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NM_201384.3(PLEC):c.13384C>T (p.Arg4462Trp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 3, 2023
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:
RCV003072003.3

Allele description [Variation Report for NM_201384.3(PLEC):c.13384C>T (p.Arg4462Trp)]

NM_201384.3(PLEC):c.13384C>T (p.Arg4462Trp)

Gene:
PLEC:plectin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q24.3
Genomic location:
Preferred name:
NM_201384.3(PLEC):c.13384C>T (p.Arg4462Trp)
HGVS:
  • NC_000008.11:g.143916437G>A
  • NG_012492.1:g.65309C>T
  • NM_000445.5:c.13465C>T
  • NM_001410941.1:c.10084C>T
  • NM_201378.4:c.13342C>T
  • NM_201379.3:c.13318C>T
  • NM_201380.4:c.13795C>T
  • NM_201381.3:c.13288C>T
  • NM_201382.4:c.13384C>T
  • NM_201383.3:c.13396C>T
  • NM_201384.3:c.13384C>TMANE SELECT
  • NP_000436.2:p.Arg4489Trp
  • NP_001397870.1:p.Arg3362Trp
  • NP_958780.1:p.Arg4448Trp
  • NP_958781.1:p.Arg4440Trp
  • NP_958782.1:p.Arg4599Trp
  • NP_958783.1:p.Arg4430Trp
  • NP_958784.1:p.Arg4462Trp
  • NP_958785.1:p.Arg4466Trp
  • NP_958786.1:p.Arg4462Trp
  • NC_000008.10:g.144990605G>A
Protein change:
R3362W
Molecular consequence:
  • NM_000445.5:c.13465C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001410941.1:c.10084C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201378.4:c.13342C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201379.3:c.13318C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201380.4:c.13795C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201381.3:c.13288C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201382.4:c.13384C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201383.3:c.13396C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201384.3:c.13384C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Epidermolysis bullosa simplex 5B, with muscular dystrophy (EBS5B)
Synonyms:
EPIDERMOLYSIS BULLOSA SIMPLEX AND LIMB-GIRDLE MUSCULAR DYSTROPHY; Epidermolysa bullosa simplex and limb girdle muscular dystrophy; Epidermolysis bullosa simplex with muscular dystrophy
Identifiers:
MONDO: MONDO:0009181; MedGen: C2931072; Orphanet: 257; OMIM: 226670
Name:
Epidermolysis bullosa simplex, Ogna type (EBS5A)
Synonyms:
EPIDERMOLYSIS BULLOSA SIMPLEX 5A, OGNA TYPE; Pidermolysis bullosa simplex 5A, Ogna type
Identifiers:
MONDO: MONDO:0007555; MedGen: C0432317; Orphanet: 79401; OMIM: 131950
Name:
Epidermolysis bullosa simplex 5C, with pyloric atresia (EBS5C)
Synonyms:
Epidermolysis bullosa simplex with pyloric atresia; PLEC1-Related Epidermolysis Bullosa with Pyloric Atresia
Identifiers:
MONDO: MONDO:0012807; MedGen: C2677349; Orphanet: 158684; OMIM: 612138
Name:
Autosomal recessive limb-girdle muscular dystrophy type 2Q (LGMDR17)
Synonyms:
Limb-girdle muscular dystrophy, type 2Q; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 17
Identifiers:
MONDO: MONDO:0013390; MedGen: C3150989; Orphanet: 254361; OMIM: 613723
Name:
Epidermolysis bullosa simplex with nail dystrophy (EBS5D)
Identifiers:
MONDO: MONDO:0014661; MedGen: C4225309; OMIM: 616487

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003460283Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 3, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003460283.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 4489 of the PLEC protein (p.Arg4489Trp). This variant is present in population databases (rs781845444, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with PLEC-related conditions. ClinVar contains an entry for this variant (Variation ID: 2150930). 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 not expected to disrupt PLEC protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024