NM_170707.4(LMNA):c.3G>A (p.Met1Ile) AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 30, 2020
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:: RCV001268969.1

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

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

HGVS:

NC_000001.11:g.156114921G>A
NG_008692.2:g.37349G>A
NM_001282625.2:c.3G>A
NM_001282626.2:c.3G>A
NM_005572.4:c.3G>A
NM_170707.4:c.3G>AMANE SELECT
NM_170708.4:c.3G>A
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>A
LRG_254:g.37349G>A
NC_000001.10:g.156084712G>A
NM_170707.2:c.3G>A
NM_170707.3:c.3G>A
p.M1I

Protein change:

M1I

Links:

dbSNP: rs794728598

NCBI 1000 Genomes Browser:

rs794728598

Molecular consequence:

NM_001282625.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001282626.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_005572.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_170707.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_170708.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001282625.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282626.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005572.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170707.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170708.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001448193	Petrovsky National Research Centre of Surgery, The Federal Agency for Scientific Organizations	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 30, 2020)	unknown, paternal	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

SCV001448193

Petrovsky National Research Centre of Surgery, The Federal Agency for Scientific Organizations

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 30, 2020)

unknown, paternal

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	paternal	no	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Petrovsky National Research Centre of Surgery, The Federal Agency for Scientific Organizations, SCV001448193.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)
2		1	not provided	not provided	clinical testing	PubMed (1)

Description

No cardiac abnormalities were observed; echocardiographic parameters are age-appropriate.

Description

We observed the genetic variant c.3G>A (p.M1I) in a 43-y.o. male proband, diagnosed with left ventricular non-compaction and dilatation of all cardiac chambers. The c.3G>A genetic variant leads to mutation in the initiation codon (PVS1 criteria). Neither population data (PM2 criteria) nor functional studies are available for this variant. Online in silico tools predict the p.M1I to have the deleterious effect (PP3 criteria). Additionally, this variant was previously reported as pathogenic (PP5). Two more nucleotide changes were reported in this codon, all of them leading to methionine-isoleucine amino acid substitution. We classify the c.3G>A genetic variant as pathogenic due to the combination of PVS1, PM2, PP3, and PP5 criteria.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
2	paternal	no	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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