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NC_000016.9:g.(?_1822222)_(2550959_?)dup AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 2, 2024
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:
RCV004582753.2

Allele description [Variation Report for NC_000016.9:g.(?_1822222)_(2550959_?)dup]

NC_000016.9:g.(?_1822222)_(2550959_?)dup

Genes:
  • ABCA3:ATP binding cassette subfamily A member 3 [Gene - OMIM - HGNC]
  • BRICD5:BRICHOS domain containing 5 [Gene - HGNC]
  • CASKIN1:CASK interacting protein 1 [Gene - OMIM - HGNC]
  • E4F1:E4F transcription factor 1 [Gene - OMIM - HGNC]
  • MLST8:MTOR associated protein, LST8 homolog [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]
  • NUBP2:NUBP iron-sulfur cluster assembly factor 2, cytosolic [Gene - OMIM - HGNC]
  • RAB26:RAB26, member RAS oncogene family [Gene - OMIM - HGNC]
  • RNPS1:RNA binding protein with serine rich domain 1 [Gene - OMIM - HGNC]
  • TBC1D24:TBC1 domain family member 24 [Gene - OMIM - HGNC]
  • TRAF7:TNF receptor associated factor 7 [Gene - OMIM - HGNC]
  • TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
  • CCNF:cyclin F [Gene - OMIM - HGNC]
  • DNASE1L2:deoxyribonuclease 1 like 2 [Gene - OMIM - HGNC]
  • ECI1:enoyl-CoA delta isomerase 1 [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]
  • HAGH:hydroxyacylglutathione hydrolase [Gene - OMIM - HGNC]
  • IGFALS:insulin like growth factor binding protein acid labile subunit [Gene - OMIM - HGNC]
  • MEIOB:meiosis specific with OB-fold [Gene - OMIM - HGNC]
  • MSRB1:methionine sulfoxide reductase B1 [Gene - OMIM - HGNC]
  • MIR1225:microRNA 1225 [Gene - OMIM - HGNC]
  • MRPS34:mitochondrial ribosomal protein S34 [Gene - OMIM - HGNC]
  • NTN3:netrin 3 [Gene - OMIM - HGNC]
  • NPW:neuropeptide W [Gene - OMIM - HGNC]
  • NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
  • PGP:phosphoglycolate phosphatase [Gene - OMIM - HGNC]
  • PKD1:polycystin 1, transient receptor potential channel interacting [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]
  • SPSB3:splA/ryanodine receptor domain and SOCS box containing 3 [Gene - OMIM - HGNC]
  • SYNGR3:synaptogyrin 3 [Gene - OMIM - HGNC]
  • TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
  • TEDC2:tubulin epsilon and delta complex 2 [Gene - HGNC]
  • ZNF598:zinc finger protein 598, E3 ubiquitin ligase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16p13.3
Genomic location:
Chr16: 1822222 - 2550959 (on Assembly GRCh37)
Preferred name:
NC_000016.9:g.(?_1822222)_(2550959_?)dup
HGVS:
NC_000016.9:g.(?_1822222)_(2550959_?)dup

Condition(s)

Name:
Developmental and epileptic encephalopathy, 1 (DEE1)
Synonyms:
INFANTILE SPASM SYNDROME, X-LINKED 1; X-linked infantile spasms; West's syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010632; MedGen: C3463992; OMIM: 308350
Name:
Autosomal dominant nonsyndromic hearing loss 65
Synonyms:
Deafness, autosomal dominant 65
Identifiers:
MONDO: MONDO:0014470; MedGen: C3892048; Orphanet: 90635; OMIM: 616044
Name:
Caused by mutation in the TBC1 domain family, member 24
Identifiers:
MedGen: CN236805

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005062343Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 2, 2024) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Diagnostic implications of genetic copy number variation in epilepsy plus.

Coppola A, Cellini E, Stamberger H, Saarentaus E, Cetica V, Lal D, Djémié T, Bartnik-Glaska M, Ceulemans B, Helen Cross J, Deconinck T, Masi S, Dorn T, Guerrini R, Hoffman-Zacharska D, Kooy F, Lagae L, Lench N, Lemke JR, Lucenteforte E, Madia F, Mefford HC, et al.

Epilepsia. 2019 Apr;60(4):689-706. doi: 10.1111/epi.14683. Epub 2019 Mar 13.

PubMed [citation]
PMID:
30866059
PMCID:
PMC6488157

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, SCV005062343.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the TBC1D24 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. A similar copy number variant has been observed in individual(s) with epilepsy and intellectual disability (PMID: 30866059). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant 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
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024