NM_014476.6(PDLIM3):c.379G>A (p.Val127Met) AND not specified

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Apr 17, 2023
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:: RCV000181008.8

Allele description [Variation Report for NM_014476.6(PDLIM3):c.379G>A (p.Val127Met)]

NM_014476.6(PDLIM3):c.379G>A (p.Val127Met)

Genes:

LOC126807246:BRD4-independent group 4 enhancer GRCh37_chr4:186434842-186436041 [Gene]
PDLIM3:PDZ and LIM domain 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q35.1

Genomic location:

Preferred name:

NM_014476.6(PDLIM3):c.379G>A (p.Val127Met)

Other names:

p.V127M:GTG>ATG

HGVS:

NC_000004.12:g.185514289C>T
NG_032576.3:g.26270G>A
NM_001114107.5:c.518+414G>A
NM_001257962.2:c.379G>A
NM_001257963.2:c.142G>A
NM_014476.6:c.379G>AMANE SELECT
NM_014476.6:c.379G>A
NP_001244891.1:p.Val127Met
NP_001244892.1:p.Val48Met
NP_055291.2:p.Val127Met
NP_055291.2:p.Val127Met
LRG_752t1:c.379G>A
LRG_752:g.26270G>A
LRG_752p1:p.Val127Met
NC_000004.11:g.186435443C>T
NG_032576.2:g.26270G>A
NM_014476.4:c.379G>A
NM_014476.5:c.379G>A
Q53GG5:p.Val127Met
p.(Val127Met)

Protein change:

V127M

Links:

Leiden Muscular Dystrophy (PDLIM3): PDLIM3_00002; UniProtKB: Q53GG5#VAR_050166; dbSNP: rs11944325

NCBI 1000 Genomes Browser:

rs11944325

Molecular consequence:

NM_001114107.5:c.518+414G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001257962.2:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001257963.2:c.142G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014476.6:c.379G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

no known functional consequence

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
SCV000170986	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Aug 5, 2014)	germline	clinical testing	Citation Link,
SCV000269632	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]
SCV001930788	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001971743	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV003928403	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Apr 17, 2023)	germline	clinical testing	Citation Link

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	10	10	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

Details of each submission

From GeneDx, SCV000170986.11

#	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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269632.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	10	not provided	not provided	clinical testing	PubMed (1)

Description

p.Val127Met in exon 4 of PDLIM3: This variant is not expected to have clinical s ignificance because it has been identified in 9.9% (437/4406) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs11944325).

#	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		10	not provided	10	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001930788.1

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

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001971743.1

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

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003928403.1

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

#	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

Last Updated: Sep 29, 2024

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