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NM_003560.4(PLA2G6):c.956C>T (p.Thr319Met) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Mar 25, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001585947.7

Allele description [Variation Report for NM_003560.4(PLA2G6):c.956C>T (p.Thr319Met)]

NM_003560.4(PLA2G6):c.956C>T (p.Thr319Met)

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.956C>T (p.Thr319Met)
HGVS:
  • NC_000022.11:g.38132952G>A
  • NG_007094.3:g.86827C>T
  • NM_001004426.3:c.956C>T
  • NM_001199562.3:c.956C>T
  • NM_001349864.2:c.956C>T
  • NM_001349865.2:c.956C>T
  • NM_001349866.2:c.956C>T
  • NM_001349867.2:c.422C>T
  • NM_001349868.2:c.278C>T
  • NM_001349869.2:c.422C>T
  • NM_003560.4:c.956C>TMANE SELECT
  • NP_001004426.1:p.Thr319Met
  • NP_001186491.1:p.Thr319Met
  • NP_001336793.1:p.Thr319Met
  • NP_001336794.1:p.Thr319Met
  • NP_001336795.1:p.Thr319Met
  • NP_001336796.1:p.Thr141Met
  • NP_001336797.1:p.Thr93Met
  • NP_001336798.1:p.Thr141Met
  • NP_003551.2:p.Thr319Met
  • LRG_1015t1:c.956C>T
  • LRG_1015:g.86827C>T
  • LRG_1015p1:p.Thr319Met
  • NC_000022.10:g.38528959G>A
  • NG_007094.2:g.77739C>T
  • NM_003560.2:c.956C>T
Protein change:
T141M
Links:
dbSNP: rs149653983
NCBI 1000 Genomes Browser:
rs149653983
Molecular consequence:
  • NM_001004426.3:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199562.3:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349864.2:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349865.2:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349866.2:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349867.2:c.422C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349868.2:c.278C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349869.2:c.422C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003560.4:c.956C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001818379GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Mar 25, 2024) 		germlineclinical testing

Citation Link,

SCV002503547AiLife Diagnostics, AiLife Diagnostics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 10, 2020) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Impaired Transferrin Receptor Palmitoylation and Recycling in Neurodegeneration with Brain Iron Accumulation.

Drecourt A, Babdor J, Dussiot M, Petit F, Goudin N, Garfa-Traoré M, Habarou F, Bole-Feysot C, Nitschké P, Ottolenghi C, Metodiev MD, Serre V, Desguerre I, Boddaert N, Hermine O, Munnich A, Rötig A.

Am J Hum Genet. 2018 Feb 1;102(2):266-277. doi: 10.1016/j.ajhg.2018.01.003.

PubMed [citation]
PMID:
29395073
PMCID:
PMC5985451

Genetic analysis of ATP13A2, PLA2G6 and FBXO7 in a cohort of Chinese patients with early-onset Parkinson's disease.

Shen T, Pu J, Lai HY, Xu L, Si X, Yan Y, Jiang Y, Zhang B.

Sci Rep. 2018 Sep 19;8(1):14028. doi: 10.1038/s41598-018-32217-4.

PubMed [citation]
PMID:
30232368
PMCID:
PMC6145881
See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV001818379.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Reported along with another PLA2G6 variant in a patient with neurodegeneration with brain iron accumulation; however, segregation information was not provided (PMID: 29395073); Reported in a cohort of patients with early-onset Parkinson disease and not detected in 83 control individuals; however, additional clinical information and segregation information were not provided (PMID: 30232368); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 35911906, Schmaderer2023[casestudy], 34758253, 33279242, 30232368, 37139542, 29913018, 34622992, 29395073, 29859652)

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

From AiLife Diagnostics, AiLife Diagnostics, SCV002503547.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 26, 2024