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NM_170707.4(LMNA):c.1163G>A (p.Arg388His) AND Charcot-Marie-Tooth disease type 2

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 7, 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:
RCV000805453.5

Allele description [Variation Report for NM_170707.4(LMNA):c.1163G>A (p.Arg388His)]

NM_170707.4(LMNA):c.1163G>A (p.Arg388His)

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.1163G>A (p.Arg388His)
HGVS:
  • NC_000001.11:g.156136219G>A
  • NG_008692.2:g.58647G>A
  • NM_001257374.3:c.827G>A
  • NM_001282624.2:c.920G>A
  • NM_001282625.2:c.1163G>A
  • NM_001282626.2:c.1163G>A
  • NM_005572.4:c.1163G>A
  • NM_170707.4:c.1163G>AMANE SELECT
  • NM_170708.4:c.1163G>A
  • NP_001244303.1:p.Arg276His
  • NP_001269553.1:p.Arg307His
  • NP_001269554.1:p.Arg388His
  • NP_001269555.1:p.Arg388His
  • NP_005563.1:p.Arg388His
  • NP_733821.1:p.Arg388His
  • NP_733822.1:p.Arg388His
  • LRG_254t2:c.1163G>A
  • LRG_254:g.58647G>A
  • NC_000001.10:g.156106010G>A
  • NM_170707.2:c.1163G>A
  • NM_170707.3:c.1163G>A
  • P02545:p.Arg388His
Protein change:
R276H
Links:
UniProtKB: P02545#VAR_070180; dbSNP: rs267607576
NCBI 1000 Genomes Browser:
rs267607576
Molecular consequence:
  • NM_001257374.3:c.827G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282624.2:c.920G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282625.2:c.1163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282626.2:c.1163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005572.4:c.1163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170707.4:c.1163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170708.4:c.1163G>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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000945410Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Nov 7, 2022)
germlineclinical testing

PubMed (4)
[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

A Novel Lamin A Mutant Responsible for Congenital Muscular Dystrophy Causes Distinct Abnormalities of the Cell Nucleus.

Barateau A, Vadrot N, Vicart P, Ferreiro A, Mayer M, Héron D, Vigouroux C, Buendia B.

PLoS One. 2017;12(1):e0169189. doi: 10.1371/journal.pone.0169189.

PubMed [citation]
PMID:
28125586
PMCID:
PMC5268432

Morphological analysis of 13 LMNA variants identified in a cohort of 324 unrelated patients with idiopathic or familial dilated cardiomyopathy.

Cowan J, Li D, Gonzalez-Quintana J, Morales A, Hershberger RE.

Circ Cardiovasc Genet. 2010 Feb;3(1):6-14. doi: 10.1161/CIRCGENETICS.109.905422. Epub 2009 Nov 17.

PubMed [citation]
PMID:
20160190
PMCID:
PMC2908895
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000945410.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg388 amino acid residue in LMNA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 28125586). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects LMNA function (PMID: 20160190). 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. ClinVar contains an entry for this variant (Variation ID: 66790). This missense change has been observed in individual(s) with dilated cardiomyopathy (PMID: 30012837). This variant is present in population databases (rs267607576, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 388 of the LMNA protein (p.Arg388His).

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

Last Updated: May 7, 2024