rs7003580

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_201384.3(PLEC):c.1264-15G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,607,214 control chromosomes in the GnomAD database, including 133,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 16523 hom., cov: 33)

Exomes 𝑓: 0.40 ( 116933 hom. )

Consequence

PLEC
NM_201384.3 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.847

Variant links:

Genes affected

PLEC (HGNC:9069): (plectin) Plectin is a prominent member of an important family of structurally and in part functionally related proteins, termed plakins or cytolinkers, that are capable of interlinking different elements of the cytoskeleton. Plakins, with their multi-domain structure and enormous size, not only play crucial roles in maintaining cell and tissue integrity and orchestrating dynamic changes in cytoarchitecture and cell shape, but also serve as scaffolding platforms for the assembly, positioning, and regulation of signaling complexes (reviewed in PMID: 9701547, 11854008, and 17499243). Plectin is expressed as several protein isoforms in a wide range of cell types and tissues from a single gene located on chromosome 8 in humans (PMID: 8633055, 8698233). Until 2010, this locus was named plectin 1 (symbol PLEC1 in human; Plec1 in mouse and rat) and the gene product had been referred to as "hemidesmosomal protein 1" or "plectin 1, intermediate filament binding 500kDa". These names were superseded by plectin. The plectin gene locus in mouse on chromosome 15 has been analyzed in detail (PMID: 10556294, 14559777), revealing a genomic exon-intron organization with well over 40 exons spanning over 62 kb and an unusual 5' transcript complexity of plectin isoforms. Eleven exons (1-1j) have been identified that alternatively splice directly into a common exon 2 which is the first exon to encode plectin's highly conserved actin binding domain (ABD). Three additional exons (-1, 0a, and 0) splice into an alternative first coding exon (1c), and two additional exons (2alpha and 3alpha) are optionally spliced within the exons encoding the acting binding domain (exons 2-8). Analysis of the human locus has identified eight of the eleven alternative 5' exons found in mouse and rat (PMID: 14672974); exons 1i, 1j and 1h have not been confirmed in human. Furthermore, isoforms lacking the central rod domain encoded by exon 31 have been detected in mouse (PMID:10556294), rat (PMID: 9177781), and human (PMID: 11441066, 10780662, 20052759). The short alternative amino-terminal sequences encoded by the different first exons direct the targeting of the various isoforms to distinct subcellular locations (PMID: 14559777). As the expression of specific plectin isoforms was found to be dependent on cell type (tissue) and stage of development (PMID: 10556294, 12542521, 17389230) it appears that each cell type (tissue) contains a unique set (proportion and composition) of plectin isoforms, as if custom-made for specific requirements of the particular cells. Concordantly, individual isoforms were found to carry out distinct and specific functions (PMID: 14559777, 12542521, 18541706). In 1996, a number of groups reported that patients suffering from epidermolysis bullosa simplex with muscular dystrophy (EBS-MD) lacked plectin expression in skin and muscle tissues due to defects in the plectin gene (PMID: 8698233, 8941634, 8636409, 8894687, 8696340). Two other subtypes of plectin-related EBS have been described: EBS-pyloric atresia (PA) and EBS-Ogna. For reviews of plectin-related diseases see PMID: 15810881, 19945614. Mutations in the plectin gene related to human diseases should be named based on the position in NM_000445 (variant 1, isoform 1c), unless the mutation is located within one of the other alternative first exons, in which case the position in the respective Reference Sequence should be used. [provided by RefSeq, Aug 2011]

PLEC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 8-143933366-C-T is Benign according to our data. Variant chr8-143933366-C-T is described in ClinVar as [Benign]. Clinvar id is 227018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-143933366-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLEC	NM_201378.4 linkuse as main transcript	c.1222-15G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000356346.7
PLEC	NM_201384.3 linkuse as main transcript	c.1264-15G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000345136.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLEC	ENST00000345136.8 linkuse as main transcript	c.1264-15G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_201384.3		Q15149-4
PLEC	ENST00000356346.7 linkuse as main transcript	c.1222-15G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_201378.4		Q15149-9

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68197

AN:

151930

Hom.:

16479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.397

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.446

GnomAD3 exomes

AF:

0.373

AC:

91127

AN:

244494

Hom.:

18434

AF XY:

0.374

AC XY:

49915

AN XY:

133482

show subpopulations

Gnomad AFR exome

AF:

0.635

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.405

Gnomad NFE exome

AF:

0.400

Gnomad OTH exome

AF:

0.394

GnomAD4 exome

AF:

0.396

AC:

575538

AN:

1455166

Hom.:

116933

Cov.:

AF XY:

0.393

AC XY:

284890

AN XY:

724110

show subpopulations

Gnomad4 AFR exome

AF:

0.646

Gnomad4 AMR exome

AF:

0.272

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.351

Gnomad4 FIN exome

AF:

0.393

Gnomad4 NFE exome

AF:

0.402

Gnomad4 OTH exome

AF:

0.405

GnomAD4 genome

AF:

0.449

AC:

68280

AN:

152048

Hom.:

16523

Cov.:

AF XY:

0.444

AC XY:

33018

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.632

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.456

Gnomad4 EAS

AF:

0.157

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.443

Alfa

AF:

0.442

Hom.:

3131

Bravo

AF:

0.452

Asia WGS

AF:

0.262

AC:

916

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 24, 2014	1675-15G>A in intron 12 of PLEC: This variant is not expected to have clinical s ignificance because it has been identified in 39.5% (3350/8484) of European Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs7003580). -

Epidermolysis bullosa simplex with nail dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

Epidermolysis bullosa simplex, Ogna type;C2677349:Epidermolysis bullosa simplex 5C, with pyloric atresia;C2931072:Epidermolysis bullosa simplex 5B, with muscular dystrophy;C3150989:Autosomal recessive limb-girdle muscular dystrophy type 2Q;C4225309:Epidermolysis bullosa simplex with nail dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Epidermolysis bullosa simplex 5C, with pyloric atresia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

Epidermolysis bullosa simplex 5B, with muscular dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Autosomal recessive limb-girdle muscular dystrophy type 2Q

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

Epidermolysis bullosa simplex, Ogna type

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

Cadd

Benign

0.076

Dann

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over