rs57983345

chr1-156115034-A-Gchr1-156115034-A-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_170707.4(LMNA):c.116A>G(p.Asn39Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N39K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LMNA NM_170707.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6 O:1
• Conservation: PhyloP100: 7.33

Genes affected

LMNA (HGNC:6636): (lamin A/C) The protein encoded by this gene is part of the nuclear lamina, a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a hotspot region, there are 13 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 11 uncertain in NM_170707.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-156115033-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2202857.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP2: Missense variant where missense usually causes diseases, LMNA
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.994
• PP5: Variant 1-156115034-A-G is Pathogenic according to our data. Variant chr1-156115034-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 66791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-156115034-A-G is described in Lovd as [Pathogenic]. Variant chr1-156115034-A-G is described in Lovd as [Pathogenic]. Variant chr1-156115034-A-G is described in Lovd as [Likely_pathogenic]. Variant chr1-156115034-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMNA	NM_170707.4	c.116A>G	p.Asn39Ser	missense_variant	1/12	ENST00000368300.9
LMNA	NM_005572.4	c.116A>G	p.Asn39Ser	missense_variant	1/10	ENST00000677389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMNA	ENST00000368300.9	c.116A>G	p.Asn39Ser	missense_variant	1/12	1	NM_170707.4	P1
LMNA	ENST00000677389.1	c.116A>G	p.Asn39Ser	missense_variant	1/10		NM_005572.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1447038 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 718414

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 02, 2022	The LMNA c.116A>G (p.Asn39Ser) missense variant results in the substitution of asparagine at amino acid position 39 with serine. Across a selection of the available literature, the c.116A>G variant has been identified in at least ten individuals with muscular disorders, and in five of these it was found to be de novo (PMID: 18551513; PMID: 24508248; PMID: 26098624; PMID: 33250842; PMID: 32571898; PMID: 32528171; PMID: 34240052). Functional studies demonstrated that this variant causes the variant LMNA protein to aggregate (PMID: 34862408). Other pathogenic missense changes at the same codon, including p.Asn39Lys and p.Asn39Tyr, have been reported in multiple individuals with muscular disorders. This variant is located within the N-terminal Coil 1A coiled-coil domain which is a part of the larger central rod region and is thought to be involved in head to tail interactions of nuclear lamins and in facilitating the unwinding of molecules into separate strands (PMID: 30083363; PMID: 15476822). Multiple lines of in silico predictions suggest that this variant may have a deleterious effect on the gene or gene product. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Based on the available evidence, the c.116A>G (p.Asn39Ser) variant is classified as pathogenic for LMNA-related muscular disorders. -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 08, 2016	- -
not provided, no classification provided	literature only	Epithelial Biology; Institute of Medical Biology, Singapore	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital	Dec 17, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 07, 2017	The N39S pathogenic variant in the LMNA gene was first initially reported in an individual with EDMD (Benedetti et al., 2007), and subsequently reported as an apparently de novo variant in additional individuals with LMNA-related disorders (Quijano-Roy et al., 2008; Pasqualin et al., 2014). The N39S variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species, and different missense variants at the same position (N39Y/K) have been previously reported in association with muscular dystrophy (Prigogine et al., 2010; Tan et al., 2015). Additionally, missense variants in nearby residues (L35V/P; R41C/S; A43T) have been reported in the Human Gene Mutation Database in association with LMNA-related disorders (Stenson et al., 2014), supporting the functional importance of this region of the protein. In silico analysis predicts this variant is probably damaging to the protein structure/function. -

Charcot-Marie-Tooth disease type 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jul 05, 2023

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. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 66791). This missense change has been observed in individual(s) with Emery-Dreifuss muscular dystrophy, congenital muscular dystrophy, and limb-girdle muscular dystrophy (PMID: 17377071, 18551513, 21520333, 24508248). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 39 of the LMNA protein (p.Asn39Ser). -

LMNA-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Mar 02, 2022

ACMG classification criteria: PS4 strong, PM2, PM5 moderated, PM6 strong, PP3 supporting -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
CardioboostCm	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.16
Cadd	Pathogenic	27
Dann	Uncertain	1.0
Eigen	Pathogenic	0.85
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;D;D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	4.8	H;.;H;H;H
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-4.3	D;D;D;D;D
REVEL	Pathogenic	0.88
Sift	Uncertain	0.0020	D;D;D;D;D
Sift4G	Uncertain	0.0040	D;D;D;D;D
Polyphen		1.0	D;.;D;D;.
Vest4		1.0
MutPred		0.96		Gain of phosphorylation at N39 (P = 0.0422);Gain of phosphorylation at N39 (P = 0.0422);Gain of phosphorylation at N39 (P = 0.0422);Gain of phosphorylation at N39 (P = 0.0422);Gain of phosphorylation at N39 (P = 0.0422);
MVP		0.97
MPC		1.8
ClinPred		1.0	D
GERP RS		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.67
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs57983345; hg19: chr1-156084825;