NM_201384.3(PLEC):c.8012G>A (p.Arg2671Gln) AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: Jan 22, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000117977.16

Allele description [Variation Report for NM_201384.3(PLEC):c.8012G>A (p.Arg2671Gln)]

NM_201384.3(PLEC):c.8012G>A (p.Arg2671Gln)

Gene:

PLEC:plectin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_201384.3(PLEC):c.8012G>A (p.Arg2671Gln)

HGVS:

NC_000008.11:g.143921809C>T
NG_012492.1:g.59937G>A
NM_000445.5:c.8093G>A
NM_201378.4:c.7970G>A
NM_201379.3:c.7946G>A
NM_201380.4:c.8423G>A
NM_201381.3:c.7916G>A
NM_201382.4:c.8012G>A
NM_201383.3:c.8024G>A
NM_201384.3:c.8012G>AMANE SELECT
NP_000436.2:p.Arg2698Gln
NP_958780.1:p.Arg2657Gln
NP_958781.1:p.Arg2649Gln
NP_958782.1:p.Arg2808Gln
NP_958783.1:p.Arg2639Gln
NP_958784.1:p.Arg2671Gln
NP_958785.1:p.Arg2675Gln
NP_958786.1:p.Arg2671Gln
NC_000008.10:g.144995977C>T
NM_000445.3:c.8093G>A
NM_000445.4:c.8093G>A
NM_201380.2:c.8423G>A

Protein change:

R2639Q

Links:

dbSNP: rs28526657

NCBI 1000 Genomes Browser:

rs28526657

Molecular consequence:

NM_000445.5:c.8093G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201378.4:c.7970G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201379.3:c.7946G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201380.4:c.8423G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201381.3:c.7916G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201382.4:c.8012G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201383.3:c.8024G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201384.3:c.8012G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000152289	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000269698	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Jan 13, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000519978	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jul 7, 2016)	germline	clinical testing	Citation Link,
SCV001475389	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jan 22, 2020)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31641117, 26467025

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Sequence variants with large effects on cardiac electrophysiology and disease.

Norland K, Sveinbjornsson G, Thorolfsdottir RB, Davidsson OB, Tragante V, Rajamani S, Helgadottir A, Gretarsdottir S, van Setten J, Asselbergs FW, Sverrisson JT, Stephensen SS, Oskarsson G, Sigurdsson EL, Andersen K, Danielsen R, Thorgeirsson G, Thorsteinsdottir U, Arnar DO, Sulem P, Holm H, Gudbjartsson DF, et al.

Nat Commun. 2019 Oct 22;10(1):4803. doi: 10.1038/s41467-019-12682-9.

PubMed [citation]

PMID:: 31641117
PMCID:: PMC6805929

See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000152289.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269698.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

p.Arg2808Gln in exon 32 of PLEC: This variant is not expected to have clinical s ignificance because it has been identified in 3.0% (131/4296) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs28526657).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

From GeneDx, SCV000519978.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics, SCV001475389.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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