NM_003560.4(PLA2G6):c.325C>G (p.His109Asp) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 6, 2022
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:: RCV000712686.15

Allele description

NM_003560.4(PLA2G6):c.325C>G (p.His109Asp)

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.325C>G (p.His109Asp)

HGVS:

NC_000022.11:g.38145538G>C
NG_007094.3:g.74241C>G
NM_001004426.3:c.325C>G
NM_001199562.3:c.325C>G
NM_001349864.2:c.325C>G
NM_001349865.2:c.325C>G
NM_001349866.2:c.325C>G
NM_001349867.2:c.-210C>G
NM_001349868.2:c.-166C>G
NM_001349869.2:c.-210C>G
NM_003560.4:c.325C>GMANE SELECT
NP_001004426.1:p.His109Asp
NP_001186491.1:p.His109Asp
NP_001336793.1:p.His109Asp
NP_001336794.1:p.His109Asp
NP_001336795.1:p.His109Asp
NP_003551.2:p.His109Asp
LRG_1015t1:c.325C>G
LRG_1015:g.74241C>G
LRG_1015p1:p.His109Asp
NC_000022.10:g.38541545G>C
NG_007094.2:g.65153C>G
NM_003560.2:c.325C>G
NM_003560.3:c.325C>G

Protein change:

H109D

Links:

dbSNP: rs142530390

NCBI 1000 Genomes Browser:

rs142530390

Molecular consequence:

NM_001349867.2:c.-210C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001349868.2:c.-166C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001349869.2:c.-210C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001004426.3:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001199562.3:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349864.2:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349865.2:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349866.2:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003560.4:c.325C>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000843205	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Feb 22, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002520097	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 6, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000843205

Athena Diagnostics Inc

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Feb 22, 2018)

germline

clinical testing

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

SCV002520097

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 6, 2022)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics Inc, SCV000843205.1

#	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 GeneDx, SCV002520097.2

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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

Last Updated: May 1, 2024

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