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NM_170707.4(LMNA):c.3G>T (p.Met1Ile) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Apr 28, 2017
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:
RCV000182378.7

Allele description [Variation Report for NM_170707.4(LMNA):c.3G>T (p.Met1Ile)]

NM_170707.4(LMNA):c.3G>T (p.Met1Ile)

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.3G>T (p.Met1Ile)
Other names:
p.M1I:ATG>ATT
HGVS:
  • NC_000001.11:g.156114921G>T
  • NG_008692.2:g.37349G>T
  • NM_001282625.2:c.3G>T
  • NM_001282626.2:c.3G>T
  • NM_005572.4:c.3G>T
  • NM_170707.4:c.3G>TMANE SELECT
  • NM_170708.4:c.3G>T
  • NP_001269554.1:p.Met1Ile
  • NP_001269555.1:p.Met1Ile
  • NP_005563.1:p.Met1Ile
  • NP_733821.1:p.Met1Ile
  • NP_733822.1:p.Met1Ile
  • LRG_254t2:c.3G>T
  • LRG_254:g.37349G>T
  • NC_000001.10:g.156084712G>T
  • NM_170707.2:c.3G>T
Protein change:
M1I
Links:
dbSNP: rs794728598
NCBI 1000 Genomes Browser:
rs794728598
Molecular consequence:
  • NM_001282625.2:c.3G>T - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001282626.2:c.3G>T - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_005572.4:c.3G>T - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_170707.4:c.3G>T - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_170708.4:c.3G>T - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001282625.2:c.3G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282626.2:c.3G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005572.4:c.3G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170707.4:c.3G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170708.4:c.3G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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
SCV000234715GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Apr 28, 2017)
germlineclinical testing

Citation Link,

SCV000344046Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Likely pathogenic
(Aug 15, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000234715.11

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

Description

p.Met1Ile (M1I) ATG>ATT: c.3 G>T in exon 1 of the LMNA gene (NM_170707.2). The c.3 G>T mutation in the LMNA gene has not been reported as a disease-causing mutation or as a benign polymorphism, to our knowledge. This mutation alters the initiator Methionine codon, and the resultant protein would be described as p.Met1?" using a question mark to signify that it is not known if the loss of Met1 means that all protein translation is completely prevented or if an abnormal protein is produced using an alternate Met. Two mutations which affect the Met1 residue have been reported in association with laminopathies (Walter M et al., 2005; van Tintelen et al., 2007). Walter et al. identified a 15bp deletion starting at c.-3 that includes the Met1 codon in a family with symptoms of Emery-Driefuss muscular dystrophy, limb girdle muscular dystrophy with atrioventricular disturbance and dilated cardiomyopathy with conduction defects. van Tintelen et al. identified a deletion of the 5' end of the LMNA gene, including exon 1 and the Met1 codon in a family presenting with severe, early onset myocardial fibrosis. Also, c.3 G>T in the LMNA gene has been observed in other unrelated individual tested for DCM at GeneDx. Therefore, the presence of this mutation indicates an increased risk to develop DCM. However, other genetic and environmental factors influence disease expression and severity, and some mutation carriers may never become symptomatic. The variant is found in DCM panel(s)."

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

From Eurofins Ntd Llc (ga), SCV000344046.5

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

Last Updated: Sep 29, 2024