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NM_170707.4(LMNA):c.1357C>T (p.Arg453Trp) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (9 submissions)
Last evaluated:
Oct 31, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000057273.39

Allele description [Variation Report for NM_170707.4(LMNA):c.1357C>T (p.Arg453Trp)]

NM_170707.4(LMNA):c.1357C>T (p.Arg453Trp)

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.1357C>T (p.Arg453Trp)
HGVS:
  • NC_000001.11:g.156136413C>T
  • NG_008692.2:g.58841C>T
  • NM_001257374.3:c.1021C>T
  • NM_001282624.2:c.1114C>T
  • NM_001282625.2:c.1357C>T
  • NM_001282626.2:c.1357C>T
  • NM_005572.4:c.1357C>T
  • NM_170707.4:c.1357C>TMANE SELECT
  • NM_170708.4:c.1357C>T
  • NP_001244303.1:p.Arg341Trp
  • NP_001269553.1:p.Arg372Trp
  • NP_001269554.1:p.Arg453Trp
  • NP_001269555.1:p.Arg453Trp
  • NP_005563.1:p.Arg453Trp
  • NP_733821.1:p.Arg453Trp
  • NP_733822.1:p.Arg453Trp
  • LRG_254t2:c.1357C>T
  • LRG_254:g.58841C>T
  • NC_000001.10:g.156106204C>T
  • NM_005572.4:c.1357C>T
  • NM_170707.2:c.1357C>T
  • NM_170707.3:c.1357C>T
  • P02545:p.Arg453Trp
Protein change:
R341W; ARG453TRP
Links:
UniProtKB: P02545#VAR_009988; OMIM: 150330.0002; dbSNP: rs58932704
NCBI 1000 Genomes Browser:
rs58932704
Molecular consequence:
  • NM_001257374.3:c.1021C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282624.2:c.1114C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282625.2:c.1357C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282626.2:c.1357C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005572.4:c.1357C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170707.4:c.1357C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170708.4:c.1357C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
functionally_abnormal [Sequence Ontology: SO:0002218]
Observations:
10

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000088386Epithelial Biology; Institute of Medical Biology, Singapore
no classification provided
not providednot providednot provided

SCV000292719GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Oct 31, 2022)
germlineclinical testing

Citation Link,

SCV000335899Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(Jan 31, 2018)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV001449797Clinical Genetics and Genomics, Karolinska University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 7, 2014)
germlineclinical testing

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

SCV001743435Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Likely pathogenicgermlineclinical testing

SCV001954947Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002017167Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 21, 2022)
germlineclinical testing

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

SCV002544321CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Apr 1, 2022)
germlineclinical testing

Citation Link,

SCV002771306Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)
Pathogenic
(May 26, 2022)
unknownclinical testing

PubMed (20)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown8not providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy.

Bonne G, Di Barletta MR, Varnous S, Bécane HM, Hammouda EH, Merlini L, Muntoni F, Greenberg CR, Gary F, Urtizberea JA, Duboc D, Fardeau M, Toniolo D, Schwartz K.

Nat Genet. 1999 Mar;21(3):285-8.

PubMed [citation]
PMID:
10080180

Disruption of the lamin A and matrin-3 interaction by myopathic LMNA mutations.

Depreux FF, Puckelwartz MJ, Augustynowicz A, Wolfgeher D, Labno CM, Pierre-Louis D, Cicka D, Kron SJ, Holaska J, McNally EM.

Hum Mol Genet. 2015 Aug 1;24(15):4284-95. doi: 10.1093/hmg/ddv160. Epub 2015 May 6.

PubMed [citation]
PMID:
25948554
PMCID:
PMC4492393
See all PubMed Citations (23)

Details of each submission

From Epithelial Biology; Institute of Medical Biology, Singapore, SCV000088386.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From GeneDx, SCV000292719.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Identified in patients with autosomal dominant Emery-Dreifuss muscular dystrophy, limb-girdle muscular dystrophy 1B, and congenital fiber type disproportion myopathy in published literature (Bonne et al., 1999; Mitsuhashi et al., 2010; Kajino et al., 2014); Published functional studies demonstrate the R453W variant alters lamin A protein binding characteristics, and cells expressing the variant exhibit structural abnormalities as well as anomalous differentiation and proliferation (Depreux et al., 2015; Favreau et al., 2004; Folker et al., 2011); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11503164, 18396274, 23427149, 20848652, 18646565, 11731280, 34440373, 27363342, 34862408, 24375749, 22326558, 19524666, 11792809, 21173262, 13129702, 25948554, 20980393, 24907107, 30199159, 28214269, 28987496, 25987458, 24642510, 29057633, 27854218, 23891399, 18551515, 30912254, 30764827, 30107846, 31498906, 32154989, 32576226, 31127727, 34240052, 33502018, 32571898, 32381727, 32140910, 33146414, 12783988, 33084218, 32528171, 33124102, 35741838, 35723113, 16809772, 10080180, 14749366, 10939567)

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

From Eurofins Ntd Llc (ga), SCV000335899.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided8not providednot providedclinical testing PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided8not providednot providednot provided

From Clinical Genetics and Genomics, Karolinska University Hospital, SCV001449797.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743435.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001954947.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002017167.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV002544321.16

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

LMNA: PS4, PM2, PM5, PM6, PS3:Supporting

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Athena Diagnostics, SCV002771306.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (20)

Description

This variant has been identified heterozygous in multiple unrelated individuals with Emery-Dreifuss Muscular Dystrophy (EDMD), suggesting dominant inheritance. This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). Computational tools predict that this variant is damaging.

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

Last Updated: Nov 24, 2024