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NM_003560.4(PLA2G6):c.2129G>A (p.Arg710His) AND PLA2G6-associated neurodegeneration

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 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:
RCV002526373.2

Allele description [Variation Report for NM_003560.4(PLA2G6):c.2129G>A (p.Arg710His)]

NM_003560.4(PLA2G6):c.2129G>A (p.Arg710His)

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.2129G>A (p.Arg710His)
Other names:
NM_003560.4(PLA2G6):c.2129G>A; p.Arg710His
HGVS:
  • NC_000022.11:g.38113560C>T
  • NG_007094.3:g.106219G>A
  • NG_033059.2:g.2110G>A
  • NM_001004426.3:c.1967G>A
  • NM_001199562.3:c.1967G>A
  • NM_001349864.2:c.2129G>A
  • NM_001349865.2:c.1967G>A
  • NM_001349866.2:c.1967G>A
  • NM_001349867.2:c.1595G>A
  • NM_001349868.2:c.1451G>A
  • NM_001349869.2:c.1433G>A
  • NM_003560.4:c.2129G>AMANE SELECT
  • NP_001004426.1:p.Arg656His
  • NP_001186491.1:p.Arg656His
  • NP_001336793.1:p.Arg710His
  • NP_001336794.1:p.Arg656His
  • NP_001336795.1:p.Arg656His
  • NP_001336796.1:p.Arg532His
  • NP_001336797.1:p.Arg484His
  • NP_001336798.1:p.Arg478His
  • NP_003551.2:p.Arg710His
  • LRG_1015t1:c.2129G>A
  • LRG_1015:g.106219G>A
  • LRG_1015p1:p.Arg710His
  • NC_000022.10:g.38509567C>T
  • NG_007094.2:g.97131G>A
  • NM_001199562.1:c.1967G>A
  • NM_003560.2:c.2129G>A
Protein change:
R478H
Links:
dbSNP: rs147455037
NCBI 1000 Genomes Browser:
rs147455037
Molecular consequence:
  • NM_001004426.3:c.1967G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199562.3:c.1967G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349864.2:c.2129G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349865.2:c.1967G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349866.2:c.1967G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349867.2:c.1595G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349868.2:c.1451G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349869.2:c.1433G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003560.4:c.2129G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
PLA2G6-associated neurodegeneration (PLAN)
Synonyms:
phospholipase A2-associated neurodegeneration
Identifiers:
MONDO: MONDO:0017998; MedGen: CN204472; Orphanet: 329303

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761469Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 24, 2023) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761469.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The p.Arg710His variant in PLA2G6 has been reported in 1 individual, in the homozygous state, with PLA2G6-associated neurodegeneration (PMID: 26539891) and has been identified in 0.008% (10/129094) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs147455037). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID#: 402191) and has been interpreted as likely pathogenic by Lupski Lab (Baylor-Hopkins CMG, Baylor College of Medicine), GeneDx, and 3billion, and as a variant of uncertain significance by Invitae. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Arg710His variant is uncertain. ACMG/AMP Criteria applied: PM3_supporting, PP3, PM2_supporting (Richards 2015).

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

Last Updated: May 26, 2024