rs28455570

Positions:

• chr8-143918901-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_201384.3(PLEC):​c.10920C>T​(p.Tyr3640=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 1,611,580 control chromosomes in the GnomAD database, including 7,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.069 (503 hom., cov: 33)
  • Exomes 𝑓: 0.094 (7309 hom.)
• Consequence: PLEC NM_201384.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: -0.269

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 These names were superseded by plectin.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]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant 8-143918901-G-A is Benign according to our data. Variant chr8-143918901-G-A is described in ClinVar as [Benign]. Clinvar id is 129923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-143918901-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-0.269 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEC	NM_201384.3	c.10920C>T	p.Tyr3640=	synonymous_variant	32/32	ENST00000345136.8	NP_958786.1
PLEC	NM_201378.4	c.10878C>T	p.Tyr3626=	synonymous_variant	32/32	ENST00000356346.7	NP_958780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLEC	ENST00000345136.8	c.10920C>T	p.Tyr3640=	synonymous_variant	32/32	1	NM_201384.3	ENSP00000344848
PLEC	ENST00000356346.7	c.10878C>T	p.Tyr3626=	synonymous_variant	32/32	1	NM_201378.4	ENSP00000348702

Frequencies

GnomAD3 genomes AF: 0.0689 AC: 10476 AN: 152154 Hom.: 503 Cov.: 33

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0221

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0607

GnomAD3 exomes AF: 0.0666 AC: 16414 AN: 246610 Hom.: 780 AF XY: 0.0669 AC XY: 8994 AN XY: 134430

Gnomad AFR exome AF: 0.0170

Gnomad AMR exome AF: 0.0247

Gnomad ASJ exome AF: 0.0210

Gnomad EAS exome AF: 0.0000558

Gnomad SAS exome AF: 0.0243

Gnomad FIN exome AF: 0.124

Gnomad NFE exome AF: 0.102

Gnomad OTH exome AF: 0.0616

GnomAD4 exome AF: 0.0937 AC: 136708 AN: 1459308 Hom.: 7309 Cov.: 70 AF XY: 0.0913 AC XY: 66300 AN XY: 726102

Gnomad4 AFR exome AF: 0.0132

Gnomad4 AMR exome AF: 0.0254

Gnomad4 ASJ exome AF: 0.0225

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0255

Gnomad4 FIN exome AF: 0.126

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.0774

GnomAD4 genome AF: 0.0688 AC: 10474 AN: 152272 Hom.: 503 Cov.: 33 AF XY: 0.0677 AC XY: 5038 AN XY: 74442

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0871 Hom.: 404

Bravo AF: 0.0599

Asia WGS AF: 0.00924 AC: 32 AN: 3478

EpiCase AF: 0.0915

EpiControl AF: 0.0868

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:4

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 13, 2015	p.Tyr3777Tyr in exon 32 of PLEC: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 9.6% (816/8492) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs28455570). -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 20, 2014	- -

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 21, 2018	- -

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

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.13
DANN	Benign	0.93
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

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: rs28455570; hg19: chr8-144993069;