NM_170707.4(LMNA):c.1324G>A (p.Val442Met) AND Charcot-Marie-Tooth disease type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 2022
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:: RCV000808964.4

Allele description [Variation Report for NM_170707.4(LMNA):c.1324G>A (p.Val442Met)]

NM_170707.4(LMNA):c.1324G>A (p.Val442Met)

Gene:

LMNA:lamin A/C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NM_170707.4(LMNA):c.1324G>A (p.Val442Met)

Other names:

p.Val442Met

HGVS:

NC_000001.11:g.156136380G>A
NG_008692.2:g.58808G>A
NM_001257374.3:c.988G>A
NM_001282624.2:c.1081G>A
NM_001282625.2:c.1324G>A
NM_001282626.2:c.1324G>A
NM_005572.4:c.1324G>A
NM_170707.4:c.1324G>AMANE SELECT
NM_170708.4:c.1324G>A
NP_001244303.1:p.Val330Met
NP_001269553.1:p.Val361Met
NP_001269554.1:p.Val442Met
NP_001269555.1:p.Val442Met
NP_005563.1:p.Val442Met
NP_005563.1:p.Val442Met
NP_733821.1:p.Val442Met
NP_733822.1:p.Val442Met
LRG_254t1:c.1324G>A
LRG_254t2:c.1324G>A
LRG_254:g.58808G>A
LRG_254p1:p.Val442Met
NC_000001.10:g.156106171G>A
NM_001257374.3:c.988G>A
NM_005572.3:c.1324G>A
NM_170707.2:c.1324G>A
NM_170707.3:c.1324G>A

Protein change:

V330M

Links:

dbSNP: rs368542816

NCBI 1000 Genomes Browser:

rs368542816

Molecular consequence:

NM_001257374.3:c.988G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282624.2:c.1081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282625.2:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282626.2:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005572.4:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170707.4:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170708.4:c.1324G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Charcot-Marie-Tooth disease type 2
Synonyms:: Charcot-Marie-Tooth, Type 2
Identifiers:: MONDO: MONDO:0018993; MedGen: C0270914

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000949098	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000949098

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000949098.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 442 of the LMNA protein (p.Val442Met). This variant is present in population databases (rs368542816, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LMNA-related conditions. ClinVar contains an entry for this variant (Variation ID: 519022). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LMNA protein function. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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