VCV002633687.2 - ClinVar

NM_144573.4(NEXN):c.1898G>A (p.Arg633Lys)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_144573.4(NEXN):c.1898G>A (p.Arg633Lys)

Variation ID: 2633687 Accession: VCV002633687.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p31.1 1: 77942699 (GRCh38) [ NCBI UCSC ] 1: 78408384 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 20, 2023	Aug 11, 2024	May 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_144573.4:c.1898G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_653174.3:p.Arg633Lys	missense
NM_001172309.2:c.1706G>A	NP_001165780.1:p.Arg569Lys	missense
NC_000001.11:g.77942699G>A
NC_000001.10:g.78408384G>A
NG_016625.1:g.59185G>A
NG_033243.2:g.41395C>T
LRG_442:g.59185G>A
LRG_442t1:c.1898G>A	LRG_442p1:p.Arg633Lys
LRG_995:g.41395C>T

... more HGVS ... less HGVS

Protein change

R569K, R633K

Other names

Canonical SPDI

NC_000001.11:77942698:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NEXN		-	-	GRCh38 GRCh37	648	728

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
NEXN-related disorder	Uncertain significance (1)	criteria provided, single submitter	Apr 11, 2023	RCV004531644.1
Cardiovascular phenotype	Uncertain significance (1)	criteria provided, single submitter	May 20, 2024	RCV004654208.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Apr 11, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NEXN-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004110930.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The NEXN c.1898G>A variant is predicted to result in the amino acid substitution p.Arg633Lys. This variant was reported in an individual with dilated cardiomyopathy; however, … (more) The NEXN c.1898G>A variant is predicted to result in the amino acid substitution p.Arg633Lys. This variant was reported in an individual with dilated cardiomyopathy; however, pathogenicity was not established with functional or segregation analysis (Table S3 in Mazzarotto et al. 2020. PubMed ID: 31983221). This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-78408384-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)
Uncertain significance (May 20, 2024)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Cardiovascular phenotype Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV005141702.1 First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024	Publications: PubMed (1) PubMed: 31983221 Comment: The p.R633K variant (also known as c.1898G>A), located in coding exon 12 of the NEXN gene, results from a G to A substitution at nucleotide … (more) The p.R633K variant (also known as c.1898G>A), located in coding exon 12 of the NEXN gene, results from a G to A substitution at nucleotide position 1898. The arginine at codon 633 is replaced by lysine, an amino acid with highly similar properties. This variant has been reported in a dilated cardiomyopathy (DCM) cohort (Mazzarotto F et al. Circulation, 2020 Feb;141:387-398). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. (less)

Comment:

The NEXN c.1898G>A variant is predicted to result in the amino acid substitution p.Arg633Lys. This variant was reported in an individual with dilated cardiomyopathy; however, pathogenicity was not established with functional or segregation analysis (Table S3 in Mazzarotto et al. 2020. PubMed ID: 31983221). This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-78408384-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Comment:

The p.R633K variant (also known as c.1898G>A), located in coding exon 12 of the NEXN gene, results from a G to A substitution at nucleotide position 1898. The arginine at codon 633 is replaced by lysine, an amino acid with highly similar properties. This variant has been reported in a dilated cardiomyopathy (DCM) cohort (Mazzarotto F et al. Circulation, 2020 Feb;141:387-398). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Reevaluating the Genetic Contribution of Monogenic Dilated Cardiomyopathy.	Mazzarotto F	Circulation	2020	PMID: 31983221

Text-mined citations for this variant ...

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_144573.4(NEXN):c.1898G>A (p.Arg633Lys)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...