2:ectonucleoside triphosphate diphosphohydrolase 2 [Gene - OMIM - HGNC]
  • ENTPD8:ectonucleoside triphosphate diphosphohydrolase 8 [Gene - OMIM - HGNC]
  • ENTR1:endosome associated trafficking regulator 1 [Gene - OMIM - HGNC]
  • EDF1:endothelial differentiation related factor 1 [Gene - OMIM - HGNC]
  • EHMT1:euchromatic histone lysine methyltransferase 1 [Gene - OMIM - HGNC]
  • EXD3:exonuclease 3'-5' domain containing 3 [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]
  • LRRC26:leucine rich repeat containing 26 [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]
  • MRPL41:mitochondrial ribosomal protein L41 [Gene - OMIM - HGNC]
  • NELFB:negative elongation factor complex member B [Gene - OMIM - HGNC]
  • NPDC1:neural proliferation, differentiation and control 1 [Gene - OMIM - HGNC]
  • NOTCH1:notch receptor 1 [Gene - OMIM - HGNC]
  • PNPLA7:patatin like phospholipase domain containing 7 [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]
  • RNF208:ring finger protein 208 [Gene - OMIM - HGNC]
  • RNF224:ring finger protein 224 [Gene - HGNC]
  • SNAPC4:small nuclear RNA activating complex polypeptide 4 [Gene - OMIM - HGNC]
  • SNHG7:small nucleolar RNA host gene 7 [Gene - HGNC]
  • SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]
  • STPG3:sperm-tail PG-rich repeat containing 3 [Gene - HGNC]
  • SAPCD2:suppressor APC domain containing 2 [Gene - OMIM - HGNC]
  • TPRN:taperin [Gene - OMIM - HGNC]
  • TOR4A:torsin family 4 member A [Gene - HGNC]
  • TMEM141:transmembrane protein 141 [Gene - HGNC]
  • TMEM203:transmembrane protein 203 [Gene - OMIM - HGNC]
  • TMEM210:transmembrane protein 210 [Gene - HGNC]
  • TMEM250:transmembrane protein 250 [Gene - HGNC]
  • TUBB4B:tubulin beta 4B class IVb [Gene - OMIM - HGNC]
  • LOC651337:uncharacterized LOC651337 [Gene]
  • ZMYND19:zinc finger MYND-type containing 19 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.3
Genomic location:
Chr9: 138645763 - 140729425 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_138645763)_(140729425_?)del
HGVS:
NC_000009.11:g.(?_138645763)_(140729425_?)del

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
SCV001559050Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 7, 2019) 		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, SCV001559050.5

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

Description

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. This variant has not been reported in the literature in individuals with KCNT1-related conditions. This variant is a gross deletion of the genomic region encompassing exons 5-31 of the KCNT1 gene. The 5' boundary is likely confined to intron 4. The 3' end of this event is unknown as it extends through the termination codon beyond the assayed region for this gene and may encompass additional genes. While this deletion is not anticipated to result in nonsense mediated decay, it is expected to create a truncated protein product or disrupt mRNA translation.

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

Last Updated: Jul 23, 2024