NM_003560.4(PLA2G6):c.2222G>A (p.Arg741Gln) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Nov 21, 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:: RCV001588801.9

Allele description [Variation Report for NM_003560.4(PLA2G6):c.2222G>A (p.Arg741Gln)]

NM_003560.4(PLA2G6):c.2222G>A (p.Arg741Gln)

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.2222G>A (p.Arg741Gln)

HGVS:

NC_000022.11:g.38112558C>T
NG_007094.3:g.107221G>A
NG_033059.2:g.3112G>A
NM_001004426.3:c.2060G>A
NM_001199562.3:c.2060G>A
NM_001349864.2:c.2222G>A
NM_001349865.2:c.2060G>A
NM_001349866.2:c.2060G>A
NM_001349867.2:c.1688G>A
NM_001349868.2:c.1544G>A
NM_001349869.2:c.1526G>A
NM_003560.4:c.2222G>AMANE SELECT
NP_001004426.1:p.Arg687Gln
NP_001186491.1:p.Arg687Gln
NP_001336793.1:p.Arg741Gln
NP_001336794.1:p.Arg687Gln
NP_001336795.1:p.Arg687Gln
NP_001336796.1:p.Arg563Gln
NP_001336797.1:p.Arg515Gln
NP_001336798.1:p.Arg509Gln
NP_003551.2:p.Arg741Gln
LRG_1015t1:c.2222G>A
LRG_1015:g.107221G>A
LRG_1015p1:p.Arg741Gln
NC_000022.10:g.38508565C>T
NG_007094.2:g.98133G>A
NM_003560.2:c.2222G>A
NM_003560.3:c.2222G>A
O60733:p.Arg741Gln

Protein change:

R509Q; Arg741Gln

Links:

UniProtKB: O60733#VAR_062530; OMIM: 603604.0009; dbSNP: rs121908686

NCBI 1000 Genomes Browser:

rs121908686

Molecular consequence:

NM_001004426.3:c.2060G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001199562.3:c.2060G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349864.2:c.2222G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349865.2:c.2060G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349866.2:c.2060G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349867.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349868.2:c.1544G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001349869.2:c.1526G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003560.4:c.2222G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

Unknown function

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001814453	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 21, 2023)	germline	clinical testing	Citation Link,
SCV002018843	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 27, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005413408	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 13, 2023)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 18570303, 20886109, 27268037, 32183746, 32707456, 34272103, 34520727, 34622992, 35113461, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001814453

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 21, 2023)

germline

clinical testing

Citation Link,

SCV002018843

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 27, 2021)

germline

clinical testing

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

SCV005413408

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 13, 2023)

germline

clinical testing

PubMed (10)
[See all records that cite these PMIDs]

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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterization of PLA2G6 as a locus for dystonia-parkinsonism.

Paisan-Ruiz C, Bhatia KP, Li A, Hernandez D, Davis M, Wood NW, Hardy J, Houlden H, Singleton A, Schneider SA.

Ann Neurol. 2009 Jan;65(1):19-23. doi: 10.1002/ana.21415.

PubMed [citation]

PMID:: 18570303
PMCID:: PMC9016626

Catalytic function of PLA2G6 is impaired by mutations associated with infantile neuroaxonal dystrophy but not dystonia-parkinsonism.

Engel LA, Jing Z, O'Brien DE, Sun M, Kotzbauer PT.

PLoS One. 2010 Sep 23;5(9):e12897. doi: 10.1371/journal.pone.0012897.

PubMed [citation]

PMID:: 20886109
PMCID:: PMC2944820

See all PubMed Citations (10)

Details of each submission

From GeneDx, SCV001814453.2

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

Description

Functional analyses have not demonstrated a consistent damaging effect of this variant on protein activity (PMID: 20886109, 29108286); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 18570303, 27268037, 29108286, 25601130, 31196701, 26668131, 20669327, 26196026, 24182522, 35499206, 35113461, 35016069, 31069529, 35329915, 35803092, 35152491, 34622992, 32183746, 35911906, 34520727, 32707456, 32860008, 35005075, 34758253, 20886109, 34272103, 33452780, 34365112)

#	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 Revvity Omics, Revvity, SCV002018843.3

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

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV005413408.1

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

Description

PP1_strong, PM2_moderate, PM3_strong, PM5

#	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		1	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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