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NM_002497.4(NEK2):c.1226A>G (p.Lys409Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 17, 2023
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:
RCV002667065.4

Allele description [Variation Report for NM_002497.4(NEK2):c.1226A>G (p.Lys409Arg)]

NM_002497.4(NEK2):c.1226A>G (p.Lys409Arg)

Gene:
NEK2:NIMA related kinase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q32.3
Genomic location:
Preferred name:
NM_002497.4(NEK2):c.1226A>G (p.Lys409Arg)
HGVS:
  • NC_000001.11:g.211663538T>C
  • NG_029112.1:g.17093A>G
  • NM_001204182.2:c.1111+3568A>G
  • NM_002497.4:c.1226A>GMANE SELECT
  • NP_002488.1:p.Lys409Arg
  • NC_000001.10:g.211836880T>C
Protein change:
K409R
Molecular consequence:
  • NM_001204182.2:c.1111+3568A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002497.4:c.1226A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002979948Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 17, 2023) 		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, SCV002979948.2

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

Description

This variant is present in population databases (rs576980203, gnomAD 0.007%). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1945208). This variant has not been reported in the literature in individuals affected with NEK2-related conditions. This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 409 of the NEK2 protein (p.Lys409Arg).

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

Last Updated: Sep 29, 2024