rs77303974

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000345136.8(PLEC):โ€‹c.9925C>Tโ€‹(p.Arg3309Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00758 in 1,613,096 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (โ˜…โ˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3309H) has been classified as Uncertain significance.

Frequency

Genomes: ๐‘“ 0.0049 ( 4 hom., cov: 33)
Exomes ๐‘“: 0.0079 ( 45 hom. )

Consequence

PLEC
ENST00000345136.8 missense

Scores

6
9
4

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 3.40
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 These names were superseded by plectin.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]

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 (MetaRNN=0.014019251).
BP6
Variant 8-143919896-G-A is Benign according to our data. Variant chr8-143919896-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 93014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-143919896-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00489 (745/152354) while in subpopulation NFE AF= 0.00788 (536/68040). AF 95% confidence interval is 0.00733. There are 4 homozygotes in gnomad4. There are 322 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLECNM_201384.3 linkuse as main transcriptc.9925C>T p.Arg3309Cys missense_variant 32/32 ENST00000345136.8 NP_958786.1
PLECNM_201378.4 linkuse as main transcriptc.9883C>T p.Arg3295Cys missense_variant 32/32 ENST00000356346.7 NP_958780.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLECENST00000345136.8 linkuse as main transcriptc.9925C>T p.Arg3309Cys missense_variant 32/321 NM_201384.3 ENSP00000344848 Q15149-4
PLECENST00000356346.7 linkuse as main transcriptc.9883C>T p.Arg3295Cys missense_variant 32/321 NM_201378.4 ENSP00000348702 Q15149-9

Frequencies

GnomAD3 genomes
AF:
0.00489
AC:
745
AN:
152238
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00200
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.00477
Gnomad ASJ
AF:
0.000577
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00301
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00788
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00472
AC:
1171
AN:
248052
Hom.:
4
AF XY:
0.00459
AC XY:
620
AN XY:
135000
show subpopulations
Gnomad AFR exome
AF:
0.00150
Gnomad AMR exome
AF:
0.00252
Gnomad ASJ exome
AF:
0.000997
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00160
Gnomad FIN exome
AF:
0.00302
Gnomad NFE exome
AF:
0.00812
Gnomad OTH exome
AF:
0.00447
GnomAD4 exome
AF:
0.00786
AC:
11481
AN:
1460742
Hom.:
45
Cov.:
73
AF XY:
0.00757
AC XY:
5503
AN XY:
726684
show subpopulations
Gnomad4 AFR exome
AF:
0.00111
Gnomad4 AMR exome
AF:
0.00248
Gnomad4 ASJ exome
AF:
0.00126
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00152
Gnomad4 FIN exome
AF:
0.00336
Gnomad4 NFE exome
AF:
0.00955
Gnomad4 OTH exome
AF:
0.00616
GnomAD4 genome
AF:
0.00489
AC:
745
AN:
152354
Hom.:
4
Cov.:
33
AF XY:
0.00432
AC XY:
322
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.00200
Gnomad4 AMR
AF:
0.00477
Gnomad4 ASJ
AF:
0.000577
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00301
Gnomad4 NFE
AF:
0.00788
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00793
Hom.:
6
Bravo
AF:
0.00551
TwinsUK
AF:
0.00512
AC:
19
ALSPAC
AF:
0.00882
AC:
34
ESP6500AA
AF:
0.00287
AC:
12
ESP6500EA
AF:
0.00892
AC:
75
ExAC
AF:
0.00509
AC:
616
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00758
EpiControl
AF:
0.00776

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:4
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 15, 2021This variant is associated with the following publications: (PMID: 29334134, 32707200) -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsDec 26, 2018- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024PLEC: BS2 -
not specified Benign:3
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Jun 17, 2016- -
Likely benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 03, 2016p.Arg3446Cys in exon 32 of PLEC: This variant is not expected to have clinical s ignificance because it has been identified in 0.7% (513/64856) of European chrom osomes, including two homozygotes by the Exome Aggregation Consortium (ExAC, htt p://exac.broadinstitute.org; dbSNP rs77303974). -
Likely benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoDec 08, 2016- -
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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 25, 2024- -
Autosomal recessive limb-girdle muscular dystrophy type 2Q Benign:1
Likely benign, criteria provided, single submitterclinical testingAl Jalila Childrenโ€™s Genomics Center, Al Jalila Childrens Speciality HospitalDec 29, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.77
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Uncertain
0.090
CADD
Uncertain
25
DANN
Benign
0.95
DEOGEN2
Uncertain
0.62
.;.;.;.;D;.;.;.;.;.
Eigen
Uncertain
0.66
Eigen_PC
Uncertain
0.59
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.96
D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.30
D
MetaRNN
Benign
0.014
T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.047
D
MutationAssessor
Pathogenic
3.0
.;.;.;.;M;.;.;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.64
T
PROVEAN
Uncertain
-4.2
D;D;D;D;D;D;D;D;.;D
REVEL
Pathogenic
0.74
Sift
Pathogenic
0.0
D;D;D;D;D;D;D;D;.;D
Sift4G
Pathogenic
0.0010
D;D;D;D;D;D;D;D;.;D
Polyphen
1.0
D;D;D;D;D;D;D;D;.;.
Vest4
0.71
MVP
0.73
ClinPred
0.035
T
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2
Varity_R
0.25
gMVP
0.62

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

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

Other links and lift over

dbSNP: rs77303974; hg19: chr8-144994064; COSMIC: COSV105234282; COSMIC: COSV105234282; API