NM_003560.4(PLA2G6):c.1630A>C (p.Met544Leu) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 24, 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:: RCV003324472.2

Allele description [Variation Report for NM_003560.4(PLA2G6):c.1630A>C (p.Met544Leu)]

NM_003560.4(PLA2G6):c.1630A>C (p.Met544Leu)

Gene:

PLA2G6:phospholipase A2 group VI [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.1

Genomic location:

Preferred name:

NM_003560.4(PLA2G6):c.1630A>C (p.Met544Leu)

HGVS:

NC_000022.11:g.38120871T>G
NG_007094.3:g.98908A>C
NM_001004426.3:c.1468A>C
NM_001199562.3:c.1468A>C
NM_001349864.2:c.1630A>C
NM_001349865.2:c.1468A>C
NM_001349866.2:c.1468A>C
NM_001349867.2:c.1096A>C
NM_001349868.2:c.952A>C
NM_001349869.2:c.934A>C
NM_003560.4:c.1630A>CMANE SELECT
NP_001004426.1:p.Met490Leu
NP_001186491.1:p.Met490Leu
NP_001336793.1:p.Met544Leu
NP_001336794.1:p.Met490Leu
NP_001336795.1:p.Met490Leu
NP_001336796.1:p.Met366Leu
NP_001336797.1:p.Met318Leu
NP_001336798.1:p.Met312Leu
NP_003551.2:p.Met544Leu
LRG_1015t1:c.1630A>C
LRG_1015:g.98908A>C
LRG_1015p1:p.Met544Leu
NC_000022.10:g.38516878T>G
NM_003560.2:c.1630A>C

Protein change:

M312L

Molecular consequence:

NM_001004426.3:c.1468A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001199562.3:c.1468A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349864.2:c.1630A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349865.2:c.1468A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349866.2:c.1468A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349867.2:c.1096A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349868.2:c.952A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349869.2:c.934A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003560.4:c.1630A>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004029825	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jul 24, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004029825

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jul 24, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004029825.1

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

Description

Variant summary: PLA2G6 c.1630A>C (p.Met544Leu) results in a conservative amino acid change located in the Patatin-like phospholipase domain (IPR002641) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251264 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1630A>C in individuals affected with Neurodegeneration With Brain Iron Accumulation and no experimental evidence demonstrating its impact on protein function have been reported. Other variants affecting the same residue have been classified likely pathogenic in ClinVar (p.Met544Leu CV ID:2017072, p.Met544Val CV ID:2130085). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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 3, 2023

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