NM_170707.4(LMNA):c.13del (p.Ser5fs) AND Charcot-Marie-Tooth disease type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 18, 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:: RCV001207729.5

Allele description [Variation Report for NM_170707.4(LMNA):c.13del (p.Ser5fs)]

NM_170707.4(LMNA):c.13del (p.Ser5fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NM_170707.4(LMNA):c.13del (p.Ser5fs)

HGVS:

NC_000001.11:g.156114931del
NG_008692.2:g.37359del
NM_001282625.2:c.13del
NM_001282626.2:c.13del
NM_005572.4:c.13del
NM_170707.4:c.13delMANE SELECT
NM_170708.4:c.13del
NP_001269554.1:p.Ser5fs
NP_001269555.1:p.Ser5fs
NP_005563.1:p.Ser5fs
NP_733821.1:p.Ser5fs
NP_733822.1:p.Ser5fs
LRG_254:g.37359del
NC_000001.10:g.156084722del
NM_170707.3:c.13del

Protein change:

S5fs

Links:

dbSNP: rs1649695841

NCBI 1000 Genomes Browser:

rs1649695841

Molecular consequence:

NM_001282625.2:c.13del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282626.2:c.13del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005572.4:c.13del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_170707.4:c.13del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_170708.4:c.13del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001379094	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 18, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18585512, 18926329, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001379094

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 18, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Lamin A/C mutation analysis in a cohort of 324 unrelated patients with idiopathic or familial dilated cardiomyopathy.

Parks SB, Kushner JD, Nauman D, Burgess D, Ludwigsen S, Peterson A, Li D, Jakobs P, Litt M, Porter CB, Rahko PS, Hershberger RE.

Am Heart J. 2008 Jul;156(1):161-9. doi: 10.1016/j.ahj.2008.01.026. Epub 2008 Mar 12.

PubMed [citation]

PMID:: 18585512
PMCID:: PMC2527054

Long-term outcome and risk stratification in dilated cardiolaminopathies.

Pasotti M, Klersy C, Pilotto A, Marziliano N, Rapezzi C, Serio A, Mannarino S, Gambarin F, Favalli V, Grasso M, Agozzino M, Campana C, Gavazzi A, Febo O, Marini M, Landolina M, Mortara A, Piccolo G, Viganò M, Tavazzi L, Arbustini E.

J Am Coll Cardiol. 2008 Oct 7;52(15):1250-60. doi: 10.1016/j.jacc.2008.06.044.

PubMed [citation]

PMID:: 18926329

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001379094.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 938501). This variant has not been reported in the literature in individuals affected with LMNA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser5Profs*91) in the LMNA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LMNA are known to be pathogenic (PMID: 18585512, 18926329). For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 20, 2024

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