NM_003560.4(PLA2G6):c.2215G>C (p.Asp739His) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jun 23, 2024
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:: RCV000254887.4

Allele description [Variation Report for NM_003560.4(PLA2G6):c.2215G>C (p.Asp739His)]

NM_003560.4(PLA2G6):c.2215G>C (p.Asp739His)

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.2215G>C (p.Asp739His)

Other names:

NM_003560.4(PLA2G6):c.2215G>C; p.Asp739His

HGVS:

NC_000022.11:g.38112565C>G
NG_007094.3:g.107214G>C
NG_033059.2:g.3105G>C
NM_001004426.3:c.2053G>C
NM_001199562.3:c.2053G>C
NM_001349864.2:c.2215G>C
NM_001349865.2:c.2053G>C
NM_001349866.2:c.2053G>C
NM_001349867.2:c.1681G>C
NM_001349868.2:c.1537G>C
NM_001349869.2:c.1519G>C
NM_003560.4:c.2215G>CMANE SELECT
NP_001004426.1:p.Asp685His
NP_001186491.1:p.Asp685His
NP_001336793.1:p.Asp739His
NP_001336794.1:p.Asp685His
NP_001336795.1:p.Asp685His
NP_001336796.1:p.Asp561His
NP_001336797.1:p.Asp513His
NP_001336798.1:p.Asp507His
NP_003551.2:p.Asp739His
LRG_1015t1:c.2215G>C
LRG_1015:g.107214G>C
LRG_1015p1:p.Asp739His
NC_000022.10:g.38508572C>G
NG_007094.2:g.98126G>C
NM_003560.2:c.2215G>C

Protein change:

D507H

Links:

dbSNP: rs587784349

NCBI 1000 Genomes Browser:

rs587784349

Molecular consequence:

NM_001004426.3:c.2053G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001199562.3:c.2053G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349864.2:c.2215G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349865.2:c.2053G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349866.2:c.2053G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349867.2:c.1681G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349868.2:c.1537G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349869.2:c.1519G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003560.4:c.2215G>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000322369	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 23, 2024)	germline	clinical testing	Citation Link,
SCV002502215	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 14, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16783378, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000322369

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 23, 2024)

germline

clinical testing

Citation Link,

SCV002502215

AiLife Diagnostics, AiLife Diagnostics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 14, 2022)

germline

clinical testing

PubMed (2)
[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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

PLA2G6, encoding a phospholipase A2, is mutated in neurodegenerative disorders with high brain iron.

Morgan NV, Westaway SK, Morton JE, Gregory A, Gissen P, Sonek S, Cangul H, Coryell J, Canham N, Nardocci N, Zorzi G, Pasha S, Rodriguez D, Desguerre I, Mubaidin A, Bertini E, Trembath RC, Simonati A, Schanen C, Johnson CA, Levinson B, Woods CG, et al.

Nat Genet. 2006 Jul;38(7):752-4. Epub 2006 Jun 18. Erratum in: Nat Genet. 2006 Aug;38(8):957.

PubMed [citation]

PMID:: 16783378
PMCID:: PMC2117328

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 GeneDx, SCV000322369.8

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); 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: 16783378, 30120687, 18799783)

#	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 AiLife Diagnostics, AiLife Diagnostics, SCV002502215.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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