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NM_144573.4(NEXN):c.1366G>A (p.Gly456Arg) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 19, 2021
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:
RCV001215702.8

Allele description [Variation Report for NM_144573.4(NEXN):c.1366G>A (p.Gly456Arg)]

NM_144573.4(NEXN):c.1366G>A (p.Gly456Arg)

Gene:
NEXN:nexilin F-actin binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p31.1
Genomic location:
Preferred name:
NM_144573.4(NEXN):c.1366G>A (p.Gly456Arg)
HGVS:
  • NC_000001.11:g.77935937G>A
  • NG_016625.1:g.52423G>A
  • NM_001172309.2:c.1174G>A
  • NM_144573.4:c.1366G>AMANE SELECT
  • NP_001165780.1:p.Gly392Arg
  • NP_653174.3:p.Gly456Arg
  • NP_653174.3:p.Gly456Arg
  • LRG_442t1:c.1366G>A
  • LRG_442:g.52423G>A
  • LRG_442p1:p.Gly456Arg
  • NC_000001.10:g.78401622G>A
  • NM_144573.3:c.1366G>A
  • c.1366G>A
Protein change:
G392R
Links:
dbSNP: rs397517844
NCBI 1000 Genomes Browser:
rs397517844
Molecular consequence:
  • NM_001172309.2:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_144573.4:c.1366G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Dilated cardiomyopathy 1CC (CMD1CC)
Identifiers:
MONDO: MONDO:0013147; MedGen: C2751084; Orphanet: 154; OMIM: 613122
Name:
Hypertrophic cardiomyopathy 20
Synonyms:
Familial hypertrophic cardiomyopathy 20
Identifiers:
MONDO: MONDO:0013477; MedGen: C3151267; OMIM: 613876

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001387461Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Feb 19, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples.

Walsh R, Thomson KL, Ware JS, Funke BH, Woodley J, McGuire KJ, Mazzarotto F, Blair E, Seller A, Taylor JC, Minikel EV, Exome Aggregation Consortium, MacArthur DG, Farrall M, Cook SA, Watkins H.

Genet Med. 2017 Feb;19(2):192-203. doi: 10.1038/gim.2016.90. Epub 2016 Aug 17.

PubMed [citation]
PMID:
27532257
PMCID:
PMC5116235

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, SCV001387461.5

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

Description

This variant is present in population databases (rs397517844, ExAC 0.01%). This sequence change replaces glycine with arginine at codon 456 of the NEXN protein (p.Gly456Arg). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and arginine. This variant has been observed in an individual affected with hypertrophic cardiomyopathy (PMID: 27532257). ClinVar contains an entry for this variant (Variation ID: 47888). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0").

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

Last Updated: Sep 29, 2024